# Patent

## Title
Carboxyltransferase domain of acetyl-CoA carboxylase

## Abstract

The present invention provides compositions and crystals of the carboxyltransferase (CT) domain (the C-terminal  ̃90 kDa fragment) of various acetyl-CoA carboxylase (ACC) proteins, including yeast, mouse and human ACCs. Further, the present invention provides methods for identifying and designing compounds that can modulate ACC activity. These methods are based, in part, on the X-ray crystallographic structures of the CT domain of yeast ACC, either alone or bound to acetyl-CoA or a CT inhibitor, such as haloxyfop or diclofop or CP-640186. Thus, the present invention relates to the crystal structures of the carboxyltransferase (“CT”) domain of acetyl-CoA carboxylase (“ACC”), and to the use of these structures in the design of anti-obesity compounds, anti-diabetes compounds, antibiotic compounds, herbicide compounds, and in the design of herbicide resistant plants.

## Background
This disclosure contains material that is subject to copyright protection. The copyright owner has no objection to the facsimile reproduction by anyone of the patent document or the patent disclosure, as it appears in the U.S. Patent and Trademark Office patent file or records, but otherwise reserves any and all copyright rights. This application claims the benefit of the priority of the following four U.S. Provisional Applications: U.S. Ser. No. 60/439,383, filed Jan. 10, 2003; 60/459,464, filed Mar. 31, 2003; 60/491,640, filed Jul. 31, 2003; and 60/514,636, filed Oct. 27, 2003 and the entire contents of these applications are hereby incorporated by reference into this application.
All patent applications, published patent applications, issued and granted patents, texts, and literature references cited in this specification are hereby incorporated herein by reference in their entirety to more fully describe the state of the art to which the present invention pertains.
BACKGROUND OF THE INVENTION
Acetyl-coenzyme A carboxylases (ACCs) are crucial for the biosynthesis and oxidation of long-chain fatty acids, and they are important targets for the development of therapeutic agents against obesity, diabetes, and bacterial infections. See Alberts and Vagelos, 1972, The Enzymes, Boyer, ed., Academic Press, New York, vol. 6, pp. 37-82; Wakil et al., 1983, Ann. Rev. Biochem. 52:537-579; McGarry and Brown, 1997, Eur. J. Biochem. 244:1-14; Abu-Elheiga et al., 2001, Science 291:2613-2616; Ramsay et al., 2001, Biochim. Biophys. Acta 1546:21-43; Cronan, Jr. and Waldrop, 2002, Prog. Lipid Res. 41:407-435; Lenhard and Gottschalk, 2002, Advanced Drug Delivery Reviews 54:1199-1212. In addition, the carboxyltransferase (CT) domain of this enzyme from some plants is the site of action of widely-used commercial herbicides such as haloxyfop and sethoxydim (Gronwald, 1991, Weed Science 39:435-449; Devine and Shukla, 2000, Crop Protection 19:881-889; Zagnitko et al., 2001, Proc. Natl. Acad. Sci. USA 98:6617-6622; Delye et al., 2003, Plant Physiol. 132:1716-1723).
ACCs catalyze the formation of malonyl-CoA from acetyl-CoA and CO2, a reaction that also requires the hydrolysis of ATP. Two isoforms of this enzyme have been identified in mammals. ACC 1, a cytosolic enzyme, catalyzes the committed step in the biosynthesis of long-chain fatty acids. Wakil et al, 1983, Ann. Rev. Biochem. 52:537-579. In comparison, ACC2 is associated with the mitochondrial membrane and its malonyl-CoA product potently inhibits the shuttle that transports long-chain acyl-CoAs from the cytosol to the mitochondria for oxidation. McGarry and Brown, 1997, Eur. J. Biochem. 244:1-14; Ramsay et al., 2001, Biochim. Biophys. Acta 1546:21-43.
The malonyl-CoA produced in the ACC-catalyzed reaction is a negative regulator of carnitine palmitoyltransferase 1, which is involved in fatty acid oxidation. During starvation, ACC levels and consequently malonyl-CoA levels are decreased and fatty acid oxidation is increased. The reduction of malonyl-CoA results in an increase in ATP synthesis which is directly linked to an increase in fatty acid oxidation, and also results in a decrease in ATP consumption for fatty acid synthesis which is consequently decreased. Interestingly, mice lacking ACC2 exhibit a higher rate of fatty acid oxidation and reduced body fat and body weight, while genetic ablation of ACC1 in mice was found to be embryonically lethal, possibly due to lack of C2 units for the synthesis of fatty acid needed for biomembrane synthesis. See Abu-Elheiga et al., Science 291:2613-2616 (2001); see also U.S. Patent Application Publication No. 20030028912 of Matzuk et al. published Feb. 6, 2003.
Mammalian, yeast, and most other eukaryotic ACCs are large, multi-functional enzymes, containing the biotin carboxylase (BC) domain, the biotin carboxyl carrier protein (BCCP) domain, and the carboxyltransferase (CT) domain. See FIG. 1A. BC catalyzes the ATP-dependent carboxylation of a biotin group covalently linked to a lysine residue in BCCP, and then CT catalyzes the transfer of the carboxyl group from biotin to acetyl-CoA to produce malonyl-CoA. In E. coli and other bacteria, ACCs are multi-subunit enzymes composed of 3 distinct protein subunits, with a BC subunit, a BCCP subunit, and two subunits for the CT. See FIG. 1A. Crystal structures are available for the BC and BCCP subunits of E. coli ACC (see Cronan Jr. and Waldrop, 2002, Prog. Lipid Res. 41:407-435).
SUMMARY OF THE INVENTION
The present invention provides compositions and crystals of the carboxyltransferase (CT) domain (the C-terminal  ̃90 kDa fragment) of various acetyl-CoA carboxylase (ACC) proteins, including yeast, mouse and human ACCs. Further, the present invention provides methods for identifying and designing compounds that can modulate ACC activity. These methods are based, in part, on the X-ray crystallographic structures of the CT domain of yeast ACC as produced by construct yCTACC (the yeast CT domain comprising residues 1429-2233 (SEQ ID NO:2) of the S. cerevisiae ACC set forth in GenBank Entry No. Q00955 (SEQ ID NO:1)), either alone or bound to acetyl-CoA or a CT inhibitor, such as haloxyfop or diclofop; or the CT domain of yeast ACC as produced by construct yCT2ACC (the yeast CT domain comprising residues 1476-2233 (SEQ ID NO:3) of the S. cerevisiae ACC set forth in GenBank Entry No. Q00955) either alone, or bound to a CT inhibitor, such as haloxyfop, diclofop or CP-640186. Thus, the present invention relates to the crystal structures of the carboxyltransferase (“CT”) domain of acetyl-CoA carboxylase (“ACC”), to the use of these domains for identifying inhibitors of ACCs, and to the use of these structures in the design of anti-obesity compounds, anti-diabetes compounds, antibiotic compounds, herbicide compounds, fungicide compounds and in the design of herbicide resistant plants.
The disclosure includes seven (7) tables provided as an appendix on compact disc, Tables 1, 2, 3, 4, 5, 6 and 7. The compact disc is formatted for IBM-PC using an MS-Windows operating system, and contains 7 files, entitled: “Table 1” of size 1,319 KB created on Dec. 30, 2003; “Table 2” of size 916 KB created on Dec. 30, 2003; “Table 3” of size 1,229 KB created on Dec. 30, 2003; “Table 4” of size 856 KB created on Dec. 30, 2003; “Table 5” of size 1,264 KB created on Dec. 30, 2003; “Table 6” of size 1,042 KB created on Dec. 30, 2003; and “Table 7” of size 1,236 KB created on Dec. 30, 2003. These tables contain a list of the atomic coordinates of amino acids within the crystals of carboxyltransferase (“CT”) domains of yeast acetyl-CoA carboxylase (“ACC”) either in uncomplexed (“free”) or complexed form. Table 1 presents a list of the atomic coordinates of an uncomplexed CT domain crystal, where the CT domain polypeptide has the amino acid sequence of SEQ ID NO:2. For the present invention, the sequences that refer to a CT domain, i.e. SEQ ID NOS: 2, 3, 4, 6, 8, 10 and 14, refer to the sequence of one monomer of the CT domain. A CT domain comprises a dimer composed of two identical monomers, and from the crystal structures, it is generally the case that sequence residues below 1800 (in relation to SEQ ID NO: 1 numbering) comprise one face of a binding pocket from one monomer and sequence residues above 1800 comprise the other face of a binding pocket from the other monomer. Table 2 presents a list of the atomic coordinates of a complexed CT domain crystal, where the CT domain is complexed to acetyl-CoA, and where the CT domain polypeptide has the amino acid sequence of SEQ ID NO:2. Table 3 presents a list of the atomic coordinates of a complexed CT domain crystal, where the CT domain is complexed to the inhibitor haloxyfop, and where the CT domain polypeptide has the amino acid sequence of SEQ ID NO:2. Table 4 presents a list of the atomic coordinates of a complexed CT domain crystal, where the CT domain is complexed to the inhibitor diclofop, and where the CT domain polypeptide has the amino acid sequence of SEQ ID NO:3. Table 5 presents a list of the atomic coordinates of a complexed CT domain crystal, where the CT domain is complexed to the inhibitor CP-640186, and where the CT domain polypeptide has the amino acid sequence of SEQ ID NO:3. Table 6 presents a list of the atomic coordinates of an uncomplexed CT domain crystal, where the CT domain polypeptide has the amino acid sequence of SEQ ID NO:4. Table 7 presents a list of the atomic coordinates of an uncomplexed CT domain crystal, where the CT domain polypeptide has the amino acid sequence of SEQ ID NO:3. These atomic coordinate listings will not appear in the printed patent, but are provided herewith as separate files named by Table number on duplicate copies of a single electronically readable compact disc in compliance with 37 C.F.R. §1.52(e). The contents of these files are hereby incorporated by reference in their entireties.
In one aspect of the present invention, a crystallizable composition comprises a carboxyltransferase domain of acetyl-coenzyme A (CoA) carboxylase. The carboxyltransferase domain of the crystallizable composition can comprise a human carboxyltransferase domain, a mouse carboxyltransferase domain, or a yeast carboxyltransferase domain. The carboxyltransferase domain of the crystallizable composition can be complexed with a ligand. The ligand can comprise acetyl-CoA or a compound that inhibits activity of the carboxyltransferase domain. Compounds that inhibit activity of the CT domain include, for example, haloxyfop (FIG. 5A), diclofop (FIG. 5A) and CP-640186 (FIG. 23; and see U.S. Patent Application Publication No.US2003/0187254 A1; Harwood, J. H. et al., J. Biol. Chem. 278(39): 37099-37111 (2003)).
In another aspect of the present invention, the carboxyltransferase domain of the crystallizable composition can comprise two monomers, each monomer comprising consecutive amino acid residues at least 50% identical to SEQ ID NO:2; SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO: 6, SEQ ID NO:8, SEQ ID NO:10 or SEQ ID NO:14. In other aspects, each monomer comprises consecutive amino acid residues at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 99% identical to SEQ ID NO:2; SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO: 6, SEQ ID NO:8, SEQ ID NO:10 or SEQ ID NO:14.
The present invention also provides various crystals comprising a carboxyltransferase domain of acetyl-CoA carboxylase. In one aspect, a crystal comprises a carboxyltransferase domain of acetyl-CoA carboxylase, wherein the domain comprises two monomers. In other aspects, a crystal comprises a carboxyltransferase domain of acetyl-CoA carboxylase complexed with acetyl-CoA, haloxyfop, diclofop or CP-640186. The CT domain of the crystals can comprise, for example, a human carboxyltransferase domain, a mouse carboxyltransferase domain, or a yeast carboxyltransferase domain.
In another aspect, the crystal comprises a carboxyltransferase domain of acetyl-CoA carboxylase, wherein the CT domain comprises two monomers, and the crystal comprises unit cell dimensions of about: (a) a=247±2 Å; b=125±2 Å; c=145±2 Å; α=90°; β=94±2°; γ=90°; and space group C2 (b) a=255±2 Å; b=113+2 Å; c=135±2 Å; α=90°; β=101 ±2°; γ=90°; and space group C2 (c) a=246±2 Å; b=124±2 Å; c=145±2 Å; α=90°; β=94±2°; γ=90°; and space group C2; (d) a=93±2 Å; b=138±2 Å; c=101±2 Å; c=90°; β=114±20; γ=90°; and space group P2, (e) a=137±2 Å; b=137±2 Å; c=244±2 Å; α=90°; β=90°; γ=120°; and space group P3221; or (f) a=247±2 Å; b=125±2 Å; c=146±2 Å; a=90°; β=94±°; γ=90°; and space group C2.
In another aspect, the crystal comprises a carboxyltransferase domain of acetyl-CoA carboxylase, wherein the CT domain comprises two monomers, and wherein each monomer of the carboxyltransferase domain comprises consecutive amino acid residues at least 50% identical to SEQ ID NO:2; SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO: 6, SEQ ID NO:8 or SEQ ID NO: 10. In other aspects, each monomer of the CT domain comprises consecutive amino acid residues of at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 99% identical to SEQ ID NO:2; SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO: 6, SEQ ID NO:8, SEQ ID NO:10 or SEQ ID NO:14.
In another aspect, the crystal comprises a carboxyltransferase domain of acetyl-CoA carboxylase, wherein the CT domain comprises two monomers, and wherein the carboxyltransferase domain comprises a three-dimensional structure characterized by the atomic coordinates of Table 1, Table 2, Table 3, Table 4, Table 5, Table 6 or Table 7.
The present invention also provides an isolated carboxyltransferase domain comprising two monomers, each monomer comprising consecutive amino acid residues at least 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 99% identical to SEQ ID NO:2; SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO: 6, SEQ ID NO:8, SEQ ID NO:10 or SEQ ID NO:14. The isolated CT domain can comprise, for example, a human carboxyltransferase domain, a mouse carboxyltransferase domain, or a yeast carboxyltransferase domain.
In another aspect, the isolated CT domain comprises two monomers, each monomer comprising consecutive amino acid residues at least 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 99% identical to the amino acid residues of SEQ ID NO:2; SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO: 6, SEQ ID NO:8, SEQ ID NO:10 or SEQ ID NO:14, except that amino acid residues of each of the aforementioned SEQ ID NOS. identified in Table G as corresponding to amino acid residues 11974, V2002, G1998, V2001, V2024, L1968, F1956, W1924, Y1738, S1708, A1627, 11735, G1734 and L1756 of SEQ ID NO:1 do not vary. In another aspect, these residues can vary conservatively. The residue numbering is in relation to SEQ ID NO: 1, and the corresponding residues for SEQ ID NO:2; SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO: 6, SEQ ID NO:8, SEQ ID NO:10 or SEQ ID NO:14 have been determined as listed in Table G. Further, residues corresponding to SEQ ID NO: 1 that are not listed in Table G can be determined by Blast alignment (for example, see FIG. 4). Further, the reference to a first monomer or a second monomer is in relation to the three-dimensional structure of an isolated CT domain, as a CT domain comprises two monomers that are identical in amino acid sequence. Additionally, as a CT domain comprises two monomer units, a binding site of a CT domain is comprised of residues from both monomers. Generally, where residues are listed as comprising a binding site or some other feature of a CT domain that involves both monomer units, residues below 1800 (in relation to SEQ ID NO:1 numbering) are from one monomer, and residues above 1800 are from the other monomer. Thus, in the disclosure, residues above 1800 are sometimes denoted with an apostrophe symbol (i.e. Ala 1908′) to indicate their location within a separate monomer, however, it is not necessary to denote the residue with an apostrophe.
In another aspect, the isolated CT domain comprises two monomers, each monomer comprising consecutive amino acid residues at least 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 99% identical to the amino acid residues of SEQ ID NO:2; SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO: 6, SEQ ID NO:8, SEQ ID NO:10 or SEQ ID NO:14, except that amino acid residues of each of the aforementioned SEQ ID NOS. identified in Table G as corresponding to amino acid residues A1761, K1764, L2025, E2026, G2029 of SEQ ID NO:1 do not vary, and amino acid residue Met 1765 can be Val. In another aspect, these residues can vary conservatively. The residue numbering is in relation to SEQ ID NO:1, and the corresponding residues for SEQ ID NO:2; SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO: 6, SEQ ID NO:8, SEQ ID NO:10 or SEQ ID NO:14 is listed in Table G.
In another aspect, the isolated CT domain comprises two monomers, each monomer comprising consecutive amino acid residues at least 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 99% identical to the amino acid residues of SEQ ID NO:2; SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO: 6, SEQ ID NO:8 or SEQ ID NO:10, except that amino acid residues of each of the aforementioned SEQ ID NOS. identified in Table G as corresponding to amino acid residues Ile1593, Ser1595, Phe1596, Asn1624, Ser1625, Gly1626, Ala1627, Arg1628, Ile1629, Gly1630, Gly1699, Leu1705, Arg1731, Gly1734, Ile1735, Tyr1738, Ile1755, Leu1756, Thr1757, Gly1758, Ala1759, Ala1761, Asn1774, Gly1955, Phe1956, Arg1996, Gly1997, Gly1998, Ser1999, Val2001, Val2024, Leu2025, Gly2029, Ile2033, Lys2034 and Arg2036 of SEQ ID NO:1 do not vary. In another aspect, these residues can vary conservatively. The residue numbering is in relation to SEQ ID NO:1, and the corresponding residues for SEQ ID NO:2; SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO: 6, SEQ ID NO:8, SEQ ID NO:10 or SEQ ID NO:14 are listed in Table G.
In another aspect, the isolated CT domain comprises two monomers, each monomer comprising consecutive amino acid residues at least 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 99% identical to the amino acid residues of SEQ ID NO:2; SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO: 6, SEQ ID NO:8 or SEQ ID NO:10, except that amino acid residues of each of the aforementioned SEQ ID NOS. identified in Table G as corresponding to amino acid residues Phe1596, Ser1625, Gly1626, Ala1627, Arg1628, Ile1629, Leu1705, Ser1708, Ala1712, Gly1734, Ile1735, Gly1736, Ala1737, Tyr1738, Leu1739, Arg1741, Leu1742, Ile1755, Leu1756, Thr1757, Val1923, Trp1924, Pro1926, Ser1928, Ala1929, Trp1953, Gly1955, Phe1956, Ser1957, Val1967, Leu1968, Lys1969, Gly1971, Ile1974, Arg1996, Gly1997, Gly1998, Ser1999, Trp2000, Val2001, Val2002, Val2024 and Leu2025 of SEQ ID NO:1 do not vary. In another aspect, these residues can vary conservatively. The residue numbering is in relation to SEQ ID NO: 1, and the corresponding residues for SEQ ID NO:2; SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO: 6, SEQ ID NO:8, SEQ ID NO: 10 or SEQ ID NO: 14 is listed in Table G.
In another aspect, the isolated CT domain comprises two monomers, each monomer comprising consecutive amino acid residues at least 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 99% identical to the amino acid residues of SEQ ID NO:2; SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO: 6, SEQ ID NO:8 or SEQ ID NO:10, except that amino acid residues of each of the aforementioned SEQ ID NOS. identified in Table G as corresponding to amino acid residues Ile1629, Leu1756, Thr1757, Gly1758, Ala1761, Asn1763, Lys1764, Leu1766, Tyr1771, Ala1908, Gln1922, Val1923, Trp1924, Trp1953, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Asp1962, Arg1996, Gly1997, Ser1999, Val2024, Leu2025, Glu2026, Pro2027, Gly2029, Val2031 and Ile2033 of SEQ ID NO:1 do not vary. The residue numbering is in relation to SEQ ID NO:1, and the corresponding residues for SEQ ID NO:2; SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO: 6, SEQ ID NO:8, SEQ ID NO:10 or SEQ ID NO:14 is provided in Table G.
In yet another aspect, an isolated carboxyltransferase domain comprises two monomers, each monomer comprising amino acid residues at least 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 99% identical to the amino acid residues of SEQ ID NO:2; SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO: 6, SEQ ID NO:8, SEQ ID NO:10 or SEQ ID NO:14, which are shown to be corresponding to the following amino acid residues of SEQ ID NO:1 in Table G: Met 1503, Lys 1592, Ile1593, Ser1595, Phe 1596, Asn 1624, Ser1625, Gly 1626, Ala1627, Arg1628, Ile1629, Gly1630, Met1631, Gly 1699, Gly1701, Glu1703, Cys 1704, Leu1705, Ser1708, Ala1712, Arg1731, Val1733, Gly1734, Ile1735, Gly 1736, Ala 1737, Tyr1738, Leu 1739, Arg 1741, Leu1742, Pro1753, Ile 1755, Leu1756, Thr1757, Gly1758, Ala1759, Pro1760, Ala1761,Ile1762, Asn1763, Lys1764, Met1765, Leu1766, Tyr1771, Asn1774, Ala1908, Pro1920, Gly1921, Gln1922, Val1923, Trp1924, His1925, Pro1926, Ser1928, Ala1929, Phe1930, Trp1953, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Gln1960, Arg1961, Asp1962, Met1963, Phe1964, Asn1965, Glu1966, Val1967, Leu1968, Lys1969, Tyr1970, Gly1971, Ser1972, Ile1974, Val1975, Glu1994, Arg1996, Gly1997, Gly1998, Ser1999, Trp2000, Val2001, Val2002, Val2003, Arg2021, Gly2023, Val2024, Leu2025, Glu2026, Pro2027, Gln2028, Gly 2029, Met2030, Val2031, Gly2032, Ile2033, Lys2034, Arg2036, Asp2098, Val2108 (wherein the residue numbering is in relation to SEQ ID NO:1, and the corresponding residues for SEQ ID NOS:2, 3, 4, 6, 8, 10 and 14 are listed in Table G), wherein linear spatial relationship of the residues of SEQ ID NO:1 are preserved in the CT domain.
The crystal structures of the present invention is useful, inter alia, for the rational design of compounds that modulate the activity of the CT domain of ACC. In view of the biological importance of ACC, modulators of the CT domain of ACC may be used in the treatment of various diseases and disorders, including but not limited to, obesity, metabolic syndrome, diabetes, cardiovascular disease, atherosclerosis and infections. The present invention may also be used to design and/or screen metabolic enhancers that may be used to promote endurance or survival under stressful conditions. The structural models of the present invention are based, at least in part, on the X-ray crystallographic structure of the CT domains encoded by the vectors yCTACC or yCT2ACC, both free and bound to the inhibitors haloxyfop, diclofop or CP-640186. These models are useful for the rational design of therapeutic compounds, herbicide compounds, pesticide compounds, as well as for the design and optimization of herbicide resistant plants.
Thus, the present invention provides a method for identifying a compound that modulates activity of acetyl-CoA carboxylase comprising: (a) providing the atomic coordinates for at least 10, 20, 30 or 50 amino acid residues for a carboxyltransferase domain of acetyl-CoA carboxylase as set forth in any of Tables 1 to 7, or coordinates having a root mean square deviation therefrom, with respect to at least 50% of Cα atoms, of not more than ±2 Å or ±1.5 Å in computer readable form; (b) converting the atomic coordinates into electrical signals readable by a computer processor; (c) providing a structure of a candidate compound in computer readable form; and (d) determining whether or not the candidate compound fits into a binding cavity of the carboxyltransferase domain, so as to identify a compound that modulates activity of acetyl-CoA carboxylase. This method can further comprise determining whether contacting the candidate compound to the carboxyltransferase domain under enzymatically acceptable conditions modulates carboxyltransferase domain activity.
The present invention also provides a method for rationally designing a compound that modulates activity of acetyl-CoA carboxylase, comprising: (a) generating a computer readable model of a binding site of a carboxyltransferase domain of acetyl-CoA carboxylase; and (b) using the model to design a compound having a structure and a charge distribution compatible with the binding site, wherein the compound comprises a functional group that interacts with the binding site to modulate acetyl-CoA carboxylase activity. Additionally, the method can further comprise outputting the design of the compound to a user.
In the method for rationally designing a compound that modulates activity of acetyl-CoA carboxylase, compatibility of the compound to the binding site can be determined by determining whether the compound has a proximity of at least 2-10 Å, 2-7 Å or of at least 2.5-4 Å to residues Met1503, Lys1592, Ile1593, Ser1595, Phe1596, Asn1624, Ser1625, Gly1626, Ala1627, Arg1628, Ile1629, Gly1630, Gly1699, Leu1705, Arg1731, Val1733, Gly1734, Ile1735, Tyr1738, Ile1755, Leu1756, Thr1757, Gly1758, Ala1759, Pro1760, Ala1761, Asn1774, Gly1955, Phe1956, Arg1996, Gly1997, Gly1998, Ser1999, Val2001, Val2024, Leu2025, Gly2029, Ile2033, Lys2034, Arg2036, Leu2189 of SEQ ID NO:1, or to the corresponding residues for SEQ ID NO:2, 3, 4, 6, 8, 10 and 14 as listed in Table G.
In another aspect of the method for rationally designing a compound that modulates activity of acetyl-CoA carboxylase, the compatibility of the compound to the binding site can be determined by determining whether the compound has a proximity of at least 2-10 Å, 2-7 Å or of at least 2.5-4 Å of the compound to residues Phe1596, Ser1625, Gly1626, Ala1627, Arg1628, Ile1629, Cys1704, Leu1705, Ser1708, Ala1712, Val1733, Gly1734, Ile1735, Gly1736, Ala1737, Tyr1738, Leu1739, Arg1741, Leu1742, Ile1755, Leu1756, Thr1757, Val1923, Trp1924, His1925, Pro1926, Ser1928, Ala1929, Phe1930, Trp1953, Gly1955, Phe1956, Ser1957, Asn1965, Glu1966, Val1967, Leu1968, Lys1969, Tyr1970, Gly1971, Ser1972, Ile1974, Arg1996, Gly1997, Gly1998, Ser1999, Trp2000, Val2001, Val2002, Val2003, Gly2023, Val2024, Leu2025 of SEQ ID NO: 1, or to the corresponding residues for SEQ ID NO:2, 3, 4, 6, 8, 10 or 14 as listed in Table G.
In yet another aspect, the compatibility of the compound to the binding site can be determined by determining whether the compound has a proximity of at least 2-10 Å, 2-7 Å or of at least 2.5-4 Å of the compound to residues Ile1629, Leu1756, Thr1757, Gly1758, Pro1760, Ala1761, Ile1762, Asn1763, Lys1764, Met1765, Leu1766, Tyr1771, Ala1908, Pro1920, Gln1922, Val923, Trp1924, His1925, Trp1953, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Gln1960, Asp1962, Arg1996, Gly1997, Ser1999, Val2024, Leu2025, Glu2026, Pro2027, Gln2028, Gly2029, Met2030, Val2031, Gly2032, Ile2033 of SEQ ID NO:1, or to the corresponding residues for SEQ ID NO:2, 3, 4, 6, 8, 10 or 14 as listed in Table G.
The present invention also provides a method for identifying a compound that binds to a carboxyltransferase domain of acetyl-CoA carboxylase comprising: (a) providing a set of atomic coordinates defining the three-dimensional structure of a crystal of a carboxyltransferase domain of acetyl-CoA carboxylase as in any of Table 1 to 7, or coordinates having a root mean square deviation therefrom, with respect to at least 50% of Cα atoms, of not more than ±1.5 Å or ±2 Å, in computer readable form; and (b) selecting a compound by performing rational drug design with the atomic coordinates, wherein the selecting is performed in conjunction with computer modeling, so as to identify a compound that binds to the carboxyltransferase domain of acety-CoA carboxylase. This method can further comprise outputting the identity of the compound to a user.
In another aspect, the present invention provides a method for identifying an inhibitor compound capable of binding to, and inhibiting the enzymatic activity of a carboxyltransferase domain of acetyl-CoA carboxylase comprising: (a) introducing into a suitable computer program information defining a carboxyltransferase binding site conformation of an acetyl-CoA carboxylase molecule comprising a conformation defined by at least 30 of the atomic coordinates of any of Tables 1 to 7, wherein the program displays the three-dimensional structure thereof; (b) providing a three dimensional structure of a test compound in the computer program; (c) displaying and superimposing the model of the test compound on the model of the binding site; (d) assessing whether the test compound model fits spatially into the binding site; and (e) determining whether the test compound inhibits enzymatic activity, so as to identify an inhibitor compound capable of binding to, and inhibiting the enzymatic activity of a carboxyltransferase domain of acetyl-CoA carboxylase. This method can further comprise outputting the identity of the inhibitor compound to a user.
In another aspect, the present invention provides a method for identifying a compound that modulates acetyl-CoA carboxylase activity comprising: (a) providing a model of a binding cavity of carboxyltransferase of acetyl-CoA carboxylase, wherein the model comprises atomic coordinates of residues: (i) Met 1503, Lys 1592, Ile1593, Ser1595, Phe 1596, Asn 1624, Ser1625, Gly 1626, Ala1627, Arg1628, Ile1629, Gly1630, Met1631, Gly 1699, Gly1701, Glu1703, Cys 1704, Leu1705, Ser1708, Ala1712, Arg1731, Val1733, Gly1734, Ile1735, Gly 1736, Ala 1737, Tyr1738, Leu 1739, Arg 1741, Leu1742, Pro1753, Ile 1755, Leu1756, Thr1757, Gly1758, Ala1759, Pro1760, Ala1761, Ile1762, Asn1763, Lys1764, Met1765, Leu1766, Tyr1771, Asn1774, Ala1908, Pro1920, Gly1921, Gln1922, Val1923, Trp1924, His1925, Pro1926, Ser1928, Ala1929, Phe1930, Trp1953, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Gln1960, Arg1961, Asp1962, Met1963, Phe1964, Asn1965, Glu1966, Val1967, Leu1968, Lys1969, Tyr1970, Gly1971, Ser1972, Ile1974, Val1975, Glu1994, Arg1996, Gly1997, Gly1998, Ser1999, Trp2000, Val2001, Val2002, Val2003, Arg2021, Gly2023, Val2024, Leu2025, Glu2026, Pro2027, Gln2028, Gly 2029, Met2030, Val2031, Gly2032, Ile2033, Lys2034, Arg2036, Asp2098, Val2108 and Leu2189, according to Table 1, 2, 3, 4, 5, 6 or 7, or coordinates having a root mean square deviation therefrom, with respect to at least 50% of Cα atoms, of not more than ±1.5 Å or 2 Å, in computer readable form; (ii) Met1503, Lys1592, Ile1593, Ser1595, Phe1596, Asn1624, Ser1625, Gly1626, Ala1627, Arg1628, Ile1629, Gly1630, Gly1699, Leu1705, Arg1731, Val1733, Gly1734, Ile1735, Tyr1738, Ile1755, Leu1756, Thr1757, Gly1758, Ala1759, Pro1760, Ala1761, Asn1774, Gly1955, Phe1956, Arg1996, Gly1997, Gly1998, Ser1999, Val2001, Val2024, Leu2025, Gly2029, Ile2033, Lys2034, Arg2036 and Leu2189, according to Table 1, 2, 3, 4, 5, 6 or 7, or coordinates having a root mean square deviation therefrom, with respect to at least 50% of Cα atoms, of not more than ±1.5 Å or 2 Å, in computer readable form; (iii) Phe1596, Ser1625, Gly1626, Ala1627, Arg1628, Ile1629, Cys1704, Leu1705, Ser1708, Ala1712, Val1733, Gly1734, Ile1735, Gly1736, Ala1737, Tyr1738, Leu1739, Arg1741, Leu1742, Ile1755, Leu1756, Thr1757, Val1923, Trp1924, His1925, Pro1926, Ser1928, Ala1929, Phe1930, Trp1953, Gly1955, Phe1956, Ser1957, Asn1965, Glu1966, Val1967, Leu1968, Lys1969, Tyr1970, Gly1971, Ser1972, Ile1974, Arg1996, Gly1997, Gly1998, Ser1999, Trp2000, Val2001, Val2002, Val2003, Gly2023, Val2024 and Leu2025 according to Table 1, 2, 3, 4, 5, 6 or 7, or coordinates having a root mean square deviation therefrom, with respect to at least 50% of Cα atoms, of not more than ±1.5 Å or 2 Å, in computer readable form; (iv) Ile1629, Leu1756, Thr1757, Gly1758, Pro1760, Ala1761, Ile1762, Asn1763, Lys1764, Met1765, Leu1766, Tyr1771, Ala1908, Pro1920, Gln1922, Val1923, Trp1924, His1925, Trp1953, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Gln1960, Asp1962, Arg1996, Gly1997, Ser1999, Val2024, Leu2025, Glu2026, Pro2027, Gln2028, Gly2029, Met2030, Val2031, Gly2032 and Ile2033, according to Table 1, 2, 3, 4, 5, 6 or 7, or coordinates having a root mean square deviation therefrom, with respect to at least 50% of Cα atoms, of not more than ±1.5 Å or 2 Å, in computer readable form; (v) Ile1593, Ser1595, Ser1625, Gly1626, Ala1627, Arg1628, Ile1629, Arg1731, Val1733, Gly1734, Ile1755, Leu1756, Thr1757, Gly1758, Gly1997, Gly1998, Val2024, Leu2025, Ile2033, Lys2034 and Arg2036, according to Table 1, 2, 3, 4, 5, 6 or 7, or coordinates having a root mean square deviation therefrom, with respect to at least 50% of Cα atoms, of not more than ±1.5 Å or 2 Å, in computer readable form; (vi) Thr1757, Ala1761, Ile1762, Lys1764, Met1765, Leu1766, Val1923, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Leu2025, Glu2026, Gln2028, Gly2029, Gly2032 and Ile2033, according to Table 1, 2, 3, 4, 5, 6 or 7, or coordinates having a root mean square deviation therefrom, with respect to at least 50% of Cα atoms, of not more than ±1.5 Å or 2 Å, in computer readable form; or (vii) Gly1626, Ala1627, Leu1705, Ser1708, Gly1734, Ile1735, Tyr1738, Leu1756, Trp1924, Ala1929, Phe1956, Val1967, Leu1968, Tyr1970, Gly1971, Ile1974, Gly1997, Gly1998, Ser1999, Val2001, Val2002 and Val2024, according to Table 1, 2, 3, 4, 5, 6 or 7, or coordinates having a root mean square deviation therefrom, with respect to at least 50% of Cα atoms, of not more than ±1.5 Å or 2 Å, in computer readable form; (b) providing the structure of a candidate compound; (c) determining whether the structure of the candidate compound fits into the binding cavity, comprising determining interactions between the candidate compound and at least one of the residues; and (d) selecting the fitted candidate compound, so as to identify a compound that modulates acetyl-CoA carboxylase activity. The method for identifying a compound that modulates acetyl-CoA carboxylase activity can further comprise outputting the structure of the fitted candidate compound to a user.
The present invention also provides a computer readable medium comprising: the methods for identifying a compound that modulates activity of ACC; the methods for rationally designing a compound that modulates activity of ACC; the methods for identifying a compound that binds to a CT domain of ACC; the methods for identifying an inhibitor compound capable of binding to and inhibiting the enzymatic activity of a CT domain of ACC; or any other methods of the present invention that includes the use of the atomic coordinates provided herein.
The present invention also provides an antibody that specifically binds to any one of the isolated carboxyltransferase domains described herein.
In another aspect, the present invention provides a compound from using any of the methods for identifying a compound that modulates activity of ACC; the methods for rationally designing a compound that modulates activity of ACC; the methods for identifying a compound that binds to a CT domain of ACC; the methods for identifying an inhibitor compound capable of binding to and inhibiting the enzymatic activity of a CT domain of ACC; and any other methods of the present invention that includes the use of the atomic coordinates provided herein; wherein the compound binds to a carboxyltransferase domain of acetyl-CoA carboxylase and comes within about 2-10 Å, 2-7 Å or within about 2.5-4 Å of amino acid residues Ala1761, Lys1764, Met1765 of one monomer of the carboxyltransferase domain and residues Leu2025′, Glu2026′, and Gly2029′ of a second monomer of the carboxyltransferase domain (where the residue numbering is in relation to SEQ ID NO:1, and thus encompasses corresponding residues as listed in Table G or that can be determined by alignment, for example, in FIG. 4); and wherein both monomers combined or together comprise a three-dimensional structure characterized by atomic coordinates of at least 30 amino acid amino residues according to at least one of Tables 1-7; with the proviso that the compound is not haloxyfop, diclofop, or an anthracene-containing compound.
In another aspect, the present invention provides a compound identified by any of the methods for identifying a compound that modulates activity of ACC; the methods for rationally designing a compound that modulates activity of ACC; the methods for identifying a compound that binds to a CT domain of ACC; the methods for identifying an inhibitor compound capable of binding to and inhibiting the enzymatic activity of a CT domain of ACC; and any other methods of the present invention that includes the use of the atomic coordinates provided herein; wherein the compound binds to a carboxyltransferase domain, and wherein the bound compound comes within about 2-10, 2-7 or within about 2.5-4 Å of residues Met1503, Lys1592, Ile1593, Ser1595, Phe1596, Asn1624, Ser1625, Gly1626, Ala1627, Arg1628, Ile1629, Gly1630, Gly1699, Leu1705, Arg1731, Val1733, Gly1734, Ile1735, Tyr1738, Ile1755, Leu1756, Thr1757, Gly1758, Ala1759, Pro1760, Ala1761, Asn1774, Gly1955, Phe1956, Arg1996, Gly1997, Gly1998, Ser1999, Val2001, Val2024, Leu2025, Gly2029, Ile2033, Lys2034, Arg2036, Leu2189 of the CT domain (where the residue numbering is in relation to SEQ ID NO:1, and thus encompasses corresponding residues as listed in Table G or that can be determined by alignment, for example, in FIG. 4), with the proviso that the compound is not haloxyfop, diclofop, or an anthracene-containing compound.
In another aspect, the present invention provides a compound identified by any of the methods for identifying a compound that modulates activity of ACC; the methods for rationally designing a compound that modulates activity of ACC; the methods for identifying a compound that binds to a CT domain of ACC; the methods for identifying an inhibitor compound capable of binding to and inhibiting the enzymatic activity of a CT domain of ACC; and any other methods of the present invention that includes the use of the atomic coordinates provided herein; wherein the compound binds to a carboxyltransferase domain, and wherein the bound compound comes within about 2-10, 2-7 or within about 2.5-4 Å of residues Ile1629, Leu1756, Thr1757, Gly1758, Pro1760, Ala1761, Ile1762, Asn1763, Lys1764, Met1765, Leu1766, Tyr1771, Ala1908, Pro1920, Gln1922, Val1923, Trp1924, His1925, Trp1953, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Gln1960, Asp1962, Arg1996, Gly1997, Ser1999, Val2024, Leu2025, Glu2026, Pro2027, Gln2028, Gly2029, Met2030, Val2031, Gly2032, Ile2033 of the CT domain (where the residue numbering is in relation to SEQ ID NO: 1, and thus encompasses corresponding residues as listed in Table G or that can be determined by alignment, for example, in FIG. 4), with the proviso that the compound is not haloxyfop, diclofop, or an anthracene-containing compound.
In another aspect, the present invention provides a compound identified by any of the methods for identifying a compound that modulates activity of ACC; the methods for rationally designing a compound that modulates activity of ACC; the methods for identifying a compound that binds to a CT domain of ACC; the methods for identifying an inhibitor compound capable of binding to and inhibiting the enzymatic activity of a CT domain of ACC; and any other methods of the present invention that includes the use of the atomic coordinates provided herein; wherein the compound binds to a carboxyltransferase domain, and wherein the bound compound comes within about 2-10, 2-7 or within about 2.5-4 Å of residues Phe1596, Ser1625, Gly1626, Ala1627, Arg1628, Ile1629, Cys1704, Leu1705, Ser1708, Ala1712, Val1733, Gly1734, Ile1735, Gly1736, Ala1737, Tyr1738, Leu1739, Arg1741, Leu1742, Ile1755, Leu1756, Thr1757, Val1923, Trp1924, His1925, Pro1926, Ser1928, Ala1929, Phe1930, Trp1953, Gly1955, Phe1956, Ser1957, Asn1965, Glu1966, Val1967, Leu1968, Lys1969, Tyr1970, Gly1971, Ser1972, Ile1974, Arg1996, Gly1997, Gly1998, Ser1999, Trp2000, Val2001, Val2002, Val2003, Gly2023, Val2024, Leu2025 of the CT domain (where the residue numbering is in relation to SEQ ID NO:1, and thus encompasses corresponding residues as listed in Table G or that can be determined by alignment, for example, in FIG. 4), with the proviso that the compound is not haloxyfop, diclofop, or an anthracene-containing compound.
The present invention also provides for a composition comprising any compound isolated, designed or identified by the methods described herein and a physiologically acceptable carrier.
In another aspect, the present invention provides a three-dimensional model of a carboxyltransferase domain of acetyl-CoA carboxylase, comprising two monomers, wherein both monomers combined comprise a three-dimensional structure characterized by atomic coordinates of at least 30 amino acid residues according to one or more of Tables 1-7.
In another aspect, the present invention provides a data structure comprising atomic coordinates for a carboxyltransferase domain of acetyl-CoA carboxylase, as set forth in any of Tables 1-7, or coordinates having a root mean square deviation therefrom, with respect to at least 50% of Cα atoms, of not more than 1.5 Å or 2 Å.
In one aspect, the present invention provides a computer displaying a virtual model of carboxyltranferase domain of acetyl-CoA carboxylase based on at least twenty amino acid residues having atomic coordinates as set forth in any of Tables 1-7, or coordinates having a root mean square deviation therefrom, with respect to at least 50% of Cα atoms, of not more than about 1.5 Å or 2 Å.
In yet another aspect, the present invention provides a storage medium containing atomic coordinates for a carboxyltransferase domain of acetyl-CoA carboxylase, as set forth in any of Tables 1-7, or coordinates having a root mean square deviation therefrom, with respect to at least 50% of Cα atoms, of not more than about 1.5 Å or 2 Å.
In another aspect, the invention provides a computer system for performing rational drug design comprises atomic coordinate data according to any of Tables 1-7, defining the three-dimensional structure of a crystallized carboxyltransferase domain or of a crystallized carboxyltransferase complex.
In another aspect, the invention provides a computer method for identifying a compound capable of binding to the three-dimensional structure of a carboxyltransferase domain, the computer method comprises a step of determining whether the compound fits into a binding pocket of the carboxyltransferase domain. In this method, the binding pocket can comprise a three-dimensional structure set forth by atomic coordinates of any of Tables 1-7, or any subset of atomic coordinates thereof.
In another aspect, the present invention provides a computer readable media with atomic coordinate data according to Table 1, 2, 3, 4, 5, 6 or 7, recorded thereon, said data defining the three-dimensional structure of crystallized carboxyltransferase or crystallized carboxyltransferase complex.
In one aspect, the present invention provides a method for treating a metabolic syndrome or an insulin resistance syndrome in a subject in need of such treatment, comprising administering to the subject a first compound capable of binding to a second compound having atomic coordinates defined by Table 1 or 7, or coordinates having a root mean square deviation therefrom, with respect to at least 50% of Cα atoms, of not more than 1.5 Å. The metabolic syndrome can comprise, for example, diabetes, obesity, cardiovascular disease, atherosclerosis, depression, cancer, hyperlipidemia, dislipidemia, hypertension, hyperuricemia, renal dysfunction or any combination thereof.
In another aspect, the present invention provides a method for identifying a compound that modulates activity of acetyl-CoA carboxylase, comprising: (a) contacting a carboxyltransferase domain comprising two monomers, each monomer comprising consecutive amino acid residues at least 50% identical to the amino acid residues of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10 or SEQ ID NO:14, with a test compound; (b) determining whether or not the test compound binds to the carboxyltransferase domain; where a determination that the test compound binds to the domain identifies a compound that modulates activity of acetyl-CoA carboxylase. The method can further comprise determining whether the test compound identified in step (b) increases or decreases acetyl-CoA carboxylase activity. The test compound can comprise, for example, a peptide, an organic compound, an antibody or a nucleic acid. Additionally, such test compounds can also be from a library of compounds. The test compounds can also comprise herbicides or fungicides.



BRIEF DESCRIPTION OF THE FIGURES
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawings will be provided by the Office upon request and payment of the necessary fee.
FIGS. 1A-1B. Primary structures of ACCs. FIG. 1A presents a schematic drawing of the primary structures of an eukaryotic (yeast), multi-domain ACC (top) and a bacterial (E. coli), multi-subunit ACC (bottom) The N (terminal) sub-domain of CT is fromabout 1484-1830, and the C (terminal) sub-domain of CT is from about 1830-2233. FIG. 1B shows an alignment of CT domain sequences between yeast ACC, human ACC2 and wheat ACC. The “yeast” sequence spans residues 1481-2210 of SEQ ID NO:1 (GenBank No. Q00955). The “human” sequence spans residues 1715-2452 of SEQ ID NO:7 (GenBank No. AAH22940 (Q13805)). The “wheat” sequence spans residues 1546-2303 of SEQ ID NO:12 (GenBank No. T06161). The residue numbers shown are for yeast ACC. Residues in the core of the monomer structure of the CT domain are colored green, while residues in the dimer interface are colored magenta. The “s.s” abbreviation stands for “secondary structure”, which is either an alpha-helix (α) or a beta-strand (β). A dash “−” represents a residue that is identical to that in yeast ACC, whereas an equal sign represents a residue that is strictly conserved among ACCs (for example, see GenBank Nos. BAA11238; T30568; P32874; S60200; AAK16499; T30568; AAL02056; T02235; AAA81579; T09538; BAA07012; CAA54683; NP—776649; CAA56352; NP—071529; AAP94122; A29924; NP—446374; XP—132282; CAE01471; NP—610342; and NP—493922; the sequence conservation between species in the CT domain (in relation to the span of residues 1484-1830 of SEQ ID NO:1) is high, generally showing a conservation of at least 50% sequence identity. Dots represent gaps in the alignment.
FIGS. 2A-2D. Structure of the CT domain. FIG. 2A presents a schematic drawing in stereo of the structure of the CT domain dimer of yeast ACC. The N and C domains of one monomer are colored cyan and yellow, while those of the other monomer are colored purple and green. The acetyl-CoA molecule bound to one monomer is shown as a stick model. The acetyl portion of the compound is not visible in the electron density map (possibly due to disorder), so only the CoA portion is shown. Only the adenine base was observed in other other monomer (labeled A). FIG. 2B shows a schematic drawing of the structure of the N sub-domain of the CT domain, in stereo. FIG. 2C shows a schematic stereo drawing of the structure of the C domain of the CT domain. Secondary structure elements that are equivalent to those in the N domain are given the same name. FIG. 2D presents a schematic drawing of the structure of crotonase in complex with octanoyl-CoA. In FIGS. 2B, 2C, and 2D, the secondary structure elements are shown and labeled. The residue numbers shown are for yeast ACC.
FIGS. 3A-3D. FIG. 3A presents a schematic drawing in stereo of the active site of the yeast CT domain. The N domain is shown in cyan, and the C domain of the other monomer in green. The side chains of residues in the active site are shown in purple. The prime (′) in the labels indicates the C domain of the other monomer of the dimer. FIG. 3B shows the molecular surface of the active site region of the CT domain, depicting a three-dimensional view of the binding mode of CoA. The side chain of Lys 1764 (α6) has been removed to facilitate the viewing of the active site. FIG. 3C presents a chemical structure of the commercial herbicide haloxyfop. FIG. 3D presents a double-reciprocal plot showing the competitive inhibition of wild-type yeast CT domain by haloxyfop.
FIGS. 4A-4H. Sequence alignment of the CT domains of ACCs from different species. The sequence alignments were conducted using the Blast alignment program (Tatiana A. et al. (1999), “Blast 2 sequences—a new tool for comparing protein and nucleotide sequences”, FEMS Microbiol Lett. 174:247-250; and see National Center for Biotechnology Information website for Blast tools). Specifically, the Blast alignment program used was BlastP Version 2.2.6, where the Matrix used was Blosum 62. FIGS. 4A-4B show an alignment between SEQ ID NO:2 (yeast CT domain) and SEQ ID NO:6 (mouse CT domain of ACC1). The alignment shows that there is a 51% sequence identity and a 65% sequence similarity (“positives”) between SEQ ID NO:2 and SEQ ID NO:6. FIGS. 4C-4D show an alignment between SEQ ID NO:2 and SEQ ID NO:8 (human ACC1 CT domain). This alignment shows that there is a 50% identity and a 66% similarity between SEQ ID NO:2 and SEQ ID NO:8. FIGS. 4E-4F show an alignment between SEQ ID NO:2 and SEQ ID NO:10 (human ACC2 CT domain). This alignment shows that there is a 51% identity and a 66% similarity between SEQ ID NO:2 and SEQ ID NO:10. FIGS. 4G-4H show an alignment between SEQ ID NO:2 and SEQ ID NO:14 (mouse ACC1 CT domain). This alignment shows that there is a 51% identity and a 67% similarity between SEQ ID NO:2 and SEQ ID NO:14.
FIGS. 5A-5C. Crystal structure of the yeast CT domain in complex with haloxyfop. FIG. 5A presents the chemical structures of the herbicides R-haloxyfop, R-diclofop, and sethoxydim. FIG. 5B shows the final 2F0-Fc electron density at 2.8 Å resolution for haloxyfop, contoured at 16. FIG. 5C presents a schematic stereo drawing of the structure of yeast CT domain dimer in complex with haloxyfop. The N domains of the two monomers are colored in cyan and magenta, while the C domains are colored in yellow and green. The inhibitor is shown in stick models. The FIG. 5B drawing was produced with SETOR (Evans, 1993, J. Mol. Graphics 11:134-138). The FIG. 5C drawing was produced with Ribbons (Carson, 1987, J. Mol. Graphics 5:103-106).
FIGS. 6A-6C. The binding mode of haloxyfop. FIG. 6A presents a stereographic drawing showing the binding site for haloxyfop. The N domain of one monomer is colored in cyan, and the C domain of the other monomer in green. The side chains of residues in the binding site are shown in yellow and magenta, respectively. The dashed segment indicates the disordered residues 1959′-1964′. Produced with Ribbons (Carson, 1987, J. Mol. Graphics 5:103-106). FIG. 6B shows a schematic drawing of the interactions between haloxyfop and the yeast CT domain. FIG. 6C presents an overylay of the binding mode of haloxyfop and diclofop. The conformations of residues Tyr1738 and Phe1956′ in the haloxyfop and diclofop complexes are also shown.
FIGS. 7A-7F. Conformational change in the yeast CT domain upon inhibitor binding. FIG. 7A presents a structural overlay of the CT domain free enzyme (in magenta) and the haloxyfop complex (in cyan and green for the N and C domains) near the inhibitor binding site. The binding mode of CoA (Zhang et al., 2003, Science 299:2064-2067) is also shown. The poorer structural overlap in the C domain is due to the change in the dimer organization. FIG. 7B shows the molecular surface of the active site of the free enzyme. The model of haloxyfop is included for reference. Most of the inhibitor is in steric clash with the enzyme. FIG. 7C shows the molecular surface of the binding site in the haloxyfop complex. For both FIGS. 7B and 7C, residues 1759-1772 and 2026′-2098′ have been removed to give a better view of the binding site. FIG. 7D presents a sequence alignment of residues in the haloxyfop binding pocket. Residues that interact with haloxyfop are colored in magenta. The two residues that confer resistance when mutated, Leu1705 and Val1967, are colored in red. A dash represents a residue that is identical to that in yeast ACC, whereas an equal sign represents a residue that is strictly conserved among ACCs. The sequence numbering is in reference to SEQ ID NO: 1 (“yeast ACC”). The human ACC1 sequence is from SEQ ID NO:7, the human ACC2 sequence is from SEQ ID NO:9; the wheat ACC sequence is from SEQ ID NO:12; and the T. gondii sequence is from SEQ ID NO: 11. FIG. 7E shows the inhibition of the wild-type and mutant yeast CT domains by haloxyfop. The activity shown is relative to that in the absence of inhibitor for each enzyme. FIG. 7F shows the inhibition of the wild-type yeast CT domain by haloxyfop, diclofop and sethoxydim. FIG. 7A was produced with Ribbons (Carson, 1987, J. Mol. Graphics 5:103-106). FIGS. 7B and 7C were produced with GRASP (Nicholls et al., 1991, Proteins 11:281-296).
FIGS. 8A-8C. Structure of the L17051/V19671 double mutant. FIG. 8A presents the structure of the dimer of the L17051/V19671 mutant, in the same color scheme as FIG. 5C. FIG. 8B shows a structural overlay of the wild-type (in magenta) and the L17051/V19671 mutant CT domains (in cyan and green for the two monomers) near the active site. FIG. 8C shows the molecular surface near the active site region of the L1705I/V1967I double mutant. The CoA molecule is shown for reference. FIGS. 8A and 8B were produced with Ribbons (Carson, 1987, J. Mol. Graphics 5:103-106). FIG. 8C was produced with GRASP (Nicholls et al., 1991, Proteins 11:281-296).
FIGS. 9A-9B. The amino acid sequence for yeast ACC (SEQ ID NO: 1; GenBank Accession No. Q00955).
FIG. 10. The amino acid sequence encompassing the yeast CT domain encoded by the vector yCTACC. This amino acid sequence (SEQ ID NO:2) corresponds to residues 1429-2233 of SEQ ID NO: 1.
FIG. 11. The amino acid sequence encompassing the yeast CT domain encoded by the vector yCT2ACC. This amino acid sequence (SEQ ID NO:3) corresponds to residues 1476-2233 of SEQ ID NO:1.
FIG. 12. The amino acid sequence of a mutated yeast CT domain (SEQ ID NO:4). The mutations are in reference to the residue numbering of SEQ ID NO: 1, and the amino acid sequence of SEQ ID NO:4 spans residues 1476-2233 as the mutations were introduced on the yCT2ACC background. The mutations consisted of changing Leu1705 into an isoleucine (“L1705I”) and of changing Val 1967 to an isoleucine (“V1967I”).
FIG. 13. The amino acid sequence of mouse ACC2 (SEQ ID NO:5; GenBank Accession No. AAH22940; the corresponding mRNA GenBank Accession No. is BC022940).
FIG. 14. The amino acid sequence (SEQ ID NO:6) encompassing the CT domain of mouse ACC2. The sequence corresponds to residues 35-767 of SEQ ID NO:5.
FIGS. 15A-15B. The amino acid sequence of human ACC1 (SEQ ID NO:7; GenBank Accession No. AAP94122; the corresponding mRNA GenBank Accession No. is AY315627).
FIG. 16. The amino acid sequence (SEQ ID NO:8) encompassing the CT domain of human ACC1. The sequence corresponds to residues 1548-2346 of SEQ ID NO:7.
FIGS. 17A-17B. The amino acid sequence of human ACC2 (SEQ ID NO:9; GenBank Accession No. AAB58382; the corresponding mRNA GenBank Accession No. is U89344).
FIG. 18. The amino acid sequence (SEQ ID NO:10) encompassing the CT domain of human ACC2. The sequence corresponds to residues 1651-2483 of SEQ ID NO:9.
FIG. 19. The amino acid sequence of T. gondii ACC (SEQ ID NO: 11; GenBank Accession No. AAK16499).
FIGS. 20A-20B. The amino acid sequence of wheat ACC (SEQ ID NO:12; GenBank Accession No. T06161).
FIGS. 21A-21B. The amino acid sequence of mouse ACC1 (SEQ ID NO:13; GenBank Accession No. XP—109883.
FIG. 22. The amino acid sequence (SEQ ID NO:14) encompassing the CT domain of mouse ACC1. The sequence corresponds to residues 1294-2110 of SEQ ID NO:13.
FIGS. 23A-23D. FIG. 23A provides the chemical structure of CP-640186. FIG. 23B presents a stereographic drawing showing the binding site for haloxyfop. FIG. 23C presents a schematic of the molecular surface of the active site of the yeast CT domain. The figure shows CP-640186 is bound in the active site, at the interface between two monomers of the ACC enzyme. FIG. 23D shows that the binding site for the CP-640186 compound is distinct or non-competitive from that for CoA or for the herbicides, and this is consistent with kinetic studies that show that the CP-640186 compound is non-competitive with respect to malonyl-CoA.
FIGS. 24A-24B. FIG. 24A shows crystals of free enzyme of yeast CT domain (1429-2233). FIG. 24B shows crystals of an acetyl-CoA complex of yeast CT domain.



DETAILED DESCRIPTION OF THE INVENTION
In general, the present invention is directed to the provision of a detailed three-dimensional structure of the CT domain of the family of acetyl-CoA carboxylases, including yeast, mouse and human ACC. The present invention also provides the three-dimensional structure of the CT domain of ACC, bound to substrates, including, but not limited to, the CT domain of ACC bound to CoA, or bound to inhibitors, including, but not limited to, the CT domain of ACC bound to haloxyfop, diclofop or CP-640186. The present invention also provides methods of using the three-dimensional crystal structures in order to identify and design compounds that can modulate ACC activity. Compositions comprising solated CT domains are also provided.
The following Index of Tables lists the Tables disclosed herein:










INDEX OF TABLES








TABLE
TITLE/DESCRIPTION OF TABLE





1
Atomic Coordinates of Yeast CT Domain (1429-2233)


2
Atomic Coordinates of Yeast CT Domain Complexed



with CoA


3
Atomic Coordinates for Yeast CT Domain Complexed



with Haloxyfop


4
Atomic Coordinates for Yeast CT Domain Complexed



with Diclofop


5
Atomic Coordinates for Yeast CT Domain Complexed



with CP-640186


6
Atomic Coordinates for Mutant Yeast CT Domain


7
Atomic Coordinates for Yeast CT Domain (1476-2233)


A
CT Domain Table


B
Constructs Created and Tested For Production of



Proteins Comprising the CT Domain of Yeast ACC


C
Summary of Crystallographic Information for the Free



Enzyme (Table 1) and the CoA Complex (Table 2)


D
Kinetic Parameters of Wild-Type and Mutant CT


E
Summary of Crystallographic Information for the



Free Enzyme (Table 7), Haloxyfop Complex (Table 3),



Diclofop Complex (Table 4) and the L1705I/V1967I



Mutant (Table 6)


F
Constructs Created and Tested for Production of



Proteins Comprising the CT Domain of Mouse ACC2


G
Corresponding Residues Between SEQ ID NO:



1, 2, 3, 4, 6, 8, 10 and 14
















TABLE A







CT DOMAIN TABLE














SEQ





Row

ID
Unit Cell
Atomic


#
Description
NO:
Info.
Coord.
Comments















1
S. cerevisiae -
1
N/A
N/A




ACC gene
FIG. 9



GenBank



Q00955


2
Yeast ACC gene
—
N/A
N/A
Prior GenBank sequence for yeast ACC -



GenBank



replaced by Q00955 due to sequence errors



AAA20073


3
Yeast CT domain
2
a = 247;
Table 1
(1) Residues in/near the active site of the



(1429-2233 of
FIG. 10
b = 125;

CT domain and/or of a binding pocket:



SEQ ID NO: 1)

c = 145;

Met 1503, Lys 1592, Ile1593, Ser1595,



Vector name:

β = 94;

Phe 1596, Asn 1624, Ser1625, Gly 1626,



yCTACC

space group

Ala1627, Arg1628, Ile1629, Gly1630,





C2;

Met1631, Gly 1699, Gly1701, Glu1703,





Cystal Form I

Cys 1704, Leu1705, Ser1708, Ala1712,







Arg1731, Val1733, Gly1734, Ile1735,







Gly1736, Ala 1737, Tyr1738, Leu 1739,







Arg1741, Leu1742, Pro1753, Ile 1755,







Leu1756, Thr1757, Gly1758, Ala1759,







Pro1760, Ala1761, Ile1762, Asn1763,







Lys1764, Met1765, Leu1766, Tyr1771,







Asn1774, Ala1908, Pro1920, Gly1921,







Gln1922, Val1923, Trp1924, His1925,







Pro1926, Ser1928, Ala1929, Phe1930,







Trp1953, Arg1954, Gly1955, Phe1956,







Ser1957, Gly1958, Gly1959, Gln1960,







Arg1961, Asp1962, Met1963, Phe1964,







Asn1965, Glu1966, Val1967, Leu1968,







Lys1969, Tyr1970, Gly1971, Ser1972,







Ile1974, Val1975, Glu1994, Arg1996,







Gly1997, Gly1998, Ser1999, Trp2000,







Val2001, Val2002, Val2003, Arg2021,







Gly2023, Val2024, Leu2025, Glu2026,







Pro2027, Gln2028, Gly 2029, Met2030,







Val2031, Gly2032, Ile2033, Lys2034,







Arg2036, Asp2098, Val2108 and Leu2189







(2) Acetyl CoA binding pocket residues







(for a compound within at least 7







angstroms of) comprise: Met1503,







Lys1592, Ile1593, Ser1595, Phe1596,







Asn1624, Ser1625, Gly1626, Ala1627,







Arg1628, Ile1629, Gly1630, Gly1699,







Leu1705, Arg1731, Val1733, Gly1734,







Ile1735, Tyr1738, Ile1755, Leu1756,







Thr1757, Gly1758, Ala1759, Pro1760,







Ala1761, Asn1774, Gly1955, Phe1956,







Arg1996, Gly1997, Gly1998, Ser1999,







Val2001, Val2024, Leu2025, Gly2029,







Ile2033, Lys2034, Arg2036, Leu2189.







(3) “Herbicide” binding pocket residues







(for a compound within at least 7







angstroms of) comprise: Phe1596,







Ser1625, Gly1626, Ala1627, Arg1628,







Ile1629, Cys1704, Leu1705, Ser1708,







Ala1712, Val1733, Gly1734, Ile1735,







Gly1736, Ala1737, Tyr1738, Leu1739,







Arg1741, Leu1742, Ile1755, Leu1756,







Thr1757, Val1923, Trp1924, His1925,







Pro1926, Ser1928, Ala1929, Phe1930,







Trp1953, Gly1955, Phe1956, Ser1957,







Asn1965, Glu1966, Val1967, Leu1968,







Lys1969, Tyr1970, Gly1971, Ser1972,







Ile1974, Arg1996, Gly1997, Gly1998,







Ser1999, Trp2000, Val2001, Val2002,







Val2003, Gly2023, Val2024, Leu2025.







(4) “CP compound” binding pocket







residues (for a compound within at least 7







angstroms of) comprise: Ile1629,







Leu1756, Thr1757, Gly1758, Pro1760,







Ala1761, Ile1762, Asn1763, Lys1764,







Met1765, Leu1766, Tyr1771, Ala1908,







Pro1920, Gln1922, Val1923, Trp1924,







His1925, Trp1953, Arg1954, Gly1955,







Phe1956, Ser1957, Gly1958, Gly1959,







Gln1960, Asp1962, Arg1996, Gly1997,







Ser1999, Val2024, Leu2025, Glu2026,







Pro2027, Gln2028, Gly2029, Met2030,







Val2031, Gly2032, Ile2033.


4
Yeast CT domain
2
A = 255;

Another Crystal Form of the Free Enzyme



1429-2233 of

b = 113;



SEQ ID NO: 1

c = 135;





β = 101; space





group C2





Crystal Form





II


5
Yeast CT domain
3
a = 246;
Table 7
See Example 2



(1476-2233 of
FIG. 11
b = 124;



SEQ ID NO: 1)

c = 145;



Vector name:

β = 94;



yCT2ACC

space group





C2


6
SEQ ID NO: 2
N/A
a = 93;
Table 2
See Example 1



complexed with

b = 138;



acetyl-CoA

c = 101;





β = 114;





space





group P21





Crystal Form





III


7
SEQ ID NO: 2
N/A
a = 247;
Table 3
See Example 2



complexed with

b = 125;



haloxyfop

c = 146;





β = 94;





space group





C2 (complex





formed by





soaking





crystals of





SEQ ID





NO: 2 with





haloxyfop)


8
SEQ ID NO: 3
N/A
a = 137;
Table 4
See Example 2



complexed with

b = 137;



diclofop

c = 244;





space





group P3221





(complex





formed by co-





crystallization





of SEQ ID





NO: 3 with





diclofop)





Crystal Form





IV


9
SEQ ID NO: 3
N/A
a = 247;
Table 5
See Example 4



Complexed with

b = 125;



CP-640186

c = 146;





β = 94;





space group





C2 (complex





formed by





soaking





crystals of





SEQ ID





NO: 3 with





CP-640186


10
Yeast CT domain
4
a = 247;
Table 6
See Example 2



of yCTACC with
FIG. 12
b = 125;



mutations: L1705I

c = 146;



and V1967I in

β = 94;



SEQ ID NO: 3

space group





C2


11
Mouse ACC2
5


See Example 3



GenBank
FIG. 13



BC022940



mRNA, this entry



refers to:



AAH22940



protein


12
CT domain of
6


FIG. 4A-B alignment



mouse ACC2 (35-
FIG. 14



767 of GenBank



AAH22940)



Vector:



mCTACC2


13
human ACC1
7


FIG. 1B, FIG. 7D alignments



GenBank
FIG. 15



AY315627



mRNA, this entry



refers to:



AAP94122



protein


14
CT domain of
8


FIG. 4C-4D alignment



human ACC1
FIG. 16



(1548-2346 of



GenBank



AAP94122)



Vector:



hCTACC1


15
Human ACC2
9


FIG. 7D alignment



GenBank U89344
FIG. 17



mRNA refers to



AAB58382



protein


16
CT domain of
10


FIG. 4E-4F alignment



human ACC2
FIG. 18



(1651-2483 of



GenBank



AAB58382)


17
T. gondii ACC
11


FIG. 7D alignment



GenBank
FIG. 19



AAK16499


18
Wheat ACC
12


FIG. 1 and FIG. 7D alignments



GenBank T06161
FIG. 20


19
Mouse ACC1
13



GenBank
FIG. 21



XP_109883


20
CT Domain of
14


FIG. 4G-H alignment



Mouse ACC1
FIG. 22



(1294-2110



of GenBank



XP_109883)









In one embodiment, the present invention provides the atomic coordinates which define the three-dimensional structure of the CT domain of ACC, or an active site, substrate binding site or modulator binding site thereof, alone or in complex with a compound, with a root mean square deviation (RMSD) in the positions of the Cα atoms for at least 50% of the amino acids, of from about 0 to about 4 Å, from about 0 to about 2 Å, 0 from about 0 to about 1.5 Å or from about 0 to about 0.5 Å. The RMSD can also apply to the positions of C, N or O atoms. The term “root mean square deviation” is used herein as it is in the art. For example, in one standard definition, RMSD means the square root of the arithmetic mean of the squares of the deviations from the mean. It is a way to express the deviation or variation from a trend or object. The RMSD defines the variation in the backbone of a polypeptide, protein or protein complex from the relevant portion of the backbone of the CT domain as defined by the atomic coordinates provided herein. The atomic coordinates may be included in a computer readable medium, including a database, and may be displayed on a computer.
In one aspect of the present invention, the isolated CT domain polypeptides are crystallizable compositions. For the first time, the present invention provides crystallizable compositions of CT domains, such that the three-dimensional structure of the CT domain has now been provided, as reflected by the tables of structure coordinates listed in Tables 1-7. This has provided for the first time, information about the shape and structure of the ACC CT domain. The atomic coordinates of Tables 1-7 refers to Cartesian coordinates derived from mathematical equations related to the patterns obtained on diffraction of a beam of X-rays by the atoms (scattering centers) of a CT domain, either in free crystal form or in complexed crystal form. The diffraction data are used to calculate an electron density map of the repeating unit of the crystal. The electron density maps are then used to establish the positions of the individual atoms of the free CT domain or a CT domain complex.
Those of skill in the art will understand that a set of atomic coordinates for a CT domain or a CT domain complex or a portion thereof, is a relative set of points that define a shape in three dimensions. Thus, it is possible that a different set of coordinates could define a similar or identical shape. Therefore, slight variations in the individual coordinates will have little effect on overall shape, i.e. see RMSD. For example, variations in coordinates can be generated because of mathematical manipulations of the coordinates. For example, the structure coordinates of Tables 1-7 could be manipulated by crystallographic permutations of the structure coordinates, integer additions or subtractions to sets of the structure coordinates, inversion of the structure coordinates or any combination of the above. Alternatively, modifications in the crystal structure due to mutations, additions, substitutions and/or deletions of amino acids, or other changes in any of the components that make up the crystal could also account for variations in the structure coordinates. If such variations are within an acceptable standard of error as compared to the original coordinates, the resulting three-dimensional shape is considered to be the same. Thus, in one aspect of the present invention, any molecule or molecular complex that has a RMSD of conserved residue backbone atoms (N, Cα, C, O) of less than about 4 Å, 2 Å, 1.5 Å, 1 Å or 0.5 Å when superimposed on the relevant backbone atoms described by the coordinates listed in any one of Tables 1-7 are considered identical.
Various computational analyses are available to determine whether a molecule or a molecular complex or a portion thereof is sufficiently similar to all or parts of a CT domain or a CT domain complex to be considered the same. Such analyses may be carried out in current software applications, for example, the Molecular Similarity application of QUANTA (Molecular Simulations Inc., San Diego, Calif.) version 4.1. The Molecular Similarity application permits comparisons between different structures, different conformations of the same structure, and different parts of the same structure. The procedure used in Molecular Similarity to compare structures is divided into foru steps: 1) load the structures to be compared; 2) define the atom equivalences in these structures; 3) perform a fitting operation; and 4) analyze the results. For structures to be compared, one structure is identified as the target (the fixed structure) and the remaining structures are working structures (the moving structures). Since atom equivalency with QUANTA is defined by user input, in one aspect of the present invention, equivalent atoms can be defined as protein backbone atoms (N, Cα, C, O) for all conserved residues between any two structures being compared. When a fitting method is used to compare whether two structures are essentially the same, the working structure is translated and rotated to obtain an optimum fit with the target structure. The fitting operation uses an algorithm that computes the optimum translation and rotation to be applied to the moving structure, such that the root mean square difference of the fit over the specified pairs of equivalent atoms is an absolute minimum. This number, given in angstroms, is thereby reported by QUANTA.
The present invention also provides for methods of using a computer to identify modulators of a target CT domain of ACC comprising using a computer-readable three-dimensional structure of the CT domain of an ACC enzyme, a substrate or modulator binding site of the CT domain of ACC, and/or an active site of the CT domain of ACC to design and/or select for a potential modulator of the CT domain of ACC based on the predicted ability of the modulator to bind to a binding site, for example, of the CT domain of ACC. The invention further provides for synthesizing and testing the designed or selected modulator for its ability to modulate the activity of the target CT domain of ACC. For example, a potential modulator may be contacted with the target enzyme in the presence of one or more substrates, and the ability of the target enzyme to act on its substrate in the presence or absence of potential modulator may be measured and compared. As another specific, non-limiting example, the designed or selected potential modulator may be synthesized and introduced into an in vivo or in vitro model system and then the production of malonyl-CoA may be monitored. A modulator that decreases the relative amount of malonyl-CoA may be useful in the treatment of obesity, metabolic syndrome, diabetes, cardiovascular disease, atherosclerosis and infections, whereas a modulator that increases malonyl-CoA may be useful to promote endurance or survival in stressful conditions. In one embodiment, the modulator decreases the activity of ACC2 but not ACC1. A modulator can be essentially any compound, including, a small-molecule, a peptide, a protein, a nucleic acid (including siRNA, anti-sense RNA, catalytic DNA or RNA, DNAzymes, Ribozymes) and antibodies and antibody fragments. A modulator can also be a herbicide or a fungicide.
Modulators identified according to the instant invention also may be used as herbicides. In a further specific, non-limiting example, a designed or selected potential modulator may be contacted with the target enzyme in the presence of a known herbicide that binds to the CT domain of ACC to determine whether the potential modulator competes for binding of the herbicide. The potential modulator also may be tested for its ability to inhibit the growth of certain plants, and the potential modulator may selectively inhibit the growth of “weeds” or other undesired plants. Because the acetyl-CoA carboxylase molecule is large, it is very difficult to crystallize, and has not yet been crystallized. This invention, therefore, provides a solution to a long-felt need, for providing a method to rationally design or modify compounds known to bind to ACC. The provided structure of the CT domain of ACC only now enables one to define, and therefore adjust, the binding mode of any given compound. The virtual models, atomic structure, methods and compositions provided by this invention are useful in the drug discovery of further, as yet unindentified inhibitors or modulators of ACC, and in the design or redesign of modulators of ACC activity.
The present invention also provides for molecules which comprise binding site(s) and/or active sites of the CT domain of ACC, as defined by the atomic coordinates provided by the present invention, in an otherwise synthetic molecule. Such a molecule may be used to screen test compounds, for example compounds in a combinatorial library, for binding to the active site and/or binding sites and/or for suitability as ligands. Within the present invention, a binding site of the CT domain can also be referred to as a binding cavity or a binding pocket. Further, in the present invention, a ligand of a CT domain encompasses essentially any molecule that can bind to the CT domain, including a substrate or a modulator.
The present invention further provides for a method of designing or selecting an inhibitor or agonist of ACC comprising creating a computer model of the negative space present in an unoccupied binding site and/or active site of the CT domain of ACC, which can take into account the electron densities at the boundaries of this space, and using such a model to design or select molecules that modulate the activity of ACC. Such a negative space, particularly a space presented in the context of electrophilic and electrophobic boundaries, in computer readable, electronic form, stored or storable on a floppy disc or computer hard drive, may provide a simple template for the design and/or selection of modulator compounds.
In addition, the present invention provides for a method of evaluating the binding properties of a potential modulator comprising co-crystallizing the modulator with the CT domain of ACC, determining the three-dimensional structure of the modulator bound to the CT domain of ACC and analyzing the three-dimensional structure of the CT domain of ACC bound to the modulator to evaluate the structural aspects of binding. Such a structure may further be used to design and/or select improved potential modulator compounds.
In another embodiment, the present invention provides for polynucleotides encoding an ACC polypeptide having a mutation in one or more residues of the active site and/or a binding site of the CT domain, as those residues are defined herein. Further, CT domain polynucleotides are useful, inter alia, for producing herbicide resistant plants. Accordingly, the present invention also relates to genetically modified herbicide resistant plants.
The present invention further provides for an isolated and purified peptide fragment comprising the CT domain of ACC. In various embodiments, a CT domain of ACC is that provided by the yCTACC, yCT2ACC, mCTACC2, and hCTACC constructs. The isolated and purified peptide fragment comprising the CT domain of ACC is useful, inter alia, for the screening and assay of compounds which modulate the activity of the CT domain of ACC. As noted supra, modulators of the CT domain of ACC may be used in the treatment of various diseases and disorders, including but not limited to, obesity, metabolic syndrome, diabetes, cardiovascular disease, atherosclerosis and infections. The isolated and purified peptide fragment comprising the CT domain of ACC also may be used to design and/or screen metabolic enhancers that may be used to promote endurance or survival under stressful conditions.
The modulators of the activity of the CT domain of ACC to be screened or assayed using the isolated and purified CT domain of ACC of the instant invention may be those designed or identified using the crystal structures concerning the CT domain of ACC provided herein, or they may be existing compounds not previously known to be modulators of the CT domain of ACC.
In one aspect, the following set of amino acids, or a subset thereof: Met 1503, Lys 1592, Ile1593, Ser1595, Phe 1596, Asn 1624, Ser1625, Gly 1626, Ala1627, Arg1628, Ile1629, Gly1630, Met1631, Gly 1699, Gly1701, Glu1703, Cys 1704, Leu1705, Ser1708, Ala1712, Arg1731, Val1733, Gly1734, Ile1735, Gly 1736, Ala 1737, Tyr1738, Leu 1739, Arg 1741, Leu1742, Pro1753, Ile 1755, Leu1756, Thr1757, Gly1758, Ala1759, Pro1760, Ala1761,Ile1762, Asn1763, Lys1764, Met1765, Leu1766, Tyr1771, Asn1774, Ala1908, Pro1920, Gly1921, Gln1922, Val1923, Trp1924, His1925, Pro1926, Ser1928, Ala1929, Phe1930, Trp1953, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Gln1960, Arg1961, Asp1962, Met1963, Phe1964, Asn1965, Glu1966, Val1967, Leu1968, Lys1969, Tyr1970, Gly1971, Ser1972, Ile1974, Val1975, Glu1994, Arg1996, Gly1997, Gly1998, Ser1999, Trp2000, Val2001, Val2002, Val2003, Arg2021, Gly2023, Val2024, Leu2025, Glu2026, Pro2027, Gln2028, Gly 2029, Met2030, Val2031, Gly2032, Ile2033, Lys2034, Arg2036, Asp2098 and Val2108, can be involved as comprising a binding of a substrate or a modulator, or can be involved as comprising an active site. These residues, or a subset thereof, can help form a three-dimensional binding pocket or cavity for a substrate or a modulator and/or can actually make direct or indirect interactions with a substrate or a modulator. The residue numbering is in relation to SEQ ID NO:1. However, the corresponding residues for other polypeptides, including polypeptides of other species, can easily be determined. For example, SEQ ID NO:2 is a polypeptide identical to residues 1429-2233 of SEQ ID NO:1; and hence, Met1503 would correspond to Met75 of SEQ ID NO:2. Similarly, SEQ ID NO:3 is a polypeptide identical to residues 1476-2233 of SEQ ID NO:1; and hence, Met1503 would correspond to Met28 of SEQ ID NO:3. Further, from FIG. 4, SEQ ID NO:2 is aligned with SEQ ID NO:6 (FIGS. 4A-4B), SEQ ID NO:8 (FIGS. 4C-4D) and SEQ ID NO:10 (FIGS. 4E-4F). Thus, corresponding residues in SEQ ID NOS:6, 8 and 10 can be determined for SEQ ID NO:1 numbering. For example, as Met1503 is Met75 in SEQ ID NO:2, Met75 aligns with Leu46 of SEQ ID NO:6 in FIG. 4C; and hence, Leu46 would be the corresponding residue to Met1503. A list of corresponding residues between SEQ ID NOS:1, 2, 3, 4, 6, 8, 10 and 14 is provided in Table G.
Thus, for example, one subset of residues of the binding site that are important for CoA binding is: Ile1593, Ser1595, Ser1625, Ala1627, Arg1628, Ile1629, Gly1630, Met1631, Gly1701, Glu1703, Leu1705, Ser1708, Ala1712, Arg1731, Val1733, Gly1734, Ile1735, Tyr1738, Leu1742, Pro1753, Leu1756, Thr1757, Ala1761, Ile1762, Lys1764, Met1765, Leu 1766, Tyr1771, Pro1920, Gly1921, Val1923, Trp 1924, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Gln1960, Arg1961, Asp1962, Met1963, Phe1964, Asn1965, Val1967, Leu1968, Gly1971, Ile1974, Val1975, Glu1994, Gly1997, Gly1998, Trp2000, Val2001, Val2002, Arg2021, Gly2023, Val2024, Leu2025, Glu2026, Pro2027, Gln2028, Ile2033, Lys2034, Arg2036, Asp2098, and Val2108 (where the numbering corresponds to SEQ ID NO:1). These residues can be considered to comprise one set of residues relevant for the design/analysis of a three-dimensional binding pocket or binding cavity for acetyl-CoA or for a modulator.
Further, from the study of the crystal structure of the yeast CT domain in complex with acetyl-CoA, the following residues have been determined to be within 7 Å of acetyl-CoA, and thus comprise another subset of residues of the CoA binding site: Met1503, Lys1592, Ile1593, Ser1595, Phe1596, Asn1624, Ser1625, Gly1626, Ala1627, Arg1628, Ile1629, Gly1630, Gly1699, Leu1705, Arg1731, Val1733, Gly1734, Ile1735, Tyr1738, Ile1755, Leu1756, Thr1757, Gly1758, Ala1759, Pro1760, Ala1761, Asn1774, Gly1955, Phe1956, Arg1996, Gly1997, Gly1998, Ser1999, Val2001, Val2024, Leu2025, Gly2029, Ile2033, Lys2034, Arg2036, and Leu2189 (where the numbering corresponds to SEQ ID NO:1; and wherein residues numbered below 1800 reside on one monomer and wherein residues numbered above 1800 reside on the other monomer of the CT domain). In addition, these residues can be considered to comprise one set of residues relevant for the design/analysis of a three-dimensional binding pocket or binding cavity for acetyl-CoA or for a modulator.
Further, from the study of the crystal structure of the yeast CT domain in complex with CoA, the following residues have been determined to be within 7 Å of CoA, and thus comprise another subset of residues of the CoA binding site: Ile1593, Ser1595, Ser1625, Gly1626, Ala1627, Arg1628, Ile1629, Arg1731, Val1733, Gly1734, Ile755, Leu1756, Thr1757, Gly1758, Gly1997, Gly1998, Val2024, Leu2025, Ile2033, Lys2034, and Arg2036, (where the numbering corresponds to SEQ ID NO: 1; and wherein residues numbered below 1800 reside on one monomer and wherein residues numbered above 1800 reside on the other monomer of the CT domain). In addition, these residues can be considered to comprise one set of residues relevant for the design/analysis of a three-dimensional binding pocket or binding cavity for acetyl-CoA or for a modulator.
From the study of the crystal structure of the yeast CT domain in complex with haloxyfop, the following residues have been determined to be within 7 Å of haloxyfop, and thus comprise one set of residues for a binding site: Phe1596, Ser1625, Gly1626, Ala1627, Arg1628, Ile1629, Cys1704, Leu1705, Ser1708, Ala1712, Val1733, Gly1734, Ile1735, Gly1736, Ala1737, Tyr1738, Leu1739, Arg1741, Leu1742, Ile1755, Leu1756, Thr1757, Val923, Trp1924, His1925, Pro1926, Ser1928, Ala1929, Phe1930, Trp1953, Gly1955, Phe1956, Ser1957, Asn1965, Glu1966, Val1967, Leu1968, Lys1969, Tyr1970, Gly1971, Ser1972, Ile1974, Arg1996, Gly1997, Gly1998, Ser1999, Trp2000, Val2001, Val2002, Val2003, Gly2023, Val2024, and Leu2025 (where the numbering corresponds to SEQ ID NO: 1; and wherein residues numbered below 1800 reside on one monomer and wherein residues numbered above 1800 reside on the other monomer of the CT domain). In addition, these residues can be considered to comprise one set of residues relevant for the design/analysis of a three-dimensional binding pocket or binding cavity for modulator compounds.
From the study of the crystal structure of the yeast domain in complex with haloxyfop, the following residues have been determined to be within 7 Å of haloxyfop, and thus comprise one set of residues for a binding site: Gly1626, Ala1627, Leu1705, Ser1708, Gly1734, Ile1735, Tyr1738, Leu1756, Trp1924, Ala1929, Phe1956, Val1967, Leu1968, Tyr1970, Gly1971, Ile1974, Gly1997, Gly1998, Ser1999, Val2001, Val2002 and Val2024, (where the numbering corresponds to SEQ ID NO: 1; and wherein residues numbered below 1800 reside on one monomer and wherein residues numbered above 1800 reside on the other monomer of the CT domain). In addition, these residues can be considered to comprise one set of residues relevant for the design/analysis of a three-dimensional binding pocket or binding cavity for modulator compounds.
From the study of the crystal structure of the yeast CT domain in complex with CP-640186, the following residues have been determined to be within 7 Å of CP-640186, and thus comprise yet another subset of residues of a binding site: Ile1629, Leu1756, Thr1757, Gly1758, Pro1760, Ala1761, Ile1762, Asn1763, Lys1764, Met1765, Leu1766, Tyr1771, Ala1908, Pro1920, Gln1922, Val1923, Trp1924, His1925, Trp1953, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Gln1960, Asp1962, Arg1996, Gly1997, Ser1999, Val2024, Leu2025, Glu2026, Pro2027, Gln2028, Gly2029, Met2030, Val2031, Gly2032, and Ile2033 (where the numbering corresponds to SEQ ID NO:1; and wherein residues numbered below 1800 reside on one monomer and wherein residues numbered above 1800 reside on the other monomer of the CT domain). In addition, these residues can be considered to comprise one set of residues relevant for the design/analysis of a three-dimensional binding pocket or binding cavity for non-competitive (non-competitive in respect to the concentration of acetyl-CoA, for example, as acetyl-CoA does not bind in a pocket or cavity that is comprised by the above list of residues) modulator compounds.
From the study of the crystal structure of the yeast CT domain in complex with CP-640186, the following residues have been determined to be within 7 Å of CP-640186, and thus comprise yet another subset of residues of a binding site: Thr1757, Ala1761, Ile1762, Lys1764, Met1765, Leu1766, Val1923, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Leu2025, Glu2026, Gln2028, Gly2029, Gly2032, Ile2033, (where the numbering corresponds to SEQ ID NO: 1; and wherein residues numbered below 1800 reside on one monomer and wherein residues numbered above 1800 reside on the other monomer of the CT domain). In addition, these residues can be considered to comprise one set of residues relevant for the design/analysis of a three-dimensional binding pocket or binding cavity for non-competitive (non-competitive in respect to the concentration of acetyl-CoA, for example, as acetyl-CoA does not bind in a pocket or cavity that is comprised by the above list of residues) modulator compounds.
An α-helix refers to the most abundant helical conformation found in globular proteins and the term is used in accordance with the standard meaning of the art. In an α helix, all amide protons point toward the N-terminus and all carbonyl oxygens point toward the C-terminus. The repeating nature of the phi, psi pairs ensure this orientation. Hydrogen bonds within an α helix also display a repeating pattern in which the backbone C═O of residue X (wherein X refers to any amino acid) hydrogen bonds to the backbone HN of residue X+4. The α helix is a coiled structure characterized by 3.6 residues per turn, and translating along its axis 1.5 Å per amino acid. Thus the pitch is 3.6×1.5 or 5.4 Å. The screw sense of alpha helices is always right-handed.
A β-sheet refers to two or more polypeptide chains (or β-strands) that run alongside each other and are linked in a regular manner by hydrogen bonds between the main chain C═O and N—H groups. Therefore all hydrogen bonds in a beta-sheet are between different segments of polypeptide. Hydrogen bonds in anti-parallel sheets are perpendicular to the chain direction and spaced evenly as pairs between strands. Hydrogen bonds in parallel sheets are slanted with respect to the chain direction and spaced evenly between strands.
A loop refers to any other conformation of amino acids (i.e. not a helix, strand or sheet). Additionally, a loop may contain bond interactions between amino acid side chains, but not in a repetitive, regular fashion.
In one embodiment, the present invention encompasses allelic variants and mutations of the CT domain sequences disclosed herein that are at least 85 percent, at least 90 percent, or at least 95 percent homologous to the naturally occurring CT domain, with homology being determined by standard computer software, such as BLASTP, or ClustalW used with a scoring matrix such as BLOSUM or PAM.
A modulator of ACC enzyme activity refers to a compound which can alter the amount of product generated by a reaction catalyzed by the enzyme. The alteration may be an increase or a decrease. A compound that increases the amount of product is considered an agonist and a compound that decreases the amount of product is considered an inhibitor. Where the biological function of an enzyme encompasses both directions of a reaction (for example ACC catalyzes the carboxylation of acetyl-CoA to produce malonyl-CoA and the decarboxylation of malonyl-CoA to produce acetyl-CoA), whether a modulator is acting as an agonist or an inhibitor depends upon the amount of malonyl-CoA produced. A modulator which decreases the production of malonyl-CoA is an inhibitor. A decrease in malonyl-CoA results in an increase in fatty acid oxidation and a decrease in fatty acid synthesis. Such a decrease may be useful for the treatment of obesity, metabolic syndrome, diabetes, cardiovascular disease, atherosclerosis and infections.
A substrate binding site refers to a region of the CT domain of ACC that retains substrate (for example, acetyl-CoA, malonyl-CoA, biotin) in a position suitable for acyl transfer to occur. The configuration of the substrate binding site is likely to be different in the presence and absence of bound substrate, and both configurations are optimally considered in the design and/or selection of enzyme modulators. Specifically, for the CT domain of yeast ACC, the substrate binding site is schematically depicted in FIGS. 3A and 3B. In one set of non-limiting embodiments of the invention, the acetyl-CoA binding site of ACC is comprised in a protein structure in which the following amino acids, or a subset thereof, may directly contact substrate or otherwise participate in or affect acetyl transfer: Ile1593, Ser1595, Ser1625, Ala1627, Arg1628, Ile1629, Gly1630, Met1631, Gly1701, Glu1703, Leu1705, Ser1708, Ala1712, Arg1731, Val1733, Gly1734, Ile1735, Tyr1738, Leu1742, Pro1753, Leu1756, Thr1757, Ala1761, Ile1762, Lys1764, Met1765, Leu1766, Tyr1771, Pro1920, Gly1921, Val1923, Trp1924, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Gln1960, Arg1961, Asp1962, Met1963, Phe1964, Asn1965, Val1967, Leu1968, Gly1971, Ile1974, Val1975, Glu1994, Gly1997, Gly1998, Trp2000, Val2001, Val2002, Arg2021, Gly2023, Val2024, Leu2025, Glu2026, Pro2027, Gln2028, Ile2033, Lys2034, Arg2036, Asp2098, and Val2108 of yeast ACC and the corresponding amino acids in other ACCs and ACC-related enzymes (see Table G and FIGS. 1, 4 and 7). In another set of non-limiting embodiments of the invention, the acetyl-CoA binding site of ACC is comprised in a protein structure in which the following amino acids, or a subset thereof, may directly contact substrate or otherwise participate in or affect acetyl transfer: Ile1593, Ser1595, Ser1625, Gly1626, Ala1627, Arg1628, Ile1629, Arg1731, Val1733, Gly1734, Ile1755, Leu1756, Thr1757, Gly1758, Gly1997, Gly1998, Val2024, Leu2025, Ile2033, Lys2034, and Arg2036. In another set of non-limiting embodiments of the invention, the acetyl-CoA binding site of ACC is comprised in a protein structure in which the following amino acids, or a subset thereof, may directly contact substrate or otherwise participate in acetyl transfer: Met1503, Lys1592, Ile1593, Ser1595, Phe1596, Asn1624, Ser1625, Gly1626, Ala1627, Arg1628, Ile1629, Gly1630, Gly1699, Leu1705, Arg1731, Val1733, Gly1734, Ile1735, Tyr1738, Ile1755, Leu1756, Thr1757, Gly1758, Ala1759, Pro1760, Ala1761, Asn1774, Gly1955, Phe1956, Arg1996, Gly1997, Gly1998, Ser1999, Val2001, Val2024, Leu2025, Gly2029, Ile2033, Lys2034, Arg2036 and Leu2189 (where the residue numbering is in reference to SEQ ID NO: 1—note: whenever the disclosure lists residues with SEQ ID NO: 1 numbering, the invention encompasses the corresponding residues to other CT domains, including the corresponding residues listed in Table G, or the corresponding residues aligned in FIGS. 1, 4 and 7, or the corresponding residues of other CT domains that can be aligned to SEQ ID NO: 1).
Where amino acid residues are designated by numbers, the numbers are sometimes used to refer to specific amino acids as present in a structurally defined CT domain of ACC to convey the three-dimensional relationship between the residues. Thus, for example, a virtual model of a binding site (for CoA or for a modulator, for example) may consist essentially of residues, or a subset thereof, of: Met 1503, Lys 1592, Ile1593, Ser1595, Phe 1596, Asn 1624, Ser1625, Gly 1626, Ala1627, Arg1628, Ile1629, Gly1630, Met1631, Gly 1699, Gly1701, Glu1703, Cys 1704, Leu1705, Ser1708, Ala1712, Arg1731, Val1733, Gly1734, Ile1735, Gly 1736, Ala 1737, Tyr1738, Leu 1739, Arg 1741, Leu1742, Pro1753, Ile 1755, Leu1756, Thr1757, Gly1758, Ala1759, Pro1760, Ala1761,Ile1762, Asn1763, Lys1764, Met1765, Leu1766, Tyr1771, Asn1774, Ala1908, Pro1920, Gly1921, Gln1922, Val1923, Trp1924, His1925, Pro1926, Ser1928, Ala1929, Phe1930, Trp1953, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Gln1960, Arg1961, Asp1962, Met1963, Phe1964, Asn1965, Glu1966, Val1967, Leu1968, Lys1969, Tyr1970, Gly1971, Ser1972, Ile1974, Val1975, Glu1994, Arg1996, Gly1997, Gly1998, Ser1999, Trp2000, Val2001, Val2002, Val2003, Arg2021, Gly2023, Val2024, Leu2025, Glu2026, Pro2027, Gln2028, Gly 2029, Met2030, Val2031, Gly2032, Ile2033, Lys2034, Arg2036, Asp2098, Val2108 and Leu2189 (where the numbering is in relation to SEQ ID NO:1, and thus encompasses corresponding residues of any CT domain, where the corresponding residues can be identified/determined by Blast alignment and/or Blast homology), with their atoms oriented according to the coordinates set forth in Tables 1-7, without intervening amino acids, and may be referred to as a “molecule” despite the fact that it is only a virtual molecule. Alternatively, additional atoms may be comprised in the site.
Additionally, a virtual model of a CoA binding site may consist essentially of residues Met1503, Lys1592, Ile1593, Ser1595, Phe1596, Asn1624, Ser1625, Gly1626, Ala1627, Arg1628, Ile1629, Gly1630, Gly1699, Leu1705, Arg1731, Val1733, Gly1734, Ile1735, Tyr1738, Ile1755, Leu1756, Thr1757, Gly1758, Ala1759, Pro1760, Ala1761, Asn1774, Gly1955, Phe1956, Arg1996, Gly1997, Gly1998, Ser1999, Val2001, Val2024, Leu2025, Gly2029, Ile2033, Lys2034, Arg2036, and Leu2189, or a subset thereof (where the numbering corresponds to SEQ ID NO: 1; and wherein residues numbered below 1800 reside on one monomer and wherein residues numbered above 1800 reside on the other monomer of the CT domain), with their atoms oriented according to the coordinates set forth in any one of Tables 1-7, without intervening amino acids, and may be referred to as a “molecule” despite the fact that it is only a virtual molecule. Alternatively, additional atoms may be comprised in the site.
A virtual model of a binding site for a modulator may consist essentially of residues: Phe1596, Ser1625, Gly1626, Ala1627, Arg1628, Ile1629, Cys1704, Leu1705, Ser1708, Ala1712, Val1733, Gly1734, Ile1735, Gly1736, Ala1737, Tyr1738, Leu1739, Arg1741, Leu1742, Ile1755, Leu1756, Thr1757, Val1923, Trp1924, His1925, Pro1926, Ser1928, Ala1929, Phe1930, Trp1953, Gly1955, Phe1956, Ser1957, Asn1965, Glu1966, Val1967, Leu1968, Lys1969, Tyr1970, Gly1971, Ser1972, Ile1974, Arg1996, Gly1997, Gly1998, Ser1999, Trp2000, Val2001, Val2002, Val2003, Gly2023, Val2024, and Leu2025, or a subset thereof (where the numbering corresponds to SEQ ID NO:1; and wherein residues numbered below 1800 reside on one monomer and wherein residues numbered above 1800 reside on the other monomer of the CT domain), with their atoms oriented according to the coordinates set forth in any one of Tables 1-7, without intervening amino acids, and may be referred to as a “molecule” despite the fact that it is only a virtual molecule. Alternatively, additional atoms may be comprised in the site.
A virtual model of another binding site for a modulator may consist essentially of residues: Ile1629, Leu1756, Thr1757, Gly1758, Pro1760, Ala1761, Ile1762, Asn1763, Lys1764, Met1765, Leu1766, Tyr1771, Ala1908, Pro1920, Gln1922, Val1923, Trp1924, His1925, Trp1953, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Gln1960, Asp1962, Arg1996, Gly1997, Ser1999, Val2024, Leu2025, Glu2026, Pro2027, Gln2028, Gly2029, Met2030, Val2031, Gly2032, and Ile2033, or a subset thereof, (where the numbering corresponds to SEQ ID NO:1; and wherein residues numbered below 1800 reside on one monomer and wherein residues numbered above 1800 reside on the other monomer of the CT domain) with their atoms oriented according to the coordinates set forth in any one of Tables 1-7, without intervening amino acids, and may be referred to as a “molecule” despite the fact that it is only a virtual molecule. Alternatively, additional atoms may be comprised in the site.
A virtual model of another binding site for a modulator may consist essentially of residues: Gly1626, Ala1627, Leu1705, Ser1708, Gly1734, Ile1735, Tyr1738, Leu1756, Trp1924, Ala1929, Phe1956, Val1967, Leu1968, Tyr1970, Gly1971, Ile1974, Gly1997, Gly1998, Ser1999, Val2001, Val2002 and Val2024, or a subset thereof, (where the numbering corresponds to SEQ ID NO:1; and wherein residues numbered below 1800 reside on one monomer and wherein residues numbered above 1800 reside on the other monomer of the CT domain) with their atoms oriented according to the coordinates set forth in any one of Tables 1-7, without intervening amino acids, and may be referred to as a “molecule” despite the fact that it is only a virtual molecule. Alternatively, additional atoms may be comprised in the site.
A virtual model of another binding site for a modulator may consist essentially of residues: Thr1757, Ala1761, Ile1762, Lys1764, Met1765, Leu1766, Val1923, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Leu2025, Glu2026, Gln2028, Gly2029, Gly2032, Ile2033, or a subset thereof, (where the numbering corresponds to SEQ ID NO:1; and wherein residues numbered below 1800 reside on one monomer and wherein residues numbered above 1800 reside on the other monomer of the CT domain) with their atoms oriented according to the coordinates set forth in any one of Tables 1-7, without intervening amino acids, and may be referred to as a “molecule” despite the fact that it is only a virtual molecule. Alternatively, additional atoms may be comprised in the site.
For purposes of clarity, and not by way of limitation, the detailed description is divided into the following subsections:

    
    
        a. determination of crystal structure;
        b. design of modulators;
        c. screening for modulators;
        d. assay systems;
        e. mutant ACC polypeptides and polynucleotides encoding them
        f. herbicide resistant plants
    
    


Determination of Crystal Structure
The three-dimensional structure of a CT domain of ACC may be determined by obtaining its crystal structure directly and/or by comparing the primary and/or secondary structure of the CT domain of ACC, and/or an incomplete set of components of its three-dimensional structure, with a crystal structure that has already been solved.
The three-dimensional structures obtained from crystals of the CT domain of yeast ACC (“yACC”) and the CT domain in complex with a modulator, may be employed to solve the structures of the CT domains of other ACC species, including but not limited to the CT domains of human ACC (hACC) and mouse ACC (mACC), as well as the structures of the CT domains of other acetyl-CoA carboxylases. The atomic coordinates calculated for yCTACC (SEQ ID NO:2) are set forth in Table 1. The atomic coordinates calculated for yCTACC in complex with CoA are set forth in Table 2. The atomic coordinates calculated for yCTACC in complex with haloxyfop are set forth in Table 3. The atomic coordinates calculated for yCT2ACC (SEQ ID NO:3) in complex with diclofop are set forth in Table 4. The atomic coordinates calculated for yCT2ACC (SEQ ID NO:3) in complex with CP-640186 are set forth in Table 5. The atomic coordinates calculated for yCT2ACC with the L17051 and V19671 mutations (SEQ ID NO:4) are set forth in Table 6. The atomic coordinates calculated for yCT2ACC (SEQ ID NO:3) are set forth in Table 7.
The CT domain of ACC may be prepared from a natural source, may be produced by recombinant DNA technology, or may be chemically synthesized (although this last possibility would be extremely cumbersome). For example, a full-length cDNA encoding an acetyl-CoA carboxylase such as ACC may be subcloned from a cDNA preparation by the polymerase chain reaction (PCR), using at least one primer design based on known, homologous, or obtained protein sequence, and inserted into an expression vector. Standard deletion mutagenesis techniques then may be used to remove those regions of the ACC cDNA not encoding the CT domain.
In specific, non-limiting embodiments, the isolated CT domain of ACC may be obtained from ACC proteins found in yeasts, such as S. cerevisiae, or in mammalian species, such as Mus musculus or Homo sapiens. Specific, non-limiting examples of the CT domains for the ACC of S. cerevisiae comprise amino acids 1429-2233 (SEQ ID NO:2) or 1476-2233 (SEQ ID NO:3), respectively, of the amino acid sequence set forth in GenBank Entry No. Q00955 (SEQ ID NO: 1). Specific, non-limiting examples of the CT domains for the ACC of M. musculus ACC2 comprise amino acids 35-767 (SEQ ID NO:6) of the amino acid sequence set forth in GenBank Entry No. AAH22940 (SEQ ID NO:5) (the corresponding mRNA sequence is set forth in GenBank Entry No. BC022940). Specific, non-limiting examples of the CT domains for the ACC of M. musculus ACC1 comprise amino acids 1294-2110 (SEQ ID NO: 14) of the amino acid sequence set forth in GenBank Entry No. XP—109883 (SEQ ID NO:13). Specific, non-limiting examples of the CT domains for the ACC of H. sapiens ACC1 comprise amino acids 1548-2346 (SEQ ID NO:8) of GenBank Entry No. AAP94122 (SEQ ID NO:7) (the corresponding mRNA sequence is set forth in GenBank Entry No. AY315627). Specific, non-limiting examples of the CT domains for the ACC of H. sapiens ACC2 comprise amino acids 1651-2483 (SEQ ID NO:10) of GenBank Entry No. AAB58382 (SEQ ID NO:9) (the corresponding mRNA sequence is set forth in GenBank Entry No. U89344).
A nucleic acid encoding a CT domain of ACC, or a fusion protein comprising said CT domain of ACC, may be operably linked to other elements which aid in its expression, such as a promoter element. One of skill in the art would know, based on the degeneracy of the genetic code, how to set out the many possible nucleotide sequences that would code for the amino acids of SEQ ID NOS:2-14. A large number of suitable vector-host systems are known in the art. Possible vectors include, but are not limited to, plasmids or modified viruses, but the vector system must be compatible with the host cell used. Examples of vectors include E. coli bacteriophages such as lambda derivatives, or plasmids such as pBR322 derivatives or pUC plasmid derivatives, e.g., pGEX vectors (Amersham-Pharmacia, Piscataway, N.J.), pET vectors (Novagen, Madison, Wis.), pmal-c vectors (Amersham-Pharmacia, Piscataway, N.J.), pFLAG vectors (Chiang and Roeder, 1993, Pept. Res. 6:62-64), baculovirus vectors (Invitrogen, Carlsbad, Calif.; Pharmingen, San Diego, Calif.), etc. The insertion into a cloning vector can, for example, be accomplished by ligating the DNA fragment into a cloning vector which has complementary cohesive termini, by blunt end ligation if no complementary cohesive termini are available or through nucleotide linkers using techniques standard in the art. E.g., Ausubel et al. (eds.), Current Protocols in Molecular Biology, (1992). Recombinant vectors comprising the nucleic acid of interest may then be introduced into a host cell compatible with the vector (e.g. E. coli, insect cells, mammalian cells, etc.) via transformation, transfection, infection, electroporation, etc. The nucleic acid may also be placed in a shuttle vector which may be cloned and propagated to large quantities in bacteria and then introduced into a eukaryotic host cell for expression. The vector systems of the present invention may provide expression control sequences and may allow for the expression of proteins in vitro.
The CT domains of any of the afore-mentioned ACCs, produced either naturally, synthetically or by recombinant means, may be purified by methods known in the art, including, but not limited to, selective precipitation, dialysis, chromatography, and/or electrophoresis. Purification may be monitored by measuring the ability of a fraction to perform the catalytic activity. Any standard method of measuring acetyl-CoA carboxylase activity may be used.
For certain embodiments, it may be desirable to express the CT domain of ACC as a fusion protein. In specific non-limiting embodiments, the fusion protein comprises a tag which facilitates purification. As referred to herein, a “tag” is any added series of amino acids which are provided in a protein at either the C-terminus, the N-terminus, or internally. Suitable tags include but are not limited to tags known to those skilled in the art to be useful in purification such as, but not limited to, His tag, glutathione-s-transferase tag, flag tag, mbp (maltose binding protein) tag, etc. Such tagged proteins may also be engineered to comprise a cleavage site, such as a thrombin, enterokinase or factor X cleavage site, for ease of removal of the tag before, during or after purification. Vector systems which provide a tag and a cleavage site for removal of the tag are particularly useful to make the expression constructs of the present invention. A tagged ACC may be purified by immuno-affinity or conventional chromatography, including but not limited to, chromatography employing the following: glutathione-SepharoseTM (Amersham-Pharmacia, Piscataway, N.J.) or an equivalent resin, nickel or cobalt-purification resins, nickel-agarose resin, anion exchange chromatography, cation exchange chromatography, hydrophobic resins, gel filtration, antiflag epitope resin, reverse phase chromatography, etc.
In certain embodiments, the CT domain of ACC is expressed as His-tagged protein by subcloning a DNA sequence encoding residues 1429-2233 (SEQ ID NO:2) of the S. cerevisiae ACC protein disclosed by Zhang et al. (Science 2003;299:2064-2067) or SEQ ID NO:3 into the pET24 d vector (Novagen) and over-expressing the His-tagged fusion protein expressed from the resulting vector in E. coli at 20° C.; the soluble protein then may be purified by nickel-agarose affinity and anion exchange chromatography. The purified protein may be concentrated to 10 mg/ml and flash-frozen in liquid nitrogen.
After purification, at least 90 to at least 95 percent of total protein is the CT domain of ACC, the enzyme, or a mixture of the enzyme and one or more substrates or modulators thereof, may be concentrated to greater than 1 mg/ml for crystallization purposes. In one embodiment, the concentration is greater than 5 mg/ml.
Any crystallization technique known to those skilled in the art may be employed to obtain the crystals of the present invention, including, but not limited to, batch crystallization, vapor diffusion (either by sitting drop or hanging drop) and micro dialysis. Seeding of the crystals in some instances may be required to obtain X-ray quality crystals. Standard micro and/or macro seeding of crystals may therefore be used. In one embodiment, the crystals are obtained using the sitting-drop vapor diffusion method. Different crystallization methods can result in the formation of different crystal forms (i.e., polymorphs or solvates), and thus, the present invention encompasses the different crystal forms for the CT domain of ACC. For example, the yeast CT domain has been crystallized in at least four different crystal forms (denoted herein as “Form I”, “Form II”, “Form III” and “Form IV”), as manifested by their different crystal unit cell parameters: Form I refers to the crystal that comprises the unit cell information: a=247±2 Å; b=125±2 Å; c=145±2 Å; α=90°; β=94±2°; γ=90°; and space group C2. The atomic coordinates for this crystal is set forth in Table 1, and a picture of the crystals is presented in FIG. 24A. Form II refers to the crystal that comprises the unit cell information: a=255±2 Å; b=113±2 Å; c=135±2 Å; α=90°; β=101+2°; γ=90°; and space group C2. Form III refers to the crystal that comprises the unit cell information: a=93±2 Å; b=138±2 Å; c=101±2 Å; α=90′; β=114±2°; γ=90°; and space group P21. The atomic coordinates for this crystal is set forth in Table 2, and a picture of the crystals is presented in FIG. 24B. Form IV refers to the crystal that comprises the unit cell information: a=137±2 Å; b=137±2 Å; c=244±2 Å; α=90°; β=90°; γ=120; and space group P3221. The atomic coordinates for this crystal is set forth in Table 4.
To collect diffraction data from the crystals of the present invention, the crystals may be flash-frozen in the crystallization buffer employed for the growth of said crystals, however with preferably higher precipitant concentration (see, Examples below). For example, but not by way of limitation, if the precipitant used was 20% PEG 3350, the crystals may be flash frozen in the same crystallization solution employed for the crystal growth wherein the concentration of the precipitant is increased to 25% (see Examples below). If the precipitant is not a sufficient cryoprotectant (i.e. a glass is not formed upon flash-freezing), cryoprotectants (e.g. glycerol, ethylene glycol, low molecular weight PEGs, alcohols, etc.) may be added to the solution in order to achieve glass formation—upon flash-freezing, providing the cryoprotectant is compatible with preserving the integrity of the crystals. The flash-frozen crystals are maintained at a temperature of less than −110° C. or less than −150° C. during the collection of the crystallographic data by X-ray diffraction.
In certain embodiments, the protein crystals and protein-substrate complex co-crystals of the present invention diffract to a high resolution limit of at least greater than or equal to 3.5 angstrom (Å) or greater than or equal to 3 Å; it should be noted that a greater resolution is associated with the ability to distinguish atoms placed closer together. In one embodiment, the protein crystals and protein-substrate complex co-crystals of the present invention diffract to a high resolution limit of greater than 2.5 Å or 1.5 Å.
Thus, a crystal of the present invention may take a variety of forms. In one embodiment, the crystallized CT domain of ACC has a space group of C2 with three molecules in the asymmetric unit and with unit dimensions for the free enzyme of: a=247±2 Å; b=125±2 Å; c=145±2 Å; α=90°; β=94±2°; γ=90° (see e.g., Examples, below). In another embodiment, the crystallized CT domain of ACC has a space group of C2 with three molecules in the asymmetric unit and with unit dimensions for the free enzyme of: a=255±2 Å; b=113±2 Å; c=135±2 Å; α=90°; β=101±2°; γ=90°. In another embodiment, the crystallized CT domain of ACC has a space group of C2 with three molecules in the asymmetric unit and with unit dimensions for the free enzyme of: a=246±2.5 Å; b=124±2 Å; c=145±2 Å; α=90°; β=94±2°; γ=90°. In another embodiment, the crystallized mutant CT domain (SEQ ID NO:4) of ACC has a space group of C2 with three molecules in the asymmetric unit and with unit dimensions for the free enzyme of a=247±2 Å; b=125+2 Å; c=146±2 Å; α=90°; β
=94±2°; γ=90°. In another embodiment, the CT domain:acetyl-CoA complex has a crystal with a space group of P21, with two molecules in the asymmetric unit and with unit dimensions of: a=93±2 Å; b=138±2 Å; c=101+2 Å; α=90; β=114±2°; γ=90°. In another embodiment, the CT domain:diclofop complex has a crystal with a space group of P3221, with two molecules in the asymmetric unit and with unit dimensions of: a=137±2 Å; b=137+2 Å; c=244±2 Å; α=90°; β=90°; γ=1200. In another embodiment, the CT domain:haloxyfop complex has a crystal with a space group of C2, with three molecules in the asymmetric unit and with unit dimensions of: a=247±2 Å; b=125±2 Å; c=146±2 Å; α=90°; β=94±°; γ=90°. In another embodiment, the CT domain:CP-640186 complex has a crystal with a space group of C2, with three molecules in the asymmetric unit and with unit dimensions of: a=247±2 Å; b=125±2 Å; c=146±2 Å; α=90°; β=94±2oo; γ=90°.
Data obtained from the diffraction pattern may be solved directly or may be solved by comparing it to a known structure, for example, the three-dimensional structure of the CT domain of yACC (with or without substrates or modulators). If the crystals are in a different space group than the known structure, molecular replacement may be employed to solve the structure, or if the crystals are in the same space group, refinement and difference Fourier methods may be employed. The structure of the CT domain of ACC, as defined herein, exhibits no greater than about 4.0 Å, 1.5 Å or 0.5 Å root mean square deviation (RMSD) in the positions of the Cα atoms for at least 50% or more of the amino acids.
In a specific, non-limiting embodiment of the present invention, seleno-methionyl proteins may be used to directly determine the structure of a CT domain of an ACC. Hendrickson, 1991, Science, 254:51-58. For example, a seleno-methionyl single wavelength anomalous diffraction (SAD) data set may be collected at 100K on the free enzyme and native reflection data sets may be collected for enzyme/substrate complexes. X-ray diffraction data may be processed with the HKL package. Otwinowski and Minor, 1997, Methods Enzymol. 276:307-326. The location of seleno-methionyl atoms may be determined with the program SnBv2.0 (Weeks and Miller, 1999, Acta Crystallogr D Biol Crystallogr 55:492-500) and may further be confirmed with SHELXS (Sheldrick, 1990, Acta Crystal. A46:467-473). Reflection phases, which can be, for example, less than or equal to 4.0 Å, may be calculated based on the SAD data and may further be improved with the program SOLVE (Terwilliger and Berendzen, 1999, Acta Cryst. D55:849-861). The resulting atomic model may be built into the electron density with the problem O (Jones et al., 1991, Acta Crystal A47:110-119). A structure of the enzyme/substrate complex may be determined by molecular replacement with the program COMO (Jogl et al., 2001, Acta Cryst. D57:1127-1134) and structural refinement may be carried out with the program CNS (Brunger et al., 1998, Acta Cryst. D54:905-921).
Any method known to those skilled in the art may be used to process the X-ray diffraction data. In addition, in order to determine the atomic structure of an ACC according to the present invention, multiple isomorphous replacement (MIR) analysis, model building and refinement may be performed. For MIR analysis, the crystals may be soaked in heavy-atoms to produce heavy atom derivatives necessary for MIR analysis. As used herein, heavy atom derivative or derivatization refers to the method of producing a chemically modified form of a protein or protein complex crystal wherein said protein is specifically bound to a heavy atom within the crystal. In practice a crystal is soaked in a solution containing heavy metal atoms or salts, or organometallic compounds, e.g., lead chloride, gold cyanide, thimerosal, lead acetate, uranyl acetate, mercury chloride, gold chloride, etc., which can diffuse through the crystal and bind specifically to the protein. The location(s) of the bound heavy metal atom(s) or salts can be determined by X-ray diffraction analysis of the soaked crystal. This information is used to generate MIR phase information which is used to construct the three-dimensional structure of the crystallized CT domain of ACC of the present invention. Thereafter, an initial model of the three-dimensional structure may be built using the program O (Jones et al., 1991, Acta Crystallogr. A47:110-119). The interpretation and building of the structure may be further facilitated by use of the program CNS (Brunger et al, 1998, Acta Crystallogr. D54:905-921).
The method of molecular replacement broadly refers to a method that involves generating a preliminary model of the three-dimensional structure of crystal of a CT domain of an ACC of the present invention whose structural coordinates were previously unknown. Molecular replacement is achieved by orienting and positioning a molecule whose structural coordinates are known (e.g. yCTACC or yCT2ACC, as described herein) within the unit cell as defined by the X-ray diffraction pattern obtained from the CT domain of an ACC under study (or the corresponding enzyme/substrate complex or enzyme/inhibitor complex) so as to best account for the observed diffraction pattern of the unknown crystal. Phases can then be calculated from this model and combined with the observed amplitudes to give an approximate Fourier synthesis of the structure whose coordinates are unknown. This in turn can be subject to any of several forms of refinement to provide a final, accurate structure.
The molecular replacement method may be applied using techniques known to the skilled artisan. For example, the program COMO may be employed to determine the previously unknown structure of a CT domain of an ACC or its enzyme/substrate or enzyme/inhibitor complexes by molecular replacement using the coordinates or a subset of coordinates, of yCTACC set forth in Table 1, the coordinates or a subset of coordinates, of yCTACC in complex with acetyl-CoA set forth in Table 2, the coordinates or a subset of coordinates, of yCTACC in complex with haloxyfop set forth in Table 3, the coordinates or a subset of coordinates, of yCTACC in complex with diclofop set forth in Table 4, the coordinates or a subset of coordinates, of yCT2ACC in complex with CP-640186 set forth in Table 5, the coordinates or a subset of coordinates, of yCTACC with mutations LI 7051 and VI 9671 set forth in Table 6, or the coordinates or a subset of coordinates, of yCT2ACC set forth in Table 7, as reference structures.
The three-dimensional structures and the specific atomic coordinates associated with said structures of the CT domain of yeast ACC, alone or in complex with a substrate such as acetyl-CoA or a modulator, are useful for solving the structure of crystallized forms of CT domains of other ACCs. This technique may could also be applied to solve the structures of ACC-related proteins, where there is sufficient sequence identity. Such ACC-related proteins comprise a root mean square deviation (RMSD) of no greater than 2.0 Å, 1.5 Å, 1.0 Å or 0.5 Å in the positions of Cα atoms for at least 50 percent or more of the amino acids of the structure of the CT domain of ACC of the present invention. Such an RMSD may be expected based on the amino acid sequence identity. Chothia and Lesk, 1986, EMBO J. 5:823-826.
The refined three-dimensional structures of the CT domains of ACCs of the present invention, specifically different spans of the CT domain (SEQ ID NO:2; SEQ ID NO:3) of yeast ACC, a mutant CT domain of yeast ACC, the CT domain of yeast ACC in complex with CoA, the CT domain of yeast ACC in complex with haloxyfop, diclofop or CP-640186, are represented by the atomic coordinates set forth in Tables 1-7. A description of various specific features of these structures is presented in the Examples section below. Such description may be useful for solving the structures of other ACCs.
Design of Modulators
Modulators of ACC may be designed, according to the invention, using three-dimensional structures obtained as set forth in the preceding section and the Examples section below. These structures may be used to design or screen for molecules that are able to form the desired interactions with one or more binding sites of the CT domain of ACC.
The models of the CT domain (and sub-regions, including active sites, binding sites or cavities thereof) of ACC described herein may be used to either directly develop a modulator for ACC or indirectly develop a modulator of an ACC-related enzyme for which the structure has not yet been solved. A modulator designed to interact with a CT domain may be reasonably expected to interact not only with the CT domain but also with the other ACC-related enzymes. The ability for such a modulator to modulate the activity of a CT domain of ACC can be confirmed by further computer analysis, and/or by in vitro and/or in vivo testing.
In non-limiting embodiments, the present invention provides for a model, actual or virtual, of the CT domain (the whole domain, or parts, such as a particular substrate or modulator binding site) of ACC. The reactive site or the active site of the CT domain of ACC is located the interface of a dimer of CT and comprises the N and C domains of the two monomers of the dimer (see FIGS. 2A and 3A). More specifically, the active site comprises a cavity between the small β-sheets (with strands β5, β7, β9, and β11) of the β-β-α super-helix of the two domains (see Examples below and FIG. 3A). The CoA molecule is mostly associated with the N domain of one molecule in the dimer (FIG. 3A). The biotin substrate is mostly associated with the small β-sheet in the C domain of the other monomer in the active site (see FIG. 3A). The three-dimensional orientation of atoms in the cavity at the interface of the dimers is as set forth by the atomic coordinates for these elements provided for yACC herein, to within about 2 Å, 1.5 Å, or 0.5 Å thereof.
Characteristics of the active site include, but are not limited to, one or more of the following features: 1) binding of haloxyfop, diclofop, CP-640186 or other modulators to the CT active site at the interface between two monomers of the ACC enzyme; 2) interaction between the CF3 group of haloxyfop or similar ACC inhibitors with the side chains of Trp1924′, Val 1967′, Ile1974′, wherein the presence of the prime sign after the numerical identifier indicates that the designated residue is in the second monomer; 3) the pyridyl ring of haloxyfop is π-stacked with the side chains of Tyr1738 and Phe1956′; 4) the phenyl ring of haloxyfop interacts with the main chains of Gly1734-Ile1735, and Gly1997′-Gly1998′; 5) one carboxylate oxygen of haloxyfop is hydrogen-bonded to the main chain amides of Ile1735 and Ala1627, and the other carboxylate oxygen of haloxyfop is exposed to the solvent; 6) the methyl group of the propionate moiety of haloxyfop interacts with Leu1705 and Ala1627; 7) binding of haloxyfop induces significant conformational changes for the side chains of Tyr1738 and Phe1956′, which in turn open up the hydrophobic core of the dimer; 8) the trifluoropyridyl group of haloxyfop is inserted into this hydrophobic core; 9) residues Phe1956′-1965′ become disordered upon binding of haloxyfop; 10) other than Leu1705 and Val1967′, most of the residues of the binding site of the CT domain of ACC that interact with haloxyfop are strictly or highly conserved among the CT domains; 11) there are only small conformational changes in the ACC enzyme upon binding of CP-640186, in contrast to the binding of herbicides; 12) the binding site for the CP-640186 compound is distinct from that for CoA or for the herbicides; 13) the anthracene group of CP-640186 is placed in the narrow channel between helices α6 and β6′, interacting with residues Ala1761, Lys1764, Met1765 on one face and residues Leu2025′, Glu2026′, and Gly2029′ on the other; 14) the carbonyl oxygen next to the anthracene group is hydrogen-bonded to the main-chain amide of Gln2028′; 15) thc remainder of the CP-640186 compound (the two piperidine rings and morpholine ring) is placed next to the peptide segment Arg1954′-Gly1959′, and has interactions with Val 1923′, Thr1757, and Ile1762; 16) one face of these piperidine rings and morpholine ring is exposed to the solvent in the CT complex; 17) the carbonyl oxygen next to the morpholine ring is hydrogen-bonded to the main-chain amide of Gly1958′; and 18) most of the residues that interact with the CP compound are strictly or highly conserved among the CT domains, two exceptions are Met1765 which is Val in most mammalian ACCs, and Ile1762, which is Leu in most other ACCs—additional residues may also be important for binding, for example, Gly2032 is replaced by Glu in most other ACCs, and this Glu side chain could ion-pair with Lys1764, forming a lid over the anthracene group.
A model of an active site may be comprised in a virtual or actual protein structure that is smaller than, larger than, or the same size as a native CT domain of an ACC protein. The protein environment surrounding the active site model may be homologous or identical to native CT domain of an ACC, or it may be partially or completely non-homologous.
In particular non-limiting embodiments of the invention, the CoA binding site of a model is as schematically depicted in FIG. 3, In another set of specific, non-limiting embodiments, the acetyl CoA binding site comprises amino acid residues Ile1593, Ser1595, Ser1625, Ala1627, Arg1628, Ile1629, Gly1630, Met1631, Gly1701, Glu1703, Leu1705, Ser1708, Ala1712, Arg1731, Val1733, Gly1734, Ile1735, Tyr1738, Leu1742, Pro1753, Leu1756, Thr1757, Ala1761, Ile1762, Lys1764, Met1765, Leu1766, Tyr1771, Pro1920, Gly1921, Val1923, Trp 1924, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Gln1960, Arg1961, Asp1962, Met1963, Phe1964, Asn1965, Val1967, Leu1968, Gly1971, Ile1974, Val1975, Glu1994, Gly1997, Gly1998, Trp2000, Val2001, Val2002, Arg2021, Gly2023, Val2024, Leu2025, Glu2026, Pro2027, Gln2028, Ile2033, Lys2034, Arg2036, Asp2098, and Val2108, or a subset thereof, of yACC or the equivalent residues from another ACC, in a configuration as defined by the atomic coordinates set forth in Tables 1-7. In another set of specific, non-limiting embodiments, the acetyl CoA binding site comprises amino acid residues: Met1503, Lys1592, Ile1593, Ser1595, Phe1596, Asn1624, Ser1625, Gly1626, Ala1627, Arg1628, Ile1629, Gly1630, Gly1699, Leu1705, Arg1731, Val1733, Gly1734, Ile1735, Tyr1738, Ile1755, Leu1756, Thr1757, Gly1758, Ala1759, Pro1760, Ala1761, Asn1774, Gly1955, Phe1956, Arg1996, Gly1997, Gly1998, Ser1999, Val9001, Val2024, Leu2025, Gly2099, Ile2033, Lys2034, Arg2036, and Leu2189, or a subset thereof, of yACC or the equivalent residues from another ACC, in a configuration as defined by the atomic coordinates set forth in Tables 1-7.
In particular non-limiting embodiments of the invention, one binding site for modulators is schematically depicted in FIGS. 5, 6 and 7. In another set of specific, non-limiting embodiments, one modulator binding site comprises amino acid residues Phe1596, Ser1625, Gly1626, Ala1627, Arg1628, Ile1629, Cys1704, Leu1705, Ser1708, Ala1712, Val1733, Gly1734, Ile1735, Gly1736, Ala1737, Tyr1738, Leu1739, Arg1741, Leu1742, Ile1755, Leu1756, Thr1757, Val1923, Trp1924, His1925, Pro1926, Ser1928, Ala1929, Phe1930, Trp1953, Gly1955, Phe1956, Ser1957, Asn1965, Glu1966, Val1967, Leu1968, Lys1969, Tyr1970, Gly1971, Ser1972, Ile1974, Arg1996, Gly1997, Gly1998, Ser1999, Trp2000, Val2001, Val2002, Val2003, Gly2023, Val2024, and Leu2025, or a subset thereof, of yACC or the equivalent residues from another ACC, in a configuration as defined by the atomic coordinates set forth in Tables 1-7.
In particular non-limiting embodiments of the invention, one binding site for modulators is schematically depicted in FIG. 23. In another set of specific, non-limiting embodiments, one modulator binding site comprises amino acid residues Ile1629, Leu1756, Thr1757, Gly1758, Pro1760, Ala1761, Ile1762, Asn1763, Lys1764, Met1765, Leu1766, Tyr1771, Ala1908, Pro1920, Gln1922, Val923, Trp1924, His1925, Trp1953, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Gln1960, Asp1962, Arg1996, Gly1997, Ser1999, Val2024, Leu2025, Glu2026, Pro2027, Gln2028, Gly2029, Met2030, Val2031, Gly2032, and Ile2033 or a subset thereof, of yeast ACC (“yACC”) or the equivalent residues from another ACC, in a configuration as defined by the atomic coordinates set forth in Tables 1-7.
Thus, the present invention provides for a method for rationally designing a modulator of an ACC, comprising the steps of (i) producing a computer readable model of a molecule comprising a region (i.e., an active site, reactive site, or a binding site) of a CT domain of ACC (e.g. yACC); and (ii) using the model to design a test compound having a structure and a charge distribution compatible with (i.e. able to be accommodated within) the region of the CT domain, wherein the test compound can comprise a functional group that may interact with the active site to modulate acetyl-CoA carboxylase activity. If the crystal structure is not available for the CT domain to be examined, homology modeling methods known to those of ordinary skill in the art may be used to produce a model, which then may be used to design test compounds as described above.
The atomic coordinates of atoms of the CT domain (or a region/portion thereof) of an ACC or an ACC-related enzyme may be used in conjunction with computer modeling using a docking program such as GRAM, DOCK, HOOK or AUTODOCK (Dunbrack et al., 1997, Folding & Design 2:27-42) to identify potential modulators. This procedure can include computer fitting of potential modulators to a model of a CT domain (including models of regions of a CT domain, for example, an active site, or a binding site) to ascertain how well the shape and the chemical structure of the potential modulator will complement the active site or to compare the potential modulators with the binding of substrate or known inhibitor molecules in the active site.
Computer programs may be employed to estimate the attraction, repulsion and/or steric hindrance associated with a postulated interaction between the reactive site model and the potential modulator compound. Generally, characteristics of an interaction that are associated with modulator activity include, but are not limited to, tight fit, low stearic hindrance, positive attractive forces, and specificity.
Modulator compounds of the present invention may also be designed by visually inspecting the three-dimensional structure of a reactive site of the CT domain of an ACC or ACC-related enzymes, a technique known in the art as “manual” drug design. Manual drug design may employ visual inspection and analysis using a graphics visualization program known in the art.
In designing potential modulator compounds according to the invention, the functional aspect of a modulator may be directed at a particular step of the ACC catalytic mechanism, as illustrated by the following non-limiting example.
In ACC, the CT domain catalyzes the carboxylation of acetyl-CoA, by transferring a carboxyl group from biotin to acetyl-CoA, to produce malonyl-CoA, and also catalyzes the decarboxylation of malonyl-CoA, by transferring a carboxyl group to a biotin methyl ester, to produce acetyl-CoA. According to the invention, a modulator intended to decrease malonyl-CoA levels decreases the carboxylation of acetyl-CoA. Correspondingly, a modulator that is intended to increase malonyl-CoA levels facilitates the carboxylation of acetyl-CoA.
Because it is known that ACC2 knockout mice (see U.S. Patent Application Publication No. US2003/0028912 A1) are “skinny” and that knockout of ACC1 is embryonically lethal in mice, it may be desirable to design modulators which selectively inhibit ACC2 and not ACC1 (Abu-Elheiga et al., Science, 291, 2613, (2001). This may be achieved as discussed further below under the heading assay systems.
In various non-limiting embodiments, the present invention provides for virtual or actual models of the active site of the CT domain of ACC. As set forth above, such a model may or alternatively may not comprise additional amino acid residues in addition to amino acid residues of the active site. Characteristics of the active site model in the actual or virtual presence of bound haloxyfop provide a non-limiting physical description of the active site model which pertain in the presence or absence of haloxyfop. As examples, active site models of the invention may, in the presence of haloxyfop, comprise the CF3 group of haloxyfop interacting with side chains of Trp1924′, Val1967′, Ile1974 of the active site model; and/or comprise a pyridyl ring of haloxyfop π-stacked with the side chains of Tyr1738 and Phe1956′ of the active site model; and/or comprise an interaction between the phenyl ring of haloxyfop and the main chains of Gly1734-Ile1735, and Gly1997′-Gly1998′ in the active site model; and/or comprise one carboxylate oxygen of haloxyfop hydrogen-bonded to the main chain amides of Ile1735 and Ala1627 of the active site model, where the other carboxylate oxygen of haloxyfop is exposed to the exterior; and/or comprise the methyl group of the propionate moiety of haloxyfop interacting with Leu1705 and Ala1627; and/or comprise significant conformational changes for the side chains of Tyr1738 and Phe1956′ which open up a hydrophobic core into which the trifluoropyridyl group of haloxyfop is inserted; and/or comprise disordered residues Phe1956′-1965′.
Further, the binding mode of diclofop is essentially the same as for haloxyfop (see FIG. 6C and Examples). The carboxyl groups of the two inhibitors essentially have the same binding mode, and the aromatic rings of diclofop show small but recognizable differences in their positions as compared to those of halxofop, but the two chloro substituents in diclofop superimpose well with the substituents in haloxyfop. For the enzyme, the Phe1956′ side chain has a different conformation, which may be linked to the change in the position of diclofop. On the other hand, the Tyr1738 side chains show little structural differences, and the other residues in the binding site have essentially the same conformation in the two complexes. The α4 helix is disordered in the co-crystals with diclofop as well. Moreover, the dimer organization in the diclofop complex is the same as the haloxyfop complex, as it also has the 2.5° rotation of the second monomer relative to the first monomer. Thus, characteristics of the active site model in the actual or virtual presence of bound diclofop provide a non-limiting physical description of the active site model which pertain in the presence or absence of diclofop.
The present invention, in further non-limiting embodiments, provides for methods of designing an ACC inhibitor, comprising virtually or physically constructing, identifying or designing a compound which, when actually or virtually bound to the active site model, interacts with side chains of Trp1924′, Val1967′, Ile1974 of the active site model; and/or n-stacks with the side chains of Tyr1738 and Phe1956′; and/or interacts with the main chains of Gly1734-Ile1735, and Gly1997′-Gly1998′; and/or comprises one carboxylate oxygen hydrogen-bonded to the main chain amides of Ile1735 and Ala1627; and/or comprises a methyl group which interacts with Leu1705 and Ala1627; and/or induces conformational changes for the side chains of Tyr1738 and Phe1956′, which may open a hydrophobic core; and/or causes residues Phe1956′-1965′ of the model to become disordered. Such methods may comprise the step of designing the compound to have one or more of the above-listed effects on the active site model.
Further, active site models of the invention may, in the presence of CP-640186, comprise a model for a binding site that is distinct from the binding sites for CoA or for herbicides such as haloxyfop or diclofop. Such a binding site can comprise the interaction with a modulator with residues Ala1761, Lys1764, Met1765 on one face of the ACC dimer and residues Leu2025′, Glu2026′, and Gly2029′ on the other. Since the carbonyl oxygen next to the anthracene group of CP-640186 is hydrogen-bonded to the main-chain amide of Gln2028′, Gln2028′ may be involved in the binding of a modulator in this binding site. Similarly, residues Arg1954′-Gly1959′, Val1923′, Thr1757, Ile1762, Gly1958′, Met1765, Ile1762, Gly2032 and Lys1764 may comprise important residues for a model of this binding site.
Screening for Modulator Compounds
As an alternative or an adjunct to rationally designing modulators, random screening of a small molecule library, a peptide library or a phage library for compounds that interact with and/or bind to a site/region of interest (i.e., a binding site, active site or a reactive site, for example) of the CT domain of ACC or ACC-related enzymes may be used to identify useful compounds. Such screening may be virtual; small molecule databases can be computationally screened for chemical entities or compounds that can bind to or otherwise interact with a virtual model of an active site, binding site or reactive site of a CT domain of an ACC. Alternatively, screening can be against actual molecular models of the CT domain or portions thereof. In one embodiment, modulators which selectively bind ACC2 and not ACC1, or vice versa, are screened. Further, antibodies can be generated that bind to a site of interest of the CT domain. After candidate (or “test”) compounds that can bind to the CT domain are identified, the compounds can then be tested to determine whether they can modulate CT domain enzymatic activity (see Assay Systems section below).
In one embodiment, CT domain proteins, nucleic acids, and cells containing the CT domains are used in screening assays. Screens may be designed to first find candidate compounds that can bind to a CT domain or portion thereof, and then these compounds may be used in assays that evaluate the ability of the candidate compound to modulate CT domain or ACC enzymatic activity. Thus, as will be appreciated by those in the art, there are a number of different assays which may be run, including binding assays and activity assays. In one aspect, candidate compounds are first tested to determine whether they can bind to a particular binding site of the CT domain, i.e., the binding site for CoA, the binding site used by diclofop/haloxyfop or the binding site used by anthracene comprising compounds.
Thus, in one embodiment, the methods comprise combining a CT domain or portion thereof and a candidate compound, and determining the binding of the candidate compound to the CT domain or portion thereof. In some embodiments of the methods herein, the CT domain (or portion thereof) or the candidate agent is non-diffusably bound to an insoluble support having isolated sample receiving areas (e.g., a microtiter plate, an array, etc.). The insoluble supports may be made of any composition to which the compositions can be bound, is readily separated from soluble material, and is otherwise compatible with the overall method of screening. The surface of such supports may be solid or porous and of any convenient shape. Examples of suitable insoluble supports include microtiter plates, arrays, membranes and beads. These are typically made of glass, plastic (e.g., polystyrene), polysaccharides, nylon or nitrocellulose, TeflonTM, etc. Microtiter plates and arrays are especially convenient because a large number of assays can be carried out simultaneously, using small amounts of reagents and samples—i.e., they enable high-throuput screening. Following binding of the CT domain, excess unbound material is removed by washing. The sample receiving areas may then be blocked through incubation with bovine serum albumin (BSA), casein or other innocuous protein or other moiety.
A candidate compound is added to the assay. Candidate compounds include, but are not limited to, specific antibodies, compounds from chemical libraries, peptide analogs, etc. Of particular interest are screening assays for compounds that have a low toxicity for human cells. A wide variety of assays may be used for this purpose, including labeled in vitro protein-protein binding assays, immunoassays for protein binding, NMR assays to determine protein-protein or protein-chemical compound binding, and the like. Candidate compounds can also include herbicides or fungicides.
The term “candidate compound” as used herein describes any molecule, e.g., protein, oligopeptide, small organic molecule, polysaccharide, polynucleotide, etc., with the capability of directly or indirectly modulating CT domain or ACC enzymatic activity. Generally a plurality of assay mixtures are run in parallel with different compound concentrations to obtain a differential response to the various concentrations. Typically, one of these concentrations serves as a negative control, i.e., at zero concentration or below the level of detection.
Candidate compounds can encompass numerous chemical classes, though typically they are organic molecules, and in one embodiment they are small organic compounds having a molecular weight of more than 100 and less than about 2,500 daltons. Candidate compounds can comprise functional groups necessary for structural interaction with proteins, for example hydrogen bonding, and typically include at least an amine, carbonyl, hydroxyl or carboxyl group, preferably at least two of the functional chemical groups. The candidate compounds can comprise cyclical carbon or heterocyclic structures and/or aromatic or polyaromatic structures substituted with one or more of the above functional groups. Candidate agents are also found among biomolecules including peptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof.
Candidate compounds can be obtained from a wide variety of sources including libraries of synthetic or natural compounds. For example, numerous means are available for random and directed synthesis of a wide variety of organic compounds and biomolecules, including combinatorial chemical synthesis and the expression of randomized peptides or oligonucleotides. Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts are available or readily produced. Additionally, natural or synthetically produced libraries and compounds are readily modified through conventional chemical, physical and biochemical means. Known pharmacological agents may be subjected to directed or random chemical modifications, such as acylation, alkylation, esterification, amidification to produce structural analogs. In one embodiment, the library is fully randomized, with no sequence preferences or constants at any position. In another, the library is biased. That is, some positions within the sequence are either held constant, or are selected from a limited number of possibilities.
The determination of the binding of the candidate compound to the CT domain may be done in a number of ways. In one embodiment, the candidate compound is labelled, and binding determined directly. For example, this may be done by attaching all or a portion of the CT domain to a solid support, adding a labelled candidate compound (for example a fluorescent label or radioactive label), washing off excess reagent, and determining whether the label is present on the solid support. Various blocking and washing steps may be utilized as is known in the art.
By “labeled” herein is meant that the compound is either directly or indirectly labelled with a label which provides a detectable signal, e.g., radioisotope, fluorescers, enzyme, antibodies, particles such as magnetic particles, chemiluminescers, or specific binding molecules, etc. Specific binding molecules include pairs, such as biotin and streptavidin, digoxin and antidigoxin, etc. For the specific binding members, the complementary member would normally be labeled with a molecule which provides for detection, in accordance with known procedures, as outlined above. The label can directly or indirectly provide a detectable signal.
In one embodiment, the binding of the candidate compound is determined through the use of competitive binding assays. In this embodiment, the competitor is a binding moiety known to bind to the CT domain, such as an antibody, peptide, ligand (i.e., acetyl-CoA, haloxyfop, diclofop or CP-640186), etc. Under certain circumstances, there may be competitive binding as between the candidate compound and the known binding moiety, with the binding moiety displacing the bioactive agent.
In one embodiment, the candidate compound is labeled. Either the candidate compound, or the competitor, or both, is added first to the CT domain for a time sufficient to allow binding, if present. Incubations may be performed at any temperature which facilitates optimal binding, typically between 4 and 40° C. Incubation periods are selected for optimum binding but may also be optimized to facilitate rapid high-throughput screening. Typically between 0.1 and 1 hour will be sufficient. Excess reagent is generally removed or washed away. The second component is then added, and the presence or absence of the labeled component is followed, to indicate binding.
In one embodiment, the competitor is added first, followed by the candidate compound. Displacement of the competitor is an indication that the candidate compound is binding to the CT domain and thus is capable of binding to, and potentially modulating, the activity of the CT domain or ACC enzyme. In this embodiment, either component can be labeled. Thus, for example, if the competitor is labeled, the presence of label in the wash solution indicates displacement of the competitor by the candidate compound. Alternatively, if the candidate compound is labeled, the presence of the label on the support indicates displacement of the candidate compound.
In one embodiment, a potential ligand for a CT domain can be obtained by screening a recombinant bacteriophage library (Scott and Smith, Science, 249:386-390 (1990); Cwirla et al., Proc. Natl. Acad. Sci., 87:6378-6382 (1990); Devlin et al., Science, 249:404-406 (1990). Specifically, the phage library can be mixed in low dilutions with permissive E. coli in low melting point LB agar which is then poured on top of LB agar plates. After incubating the plates at 37° C. for a period of time, small clear plaques in a lawn of E. coli will form which represents active phage growth and lysis of the E. coli. A representative of these phages can be absorbed to nylon filters by placing dry filters onto the agar plates. The filters can be marked for orientation, removed, and placed in washing solutions to block any remaining absorbent sites. The filters can then be placed in a solution containing, for example, a radioactive CT domain (or portion thereof). After a specified incubation period, the filters can be thoroughly washed and developed for autoradiography. Plaques containing the phage that bind to the radioactive CT domain or portion thereof can then be identified. These phages can be further cloned and then retested for their ability to bind to the CT domain as before. Once the phages have been purified, the binding sequence contained within the phage can be determined by standard DNA sequencing techniques. Once the DNA sequence is known, synthetic peptides can be generated which represents these sequences, and further binding studies can be performed as discussed herein.
In another embodiment, a potential ligand for a CT domain can be obtained by screening a candidate compounds by NMR (see for example, U.S. Patent Application Publication No. US2003/0148297A1 or Pellecchia et al., Nature Reviews Drug Discovery, 1:211-219 (2002)). As mentioned, a CT domain or portions thereof can be immobilized to all types of solid supports. It is not needed that the binding be a covalent binding. It is only required that the target is kept immobilized in the NMR measuring environment. Moreover, the immobilization need not be directly to the solid support; it may also occur indirectly through suitable bridging moieties or molecules, or through spacers. Very suitable supports are solid polymers used in chromatography, such as polystyrene, sepharose and agarose resins and gels, e.g. in bead form or in a porous matrix form. Additionally, appropriately chemically modified silicon based materials are also very suitable supports.
Any soluble molecule can be used as a compound that is a candidate to binding to the CT domain. It is not necessary that the said soluble molecule is water-soluble. Any liquid medium that does not denature the said compound nor the CT domain molecule can be used in the NMR measurements. The CT domain target molecule is immobilized to a suitable support, such as a solid resin, and additionally placed in a suitable NMR probe, for example, a flow injection NMR probe, for the duration of the screening. Each sample of the compounds to be screened, e.g. the compounds from a library, is then applied to the immobilized target by pumping it through, along or via the solid support. The sample to be assayed may contain a single component suspected of binding to the CT domain target molecule, or may contain multiple components of a compound library or other type of collection or mixture. The flow may be stopped when a desired level of concentration of the compounds to be assayed is reached in the target containing probe or vessel.
For the acquisition of the NMR spectra, in principle any NMR pulse sequence capable of detecting resonances from dissolved molecule samples and, preferably suppressing residual solvent signals, such as by pulsed field gradients, may be used to detect binding. In practice, however, a one-dimensional 1H-NMR spectrum is acquired with sufficient resolution and sensitivity to detect and quantitate resonances derived from each compound being assayed in the presence of the control solid support. In addition, a second spectrum recorded using the same NMR protocol, is acquired for the same solution of screenable compounds in the presence of the solid support containing the immobilized CT domain target molecule. Optionally, a third spectrum may be acquired in the presence of the solid support containing the immobilized CT domain target molecule in order to detect extremely weak target binding. This spectrum can be recorded while using a diffusion or T2 filter.
After acquisition of the NMR spectrum, the sample of small compound or compounds is washed out of the NMR probe containing the target immobilized solid support. Subsequently, the next sample can be applied to the probe in a stopped-flow manner. Throughout the entire screening process a single sample of the target immobilized solid support remains in the NMR probe. The target immobilized solid support need only be changed should the target become denatured, chemically degraded or saturated by a tight-binding compound that cannot be washed away. In order to safeguard that certain compounds do not bind in such a way that the target molecule is blocked, at certain stages, a control is carried out to check the availability of binding opportunities to the target molecule.
The NMR spectra are preferably compared by subtracting one of the two NMR data sets from the other, thereby creating a difference spectrum. In general, since the target molecule is essentially in the solid phase, the resonances from compounds that bind to the target molecule are broadened beyond detection while in the bound state. Thus, binding is sensitively and reliably detectable by a decrease in height of peaks that derive exclusively from the solution form of compounds binding to the target molecule. This effect is most easily seen in the difference spectra. An alternative approach that can be used to quantitate the affinity of the target-ligand interaction is to determine peak areas (e.g. by integrating) in the control and experimental spectra and compare the values of these areas. Although it is possible to carry out the NMR screening method in batch mode, in the flow-injection set-up, one sample of target may be used to screen an entire library.
The present invention also encompasses antibodies that can specifically bind to the CT domain, including specific regions of the CT domain, such as binding sites. Antibodies include, for example, monoclonal antibodies and antibody fragments, such as Fab′, Fab, F(ab′)2, single domain antibodies (DABs), Fv, and scFv (single chain Fv). The techniques for preparing and characterizing antibodies are well known in the art (see, for example, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988). Monoclonal antibodies may be readily prepared through the use of well-known techniques, such as those exemplified in U.S. Pat. No. 4,196,265. Typically, this technique involves immunizing a suitable animal with a selected immunogen composition, e.g., a purified or partially purified ACC protein, ACC polypeptide, ACC peptide, CT domain or fragment thereof. The immunizing composition is administered in a manner effective to stimulate antibody-producing cells. These antibody-producing cells are then isolated and fused with tumor cells. The result of this cell fusion is a “hybridoma,” which will continually produce antibodies. These antibodies are called monoclonal because they come from only one type of cell, the hybridoma cell; polyclonal antibodies, on the other hand, are derived from preparations containing many kinds of cells.
Assay Systems
Potential modulators of acetyl-CoA carboxylase activity, produced, for example, by rational drug design or by screening of libraries as described above, may be subjected to one of the following assays to confirm their activity.
After identifying candidate compounds that can bind to the CT domain, these candidate compounds are then tested to determine whether they can modulate ACC enzymatic activity. For example, the candidate compounds can be tested by using enzyme kinetic assays to test the effects of a candidate compound upon CT domain catalytic activity (see, Examples, FIGS. 7E and 7F, Kuchhait et al. 1974, J. Biol. Chem. 249:6633-6645 (1974), and Harwood, H. J. et al., J. Biol. Chem. 278:37099-37111 (2003)). The CT domain can catalyze the decarboxylation of malonyl-CoA to produce acetyl-CoA in the presence of biotin methyl ester. Thus, the enzyme kinetic assays monitor the production of acetyl-CoA by coupling it to citrate synthase and malate dehydrogenase, which ultimately lead to the reduction of NAD+.
A potential modulator may be subjected to virtual testing using a computer model of the CT domain of ACC or portions thereof, using the methods set forth for screening libraries of compounds. In other embodiments, a potential modulator may be evaluated for its ability to physically interact with the CT domain of an ACC or an ACC-related enzyme by co-crystallizing the potential modulator with the CT domain of the ACC or the ACC-related enzyme and then determining the structure of the resulting co-crystal. For example, the structure of the co-crystal may be determined by molecular replacement to assess the binding characteristics. The ability of the compound to modulate enzyme activity may be correlated with its ability to physically interact with the reactive site and/or to assume an orientation that would facilitate or inhibit carboxylation of malonyl.
In one specific example, a modulator may be determined to interact with the reactive site of the CT domain of yACC if, in a co-crystal of the modulator and yACC, the modulator contains an atom, (and in one embodiment, the atom is of functional group) within about 2-10 Å, 2-7 Å or within about 2.5-4 Å of an atom comprised in one or more of the following yACC amino acid residues (or corresponding amino acid residues for other ACCs): Met 1503, Lys 1592, Ile1593, Ser1595, Phe 1596, Asn 1624, Ser1625, Gly 1626, Ala1627, Arg1628, Ile1629, Gly1630, Met1631, Gly 1699, Gly1701, Glu1703, Cys 1704, Leu1705, Ser1708, Ala1712, Arg1731, Val1733, Gly1734, Ile1735, Gly 1736, Ala 1737, Tyr1738, Leu 1739, Arg 1741, Leu1742, Pro1753, Ile 1755, Leu1756, Thr1757, Gly1758, Ala1759, Pro1760, Ala1761, Ile1762, Asn1763, Lys1764, Met1765, Leu1766, Tyr1771, Asn1774, Ala1908, Pro1920, Gly1921, Gln1922, Val1923, Trp1924, His1925, Pro1926, Ser1928, Ala1929, Phe1930, Trp1953, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Gln1960, Arg1961, Asp1962, Met1963, Phe1964, Asn1965, Glu1966, Val1967, Leu1968, Lys1969, Try1970, Gly1971, Ser1972, Ile974, Val1975, Glu1994, Arg1996, Gly1997, Gly1998, Ser1999, Trp2000, Val2001, Val2002, Val2003, Arg2021, Gly2023, Val2024, Leu2025, Glu2026, Pro2027, Gln2028, Gly 2029, Met2030, Val2031, Gly2032, Ile2033, Lys2034, Arg2036, Asp2098, Val2108 and Leu2189 (residue numbering of SEQ ID NO:1). Co-crystallization with the CT domain of ACC2 and ACC1 can be accomplished in order to determine whether the modulator is selective for either ACC2 or ACC1.
The present invention further provides for assays comprising incubating the potential modulator with a purified CT domain of an ACC, such as yACC, mACC (ACC1 or ACC2) or hACC (ACC 1 or ACC2), or a plant ACC, performing gel filtration to separate any free potential modulator from ACC-bound modulator, and determining the amount of acetyl carboxylation activity of the modulator-bound enzyme. To measure binding constants (e.g., Kd), methods known to those in the art may be employed such as BiacoreTM analysis, isothermal titration calorimetry, fluorescence, ELISA with substrate on the plate to show competitive binding, or by a malonyl carboxylation activity assay. Similarly, the reaction rate may be measured by methods known in the art. In addition, relative binding affinities can be calculated, for example, to determine whether the modulator selectively binds ACC2 and not ACC1.
The present invention further provides for methods that determine the effect of a potential modulator in vivo. Such methods may provide important information, including the effect of the modulator on molecules involved in interrelated pathways may be determined. For example, a potential modulator may be administered to a cell, such as a liver cell, a fat cell, a heart cell, or a skeletal cell, that is capable of regulating fatty acid oxidation, and/or the biosynthesis of long-chain fatty acids, and then the level of one or more molecules involved in fatty oxidation, the Embden-Meyerhoff pathway, the Krebs cycle, mitochondrial electron transport, fatty acid synthesis, and gluconeogenesis, including insulin, glycogen, cholesterol, and ketone bodies, may be measured, and the success or failure of the potential modulator to achieve the desired effect may be determined. For example, a modulator intended to effect preferential metabolism of fats (for example, in the treatment of obesity) may have one or more of the following effects: an increase in the acetyl-CoA/CoA ratio; increased intermediates or products of fatty acid oxidation; decreased intermediates or products of the Embden-Meyerhoff pathway, including lactic acid or lactate; decreased intermediates and products of fatty acid synthesis; decreased glycogen stores, increased ATP production, decreased ATP consumption, and decreased insulin sensitivity. The foregoing in vivo assays may be performed in a cell in the context of a cell culture, a tissue explant, and/or an organism. Equivalent in vitro systems that duplicate one or more of the recited pathways may also be used to assay the modulator for desired activity.
Further in vivo systems include plant in vivo systems in which the modulators of the present invention are administered to plants, and in particular weeds, to determine whether the modulator is a potential herbicide. The ability to slow or inhibit plant growth indicates that the modulator is a candidate herbicide. Alternatively, a modulator may improve the growth of plants, in which case, the modulator may be useful as a fertilizer. The modulators may also be tested for their ability to selectively slow or inhibit unwanted plant growth, while having a lesser effect on the herbicide resistant plants of the present invention.
Mutant Acc Polynucleotides and Polypeptides
The amino acid sequences of the CT domains are highly conserved among the eukaryotic multi-functional ACCs (FIG. 1B and FIG. 4), and they share very limited homology to the two subunits of the bacterial ACCs (FIG. 1A). However, the CT domains do not share any recognizable sequence homology with other proteins in public databases. The carboxyltransferase (CT) domain contains about 800 residues (90 kD) (about residues 1429-2233 or residues 1476-2233 or residues 1484-2233 of SEQ ID NO:1, where SEQ ID NO:1 has the Genbank accession number Q00955), and constitutes approximately the C-terminal one-third of the eukaryotic, multi-domain ACCs. The amino acid sequences of this domain are highly conserved; for example, there is about 50% sequence identity between the CT domains of yeast ACC and mouse ACC2, human ACC1 and human ACC2 (see FIG. 4A-F). Further, when the degree of conservation is even higher when examining particular residues of the CT that are considered important in a structural sense. For example, Table G provides a list of residues that are important for substrate and modulator binding, and the degree of identity of these residues between yeast and mouse or human is greater than about 70%. Further, the present invention provides the crystal structures of the free enzyme and CoA complex of the CT domain of yeast ACC, as well as the crystal structures of the haloxyfop, diclofop and CP-640186 complexes. The structure contains two sub-domains, the N and C domains, and the active site is located at the interface of a dimer of the enzyme.
The present invention provides for isolated and purified CT domains of ACCs comprising at least one amino acid mutation. The present invention further provides for polynucleotides encoding these isolated and purified polypeptides. Such polypeptides preferably include a mutation in one or more amino acids selected from the group consisting of Met 1503, Lys 1592, Ile1593, Ser1595, Phe 1596, Asn 1624, Ser1625, Gly 1626, Ala1627, Arg1628, Ile1629, Gly1630, Met1631, Gly 1699, Gly1701, Glu1703, Cys 1704, Leu1705, Ser1708, Ala1712, Arg1731, Val1733, Gly1734, Ile1735, Gly 1736, Ala 1737, Tyr1738, Leu 1739, Arg 1741, Leu1742, Pro1753, Ile 1755, Leu1756, Thr1757, Gly1758, Ala1759, Pro1760, Ala1761, Ile1762, Asn1763, Lys1764, Met1765, Leu1766, Tyr1771, Asn1774, Ala1908, Pro1920, Gly1921, Gln1922, Val1923, Trp1924, His1925, Pro1926, Ser1928, Ala1929, Phe1930, Trp1953, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Gln1960, Arg1961, Asp1962, Met1963, Phe1964, Asn1965, Glu1966, Val1967, Leu1968, Lys1969, Try1970, Gly1971, Ser1972, Ile1974, Val1975, Glu1994, Arg1996, Gly1997, Gly1998, Ser1999, Trp2000, Val2001, Val2002, Val2003, Arg2021, Gly2023, Val2024, Leu2025, Glu2026, Pro2027, Gln2028, Gly 2029, Met2030, Val2031, Gly2032, Ile2033, Lys2034, Arg2036, Asp2098, Val2108 and Leu2189 of yACC (residue numbering of SEQ ID NO:1) or the corresponding amino acid from any ACC or ACC-related enzyme. The corresponding amino acids may be determined by amino acid alignment methods known in the art and referenced herein above. For a review of sequence alignment methodology, see Phillips et al., 2000, Mol Phylogenet Evol. 16:317-330.
The mutant CT domain polypeptides of the present invention may comprise a deletion and/or mutation in one or more of the above-enumerated amino acids. As used herein, a mutation includes a deletion, a conserved amino acid change and/or non-conserved amino acid change. The polypeptides of the present invention may comprise all or a portion of the remaining amino acids of the CT domain of ACC. For example, the polypeptide may comprise one or more mutations in the above-enumerated amino acids. The polypeptide may further comprise additional deletions/additions/mutations, so long as the resultant polypeptide comprises one or more mutations in the above-enumerated amino acids and the resultant polypeptide has reduced or increased acetyl-CoA carboxylase activity as compared to the CT domain of wild-type ACC, wherein the reduction or increase in the activity is a direct result of the mutation in one or more of the above-enumerated amino acid residues.
The polynucleotides of the present invention which encode the mutated CT domain polypeptide can be made by any means known in the art. For example, PCR may be employed to generate a polynucleotide comprising codons which result in a mutation in one or more of the above-enumerated amino acid residues. Commercial kits are also available for producing mutants, such as QuikChangeTM (Stratagene). In addition, site directed mutagenesis may be employed, as well as chemical synthesis. The skilled artisan is well versed in the methods available for producing the polynucleotides and polypeptides of the present invention.
The present invention further provides for vectors comprising the polynucleotides of the present invention, including expression vectors in which the polynucleotide is operably linked to expression control sequences. In one embodiment, the vector is suitable for expression in plants and/or suitable for creating a genetically modified plant, such as a plant in which the native CT domain of ACC is replaced by the mutated CT domain of ACC of the present invention or a plant in which the mutated CT domain of ACC of the present invention is overexpressed, as further described in the following section.
Herbicide Resistant Plants
The CT domain of ACC is also the site of action of two different classes of commercial herbicides (Gronwald, 1991, Weed Science 39:435-449; Devine and Shukla, 2000, Crop Protection 19:881-889; Zagnitko et al., 2001, Proc. Natl. Acad. Sci. USA 98:6617-6622; Delye et al., 2003, Plant Physiol. 132:1716-1723), as represented by haloxyfop and sethoxydim, respectively. See FIG. 5A. These compounds are potent inhibitors of ACCs from sensitive plants and kill them by shutting down fatty acid biosynthesis. This observation confirms that an inhibitor of the CT domain is sufficient to block the function of ACC, and establishes this domain as a valid target for the development of inhibitors against these enzymes, especially the human ACCs.
The present invention also provides for herbicide resistant plants. Such plants are resistant to herbicides which modulate the activity of the CT domain of ACC and ACC-related enzymes. An herbicide resistant plant made in accordance with the present invention has a mutation in one or more amino acids, possibly in or near the active site of the CT domain of ACC or an ACC-related enzyme. Such mutations reduce or inhibit the acetyl-CoA carboxylase activity of ACC and include mutations in one or more of the amino acids of the CT domains of plant ACCs and/or ACC-related enzymes which correspond to Met 1503, Lys 1592, Ile1593, Ser1595, Phe 1596, Asn 1624, Ser1625, Gly 1626, Ala1627, Arg1628, Ile1629, Gly1630, Met1631, Gly 1699, Gly1701, Glu1703, Cys 1704, Leu1705, Ser1708, Ala1712, Arg1731; Val1733, Gly1734, Ile1735, Gly 1736, Ala 1737, Tyr1738, Leu 1739, Arg 1741, Leu1742, Pro1753, Ile 1755, Leu1756, Thr1757, Gly1758, Ala1759, Pro1760, Ala1761, Ile1762, Asn1763, Lys1764, Met1765, Leu1766, Tyr1771, Asn1774, Ala1908, Pro1920, Gly1921, Gln1922, Val1923, Trp1924, His1925, Pro1926, Ser1928, Ala1929, Phe1930, Trp1953, Arg1954, Gly1955, Phe1956, Ser1957, Gly1958, Gly1959, Gln1960, Arg1961, Asp1962, Met1963, Phe1964, Asn1965, Glu1966, Val1967, Leu1968, Lys1969, Try1970, Gly1971, Ser1972, Ile1974, Val1975, Glu1994, Arg1996, Gly1997, Gly1998, Ser1999, Trp2000, Val2001, Val2002, Val2003, Arg2021, Gly2023, Val2024, Leu2025, Glu2026, Pro2027, Gln2028, Gly 2029, Met2030, Val2031, Gly2032, Ile2033, Lys2034, Arg2036, Asp2098, Val2108 and Leu2189 of yACC (residue numbering of SEQ ID NO:1). In a specific subset of the above residues, mutations reduce or inhibit the acetyl-CoA carboxylase activity of ACC and include mutations in one or more of the amino acids of the CT domains of plant ACCs and/or ACC-related enzymes which correspond to Phe1596, Ser1625, Gly1626, Ala1627, Arg1628, Ile1629, Cys1704, Leu1705, Ser1708, Ala1712, Val1733, Gly1734, Ile1735, Gly1736, Ala1737, Tyr1738, Leu1739, Arg1741, Leu1742, Ile1755, Leu1756, Thr1757, Val1923, Trp1924, His1925, Pro1926, Ser1928, Ala1929, Phe1930, Trp1953, Gly1955, Phe1956, Ser1957, Asn1965, Glu1966, Val1967, Leu1968, Lys1969, Tyr1970, Gly1971, Ser1972, Ile1974, Arg1996, Gly1997, Gly1998, Ser1999, Trp2000, Val2001, Val2002, Val2003, Gly2023, Val2024, Leu2025 (residue numbering of SEQ ID NO:1). A genetically modified herbicide resistant plant of the present invention may be made by any technique known in the art.
Prior to constructing a genetically modified plant, it may first be desirable to select a candidate polynucleotide encoding a mutant CT domain of an ACC polypeptide by determining whether it has reduced acetyl-CoA carboxylase activity.
Once a candidate polynucleotide encoding the mutant CT domain of an ACC polypeptide is selected, the genome of a target plant may be modified by incorporation of the polynucleotide. Modification includes providing a vector comprising the polynucleotide, insertion of the polynucleotide into the genome at any location, insertion of the polynucleotide into the endogenous ACC gene, replacement of all or part of the endogenous ACC gene with the polynucleotide.
To produce a herbicide resistant plant of the present invention shoot cultures of the target plant material may be employed as a starting material. Micropropagated shoot cultures may be generated by surface sterilizing young shoots from field grown juvenile and mature stage target plants in a sterilization medium, rinsing the sterilized shoots, and then exposing them to a multiplication or elongation medium. Suitable sterilization media, such as 0.01% mercuric chloride solution, are known, and repeated rinsing may be performed with sterile, distilled water. Alternatively, micropropagated shoot cultures may be obtained from forestry companies.
According to certain embodiments, in vitro micropropagated shoot cultures are grown for a period of from one week to several weeks, preferably three weeks, on a multiplication medium. The shoot cultures may preferably be transferred to a shoot elongation medium. The shoot elongation medium additionally comprises a plant growth promoter. Shoot cultures are preferably exposed to the shoot elongation medium for at least three weeks, more preferably for four to six weeks. Shoot cultures are preferably subcultured to fresh medium every two to four weeks, and are preferably transferred to fresh medium about two to three weeks before transformation. Shoots of the target plant material are preferably allowed to grow to a size of from 1 to 8 cm in length, more preferably from about 3 to 4 cm in length, before they are transformed to incorporate the desired polynucleotide encoding a mutant CT domain of an ACC polypeptide of the present invention.
The polynucleotide encoding the mutant CT domain of an ACC polypeptide of the invention may be transformed into the target plant material, by, for example, introducing a genetic construct, such as a vector, into the target plant. Genetic constructs introduced into the target plant material may comprise. The mutant CT domain of an ACC polypeptide encoded by the polynucleotide is preferably functional in the target plant.
According to one embodiment, the polynucleotide is incorporated into a vector which includes expression control sequences. A target plant may be transformed with more than one vector of the present invention, thereby expressing more than one mutant CT domain of an ACC polypeptide capable of modulating acetyl-CoA carboxylase activity. Similarly, a vector may be assembled containing more than one open reading frame coding for one or more mutant CT domains of ACC polypeptides of the present invention.
Polynucleotides include, but are not limited to, a polymeric collection of nucleotides and includes DNA and corresponding RNA molecules, both sense and anti-sense strands, and comprehends cDNA, genomic DNA and recombinant DNA, as well as wholly or partially synthesized polynucleotides. A polynucleotide may be an entire gene, or any portion thereof. All of the polynucleotides described herein are isolated and purified, as those ten-s are commonly used in the art.
The vector may further comprise expression control sequences, as indicated above, such as, a gene promoter sequence and a gene termination sequence operably linked to the polynucleotide to be transcribed. The gene promoter sequence is generally positioned at the 5′ end of the polynucleotide to be transcribed, and is employed to initiate transcription of the polynucleotide. Promoter sequences are generally found in the 5′ non-coding region of a gene but they may exist in introns or in the coding region. When the vector includes an open reading frame in a sense orientation, the gene promoter sequence also initiates translation of the open reading frame.
A variety of gene promoter sequences which may be usefully employed in the vectors of the present invention are well known in the art. The promoter gene sequence, and also the gene termination sequence, may be endogenous to the target plant host or may be exogenous, provided the promoter is functional in the target host. For example, the promoter and termination sequences may be from other plant species, plant viruses, bacterial plasmids and the like.
Factors influencing the choice of promoter include the desired tissue specificity of the construct, and the timing of transcription and translation. For example, constitutive promoters, such as the 35S Cauliflower Mosaic Virus (CaMV 35S) promoter, will affect the activity of a polypeptide in all parts of the plant. Use of a tissue specific promoter will result in production of the desired RNA only in the tissue of interest. With vectors employing inducible gene promoter sequences, the rate of RNA polymerase binding and initiation may be modulated by external stimuli, such as light, heat, anaerobic stress, alteration in nutrient conditions and the like. Temporally regulated promoters may be employed to effect modulation of the rate of RNA polymerase binding and initiation at a specific time during development of a transformed cell. Preferably, the original promoters from the enzyme gene in question, or promoters from a specific tissue-targeted gene in the organism to be transformed, are used. Other examples of gene promoters which may be usefully employed in the present invention include mannopine synthase (mas), octopine synthase (ocs) and those reviewed by Chua et al (Science 1989;244:174-181).
The gene termination sequence, which is located 3′ to the DNA sequence to be transcribed, may come from the same gene as the gene promoter sequence or may be from a different gene. Many gene termination sequences known in the art may be usefully employed in the present invention, such as the 3′ end of the Agrobacterium tumefaciens nopaline synthase gene. However, gene terminator sequences may be those from the original ACC polypeptide gene, or from the target species being transformed.
The vectors of the present invention may also comprise a reporter gene or a selection marker that is effective in target plant cells to permit the detection of transformed cells containing the vector. Such reporter genes and selection markers, which are well known in the art, typically confer resistance to one or more toxins. A chimeric gene that expresses β-D-glucuronidase (GUS) in transformed plant tissues but not in bacterial cells is a preferred selection marker for use in methods of the present invention. The binary vector pKIWI 105, constructed as described by Janssen and Gardner, 1989, Plant Molecular Biology 14:61-72, is one such selection marker. Plant material expressing GUS is resistant to antibiotics such as kanamycin. Another suitable marker is the NPTII gene, whose expression results in resistance to kanamycin or hygromycin, antibiotics which are generally toxic to plant cells at a moderate concentration. Rogers et al., 1988, Methods for Plant Molecular Biology, Weissbach and Weissbach, eds., Academic Press Inc., San Diego, Calif. Alternatively, the presence of the desired polynucleotide encoding a mutant CT domain of an ACC polypeptide of the present invention in transformed cells may be determined by means of other techniques that are well known in the art, such as Southern and Western blots.
In another embodiment, nucleotide sequences including a non-coding region of a polynucleotide encoding for an endogenous ACC, or a nucleotide sequence complementary to such a non-coding region may be employed. As used herein the term “non-coding region” includes both transcribed sequences which are not translated, and non-transcribed sequences within about 2000 base pairs 5′ or 3′ of the translated sequences or open reading frames. Examples of non-coding regions which may be usefully employed in the inventive constructs include introns and 5′-non-coding leader sequences of endogenous ACC. Transformation of a target plant with a vector comprising such non-coding sequences of an endogenous ACC may lead to a reduction in the amount of endogenous ACC synthesized by the plant by the process of cosuppression, in a manner similar to that discussed, for example, by Napoli et al. (Plant Cell 1990;2:279-290) and de Carvalho Niebel et al. (Plant Cell 1995;7:347-358).
The vectors of the present invention may be used to transform a variety of plants using the methods of the present invention, including monocotyledons (e.g. grasses, corn, grains, oat, wheat and barley), dicotyledons (e.g. Arabidopsis, tobacco, legumes, alfalfa, oaks, eucalyptus, maple), and Gymnosperms (e.g. Scots pine; Aronen, 1996, Finnish Forest Res. Papers, vol. 595), white spruce (Ellis et al, 1993, Biotechnology 11:94-92), larch (Huang et al., 1991, In vitro Cell 27:201-207).
Techniques for stably incorporating vectors into the genome of target plants are well known in the art and include Agrobactenum-mediated introduction, electroporation, protoplast fusion, injection into reproductive organs, injection into immature embryos, high velocity projectile introduction, and the like. The choice of technique will depend upon the target plant to be transformed. For example, dicotyledonous plants and certain monocots and gymnosperms may be transformed by Agrobacterium Ti plasmid technology as described, for example by Bevan (Nucl. Acid Res. 1984;12:8711-8721). Targets for the introduction of the genetic constructs of the present invention include tissues, such as leaf tissue, disseminated cells, protoplasts, seeds, embryos, meristematic regions, cotyledons, hypocotyls, and the like. Target plant materials for transformation according to methods of the present invention include in vitro micropropagated shoot cultures prepared as described above.
Transfer of one or more vectors into target plant shoots may be accomplished using Agrobacterium-mediated transformation techniques. Agrobacterium strains are suitable and are commercially available. Agrobacterium tumefaciens strain AGL1 (Bio-Technology 1991;9:963-967) is available. Methods for transforming a population of the Agrobacterium strain with a vector are well known. The freeze thaw method described in An et al., 1988, Plant Molecular Biology Manual, Dordrecht: Kluwer Academic Publishers, 1988, pp. A3/1-A3119, is one method for transforming the Agrobacterium culture with the vector of interest.
Colonies of Agrobacterium carrying the genetic construct of interest are prepared for inoculation of the target plant material according to known techniques. See e.g. U.S. Pat. No. 6,255,559. Mature shoots of the target plant material are selected for transformation. Stem segments from each node are excised. Stem segments from the second and third nodes are possible. All leaves are peeled from the stems, and additional wounding may be inflicted, for example, by light longitudinal cutting of both sides of the stem with a scalpel blade. The selected stem segments, preferably including the second and third nodes, are inoculated with the Agrobacterium culture prepared as described above.
Inoculation of stem segments with the Agrobacterium suspension takes place under conditions that optimize infection of the stem segments. Suitable techniques are well known. After incubation, excess suspension is removed and stem segments are transferred to a co-cultivation medium. Following the co-cultivation period, stem segments are removed from the medium and washed. Stem segments are cultured until adventitious buds are produced from the stem segments.
Putative transformed shoots are excised from the stem segments and transferred to growth medium which may include a selection agent, such as kanamycin. Transformed shoots are transferred to a suitable rooting medium known in the art. Rooting is accomplished in a period of from about two to four weeks and may involve an initial culture period in the dark to allow initial root development, followed by transfer to standard photoperiod conditions. During elongation and rooting, explants may be transferred to larger culture vessels. Rooted shoots, or plantlets, may be transferred to a growth medium and grown to mature, genetically modified plants. Genetically modified plants produced according to the methods disclosed herein may be reproduced, for example, using standard clonal propagation techniques such as axillary bud multiplication techniques. The genetically modified plants may then be tested for herbicide resistance by growing the plants in the presence of an herbicide. The polypeptide encoded by the polynucleotides of the present invention can be preselected for its inability to bind to and/or be inhibited by an herbicide compound of interest before the genetically modified plants of the present invention are prepared.
The following examples are representative of techniques employed by the inventors in carrying out aspects of the present invention. It should be appreciated that while these techniques are exemplary for the practice of the invention, those of skill in the art, in light of the present disclosure, will recognize that numerous modifications can be made without departing from the spirit and intended scope of the invention.
EXAMPLES
The examples described below are provided to illustrate the present invention and are not included for the purpose of limiting the invention.
As various changes can be made in the above methods and compositions without departing from the scope and spirit of the invention as described, it is intended that all subject matter contained in the above description, shown in the accompanying drawings, or defined in the appended claims be interpreted as illustrative, and not in a limiting sense.
Example 1
Determination of the Crystal Structure of the CT Domain of Yeast ACC, Alone or Complexed with Acetyl CoA
Materials and Methods
Protein expression and purification. Various constructs comprising the CT domain of S. cerevisiae ACC were subcloned into the pET24d vector (Novagen) to produce the constructs listed in Table A, which were then over-expressed in E. coli incubated at 20° C. The soluble proteins that were produced were purified by nickel-agarose affinity and anion exchange chromatography. The proteins were concentrated to 10 mg/ml in a buffer containing 20 mM Tris (pH 7.0), 100 mM NaCl, 5% (v/v) glycerol, and 10 mM DTT. The samples were flash-frozen in liquid nitrogen and stored at −80° C. The C-terminal His-tag was not removed for crystallization. For the production of selenomethionyl proteins, the expression constructs were transformed into DL41 (DE3) cells. The bacterial growth was carried out in defined LeMaster media, and the proteins were purified using the same protocol as for the wild-type protein.
Protein Crystallization. Crystals of the proteins were obtained at 4° C. by the vapor diffusion method. The reservoir solution contained 100 mM NaCitrate (pH 5.5), 10% (w/v) PEG8000, and 5% (v/v) glycerol. The protein was at 7 mg/ml in a solution that also contained 1 mM acetyl-CoA. Micro-seeding was used to obtain crystals of sufficient size for data collection. Three different crystal forms were observed under this condition, and our structural analyses showed only very weak electron density for the acetyl-CoA. A fourth crystal form was obtained using the crystallization condition 100 mM Tris (pH 7.0), 13% (w/v) PEG8000 and 10% (v/v) glycerol. The protein was pre-incubated with 2 mM acetyl-CoA, and the binding of this compound to the enzyme was observed in the electron density map. The crystals were cryo-protected with the introduction of 25% (v/v) ethylene glycol and flash frozen in liquid propane.
Data Collection. X-ray diffraction data were collected on an ADSC CCD at the X4A beamline of Brookhaven National Laboratory. For initial structure determination, a seleno-methionyl single-wavelength anomalous diffraction (SAD) data set to 2.7 Å resolution was collected at 100K on a crystal grown at pH 5.5. Significant decay in the crystal diffraction quality precluded data collection at other wavelengths. The diffraction images were processed and scaled with the HKL package. See Otwinowski and Minor, 1997, Meth. Enzymol. 276:307-326. One crystal form (Form 1) of the CT domain encoded by SEQ ID NO:2 belongs to the space group C2, with unit cell dimensions of a=247 Å, b=125 Å, c=145 Å, and β=94°. There are three molecules in the asymmetric unit. Another crystal form (Form II) of the CT domain encoded by SEQ ID NO:2 belongs to the space group C2, with unit cell dimensions of a=255 Å, b=113 Å, c=135 Å, and β=101°. To determine the binding mode for acetyl-CoA, a native data set to 2.7 Å resolution was collected on a crystal grown at pH 7. It belongs to space group P21, with cell dimensions of a=92.9 Å, b=138.1 Å, c=101.4 Å, and β=114.40. There are two molecules in the asymmetric unit. The data processing statistics are summarized in Table C.
Structure determination and refinement. The locations of Se atoms were determined with the program SnB (Weeks and Miller, 1999, J. Appl. Cryst. 32:120-124) and further confirmed with SHELXS (Sheldrick, 1990, Acta Cryst. A46:467-473) based on the anomalous differences in the SAD data set. Reflection phases to 2.7 Å resolution were calculated and improved with the program SOLVE (Terwilliger and Berendzen, Acta Cryst. D55:849-861). The atomic model was built into the electron density with the program O (Jones et al., 1991, Acta Cryst. A47:110-119). The structure of the CoA complex was determined by the molecular replacement method with the program COMO (Jogl et al., 2001, Acta Cryst. D57:1127-1134). The structure refinement was carried out with the program CNS (Brunger et al., Acta Cryst. D54:905-921). The statistics on the structure refinement are summarized in Table C.
Enzyme kinetic assays. The CT domain can catalyze the decarboxylation of malonyl-CoA to produce acetyl-CoA in the presence of biotin methyl ester. The kinetic assays monitored the production of acetyl-CoA by coupling it to citrate synthase and malate dehydronase, which ultimately lead to the reduction of NAD+ (Guchhait et al., 1974, J. Biol. Chem. 9:6633-6645). Mutations in the active site were designed based on the structural information. The mutants were made with the QuikChange kit (Stratagene) and sequenced for confirmation. They were purified and assayed kinetically under the same condition as the wild-type protein. The kinetic parameters for each enzyme were obtained by non-linear least-squares fitting to the initial velocity data.







TABLE B







Constructs created and tested for production of


proteins comprising the CT domain of yeast ACC













1st
Last





Construct
residue*
residue*
Induced
Soluble
Crystallized















1
1476
2147
−
 NA†
NA


2
1429
2233
+
+
+


(yCTACC)


(SEQ ID


NO: 2)


3
1476
2233
−
NA
NA


4
1412
2041
−
NA
NA


5
1423
2041
+
−
NA


6
1435
2041
−
NA
NA


7
1441
2041
+
−
NA


8
1429
2041
+
+


9
1412
2135
+
−
NA


10
1435
2135
−
NA
NA


11
1441
2135
+
+


12
1429
2135
−
NA
NA


13
1493
2135
+
−
NA


14
1525
2233
+
−
NA


15
1452
2233
+
−
NA


16
1476
2135
+
−
NA


17
1476
2190
+
+


18
1485
2135
+
−
NA


19
1493
2135
+
−
NA


20
1493
2190
+
+


21
1476
2210
+
+


22
1476
2233
+
+
+


(yCT2ACC)


(SEQ ID


NO: 3)


23
1493
2210
+
+


24
1493
2233
+
+





*Residue numbering based on GenBank Entry No. Q00955


†NA—Not applicable













TABLE C







Summary of crystallographic information










Free enzyme
CoA complex



(see Table 1 for atomic
(see Table 2 for atomic


Crystal
coordinates)
coordinates)





Maximum resolution (Å)
2.7
2.7


Number of observations
533,916
168,936


Rmerge1 (%)
7.6 (18.1)
5.2 (11.6)


Resolution range for
30-2.7 Å
30-2.7 Å


refinement


Number of reflections
113,103
59,546


Completeness (%)
94.5
93.1


R factor2 (%)
22.9 (35.4)
22.7 (33.0)


free R factor (%)
26.4 (40.4)
27.9 (36.4)


rms deviation in bond
0.009
0.009


lengths (Å)


rms deviation in bond
1.4
1.4


angles (°)














  
    
      
    
    1
  
  ⁢
  
    R
    merge
  
  =
  
    
      ∑
      h
    
    ⁢
    
      
        ∑
        i
      
      ⁢
      
        
          
          
            
              I
              hi
            
            -
            
              〈
              
                I
                h
              
              〉
            
          
          
        
        /
        
          
            ∑
            h
          
          ⁢
          
            
              ∑
              i
            
            ⁢
            
              I
              hi
            
          
        
      
    
  






 


The numbers in parentheses are for the highest resolution shell.


 






  
    
      
    
    2
  
  ⁢
  R
  =
  
    
      ∑
      h
    
    ⁢
    
      
        
        
          
            F
            h
            o
          
          -
          
            F
            h
            c
          
        
        
      
      /
      
        
          ∑
          h
        
        ⁢
        
          F
          h
          o
        
      
    
  










Results

To obtain crystals for structural analysis, the CT domain of yeast ACC, which constitutes the 90 kD fragment at the C-terminus of the protein was expressed and purified. The CT domain of yeast ACC shares 50% sequence identity with those of human ACCs, and its structure is therefore a good model for the human enzymes. The structure of the free enzyme was determined at 2.7 Å resolution by the seleno-methionyl single-wavelength anomalous diffraction (SAD) method (Table C) (Hendrickson, 1991, Science 254:51-58) and the atomic coordinates are shown in Table 1. The structure of CT in complex with CoA was determined at 2.7 Å resolution from a crystal grown in the presence of 2 mM acetyl-CoA (Table C) and the atomic coordinates are shown in Table 2.
The crystal structures show that each CT domain molecule is made up of two sub-domains, which are intimately associated with each other (FIG. 2A). The N domain contains residues 1484-1824, in the N-terminal half of the CT (FIG. 2B), whereas the C domain contains residues 1825-2202, in the C-terminal half (FIG. 2C). In FIGS. 2A, 2B, and 2C, the schematics were generated with Ribbons (Carson, 1987, J. Mol. Graphics 5:103-106). This domain organization of CT is consistent with the fact that the N- and C-terminal halves show limited sequence homology to the β and α subunits of the bacterial CT, respectively (FIG. 1A). More than 50 residues at the N-terminus and 30 residues at the C-terminus (together with the His-tag) are disordered in the crystal of the CoA complex.
The N and C domains share similar polypeptide backbone folds, with a central β-β-α super-helix (FIGS. 2A, 2B). A total of 127 equivalent Cot atoms can be superimposed to within 2.5 Å of each other between the two domains, and the root-mean-squares (rms) distance for these atoms is 1.3 Å. However, the amino acid sequence identity among these structurally equivalent residues is only 12%, underscoring the lack of sequence conservation between the two domains. The backbone fold of the two domains is also similar to that of the crotonase/ClpP superfamily (FIG. 2D) (Benning et al. 1996, Biochem. 35:8103-8109; Engel et al., 1996, EMBO J. 15:5135-5145; Wang et al., 1997, Cell 91:447-456; Benning et al., 2000, Biochem. 39:4630-4639; Mursula et al., 2001, J. Mol. Biol. 309:845-853), even though the amino acid sequence identity between the domains in CT and these other proteins are less than 14%. Interestingly, crotonase and several other members of the family are acyl-CoA-dependent enzymes that catalyze various reactions for fatty-acid P-oxidation (Engel et al., 1996, EMBO J. 15:5135-5145; Benning et al., 2000, Biochem. 39:4630-4639; Mursula et al., 2001, J. Mol. Biol. 309:845-853; Cronan, Jr. and Waldrop, 2002, Prog. Lipid Res. 41:407-435). Despite the similarity in their backbone folds, however, there are significant differences in the oligomerization state and the composition of the active site between CT and other crotonase family members (see below). In addition, the domains in CT contain significant insertions to the crotonase/Clp fold (FIGS. 2B-D), and some of these inserted segments are important for the oligomerization of the enzyme (FIG. 2A).
A dimer of the CT domain is observed in all the structures of the present invention (FIG. 2A), and the organization of this dimer is essentially the same in these different structures. About 5300 Å2 of the surface area of each monomer is buried in the dimer interface, involving mostly residues that are highly conserved among the ACCs (FIG. 2B). This suggests that the observed dimer should be a stable and conserved oligomerization state of the domain, in agreement with gel-filtration and light-scattering studies performed in solution as well as the α2β2 stoichiometry of the bacterial CT subunits (Cronan, Jr. and Waldrop, 2002, Prog. Lipid Res. 41:407-435). The dimer is formed by the side-to-side arrangement of the two monomers, such that the N domain of one molecule is placed next to the C domain of the other (FIG. 2A). The α6A-α6D insertion in the C domain of one monomer (FIG. 2C) is inter-digitated between the β7A-β7D insertion (FIG. 2B) and the core of the N domain of the other monomer (FIG. 2A). The insertion between β4 and β5 of the C domain (FIG. 2C) also contributes to the formation of the dimer.
The structure of the CoA complex of the present invention, at 2.7 Å resolution, revealed that the active site of the enzyme is located at the interface of the dimer and with mostly equal contribution from the N and C domains of the two monomers (FIGS. 2A, 3A). This is in sharp contrast to other members of the crotonase family where the active site is either located within the monomer or has only small contributions from another monomer, and where the enzyme is generally a trimer or hexamer (dimer of trimers). Engel et al., 1996, EMBO J. 15:5135-5145; Benning et al., 2000, Biochem. 39:4630-4639; Mursula et al., 2001, J. Mol. Biol. 309:845-853. In the structures of the present invention, the active site is located in a cavity between the small β-sheets (with strands β5, β7, β9 and β11) of the β-β-α super-helix of the two domains (FIG. 3A). Above these two β-sheets, the α6 helices of the two domains form two walls, providing additional binding surfaces for the CoA and biotin substrates as well as restricting their directions of approach (FIGS. 3A, 3B). FIG. 3A was produced with Ribbons (Carson, 1987, J. Mol. Graphics 5:103-106), and FIG. 3B was produced with GRASP (Nicholls et al., 1991, Proteins 11:281-296). Residues in this active site are generally well conserved among the various CT domains (FIG. 1B). FIG. 4 is a sequence alignment of ACC from different species showing that the amino acids in or near the active site are conserved.
The CoA molecule is mostly associated with the N domain of one molecule in the dimer (FIG. 3A). The N1 and N6 atoms of the adenine base are recognized by hydrogen-bonds with the main chain of residues immediately after β7 in the N domain (FIG. 3A). The phosphate groups of CoA are located near the side chains of Arg1731, Lys2034′ and Arg2036′ (the primed residue numbers indicate the second monomer). The pantotheine arm lies on the surface of the small β-sheet in the N domain, and the thiol group is placed in the cavity between the two domains (FIG. 3A). Although acetyl-CoA was used in the crystallization, there was no electron density for the acetyl group, and only the CoA molecule is included in the current atomic model. In the other active site of the dimer, only the electron density for the adenine base of the coenzyme was observed (FIG. 2A).
Based on the structures of the present invention, it is likely that the biotin substrate is mostly associated with the small β-sheet in the C domain of the other monomer in the active site (FIG. 3A). This is partly supported by observations with the E. coli biotin ligase/repressor BirA, where the biotin molecule is bound on the surface of a β-sheet. Weaver et al., 2001, Protein Sci 10:2618-2622. Therefore, two domains with similar backbone folds are used to recognize completely different chemical entities in CT.
There are only minor changes in the conformation of the core of the monomer or the organization of the dimer when CoA is bound to the enzyme. The RMS distance between 1200 equivalent Cα atoms of the dimers of the free enzyme and CoA complex is 0.4 Å. Residues in α6B-α6C (2046-2080) of the C domain are disordered in the free enzyme structure, but this is most likely due to differences in crystal packing interactions between the two crystals.
To characterize the functional roles of the conserved residues in the active site, many of them were mutated and the kinetic parameters of the mutants for the reverse reaction, which transfers the carboxyl group of malonyl-CoA to biotin (Table D) were determined. The largest effect on the catalytic activity was observed with the mutation of the Arg1954 residue, in the C domain (FIG. 3A), which lead to a 75-fold increase in the Km for malonyl-CoA and a 300-fold decrease in the overall kcat/Km of the enzyme (Table D). Based on the structures of the invention, it is likely that this residue is important for recognizing the carboxyl group of malonyl-CoA, and this is also consistent with the hypothesis that the biotin substrate may be mostly associated with the C domain. Of the charged side chains that interact with the phosphate groups of CoA, mutation of Arg1731 gave rise to a 14-fold increase in the Km for malonyl-CoA (Table D), consistent with the structural observations. On the other hand, mutation of Arg2036 had minimal effects on the enzyme catalysis.







TABLE D







Kinetic parameters of wild-type and mutant CT











Vmax*
Km (μM)



Enzyme
(×10−5 AU/s)
(for malonyl-CoA)
Vmax/Km





Wild-type
148 ± 3
67 ± 5
2.2 ± 0.1


L1705I
  12 ± 0.3
1342 ± 180
0.009 ± 0.001


R1731S
 385 ± 10
909 ± 72
0.42 ± 0.02


Y1738F
152 ± 3
53 ± 6
2.9 ± 0.3


R1954S
 39 ± 6
 5100 ± 1200
0.0076 ± 0.0008


E1994Q
272 ± 3
109 ± 5 
2.5 ± 0.1


E2026Q
144 ± 6
218 ± 24
0.66 ± 0.05


R2036E
133 ± 3
41 ± 4
3.3 ± 0.3





*All reactions contain 2.5 μM of the enzyme.






The results of the structure-based mutagenesis experiments of the invention also help to clarify the catalytic mechanism of this enzyme. A general base is needed to extract the proton from the acetyl group of acetyl-CoA to initiate the carboxylation reaction. Kinetic and chemical modification studies of E. coli CT have suggested that a cysteine residue may serve this function. Cronan, Jr. and Waldrop, 2002, Prog. Lipid Res. 41:407-435. However, the structures of the invention do not show a cysteine residue in the active site (FIG. 3A). In addition, those residues in the active site that could function as a general base (Tyr1738, Glu1994, Glu2026) were mutated, and kinetic studies were performed which showed that these residues are not required for the catalysis (Table D). Therefore, the structural and mutagenesis studies support the catalytic mechanism where the N1 atom of biotin itself functions as the general base. Knowles, 1989, Ann. Rev. Biochem. 58:195-221. This is in strong contrast to the crotonases where an acidic side chain of the enzyme is required for catalysis (FIG. 2D).
Example 2
Molecular Basis for the Inhibition of the CT Domain of ACC
Obesity is associated with a variety of serious human diseases, especially type 2 diabetes, cardiovascular diseases, depression, and cancer. There is clearly a critical need for therapeutic agents that can regulate body weight and obesity. Acetyl-coenzyme A carboxylases (ACCs) are crucial for the metabolism of longchain fatty acids. They catalyze the production of malonyl-CoA from acetyl-CoA and CO2, a reaction that also requires the hydrolysis of ATP. Two isoforms of this enzyme have been identified in mammals. ACC1, a cytosolic enzyme, catalyzes the first and the committed step in the biosynthesis of long-chain fatty acids. In comparison, ACC2 is associated with the mitochondrial membrane and its malonyl-CoA product potently inhibits the shuttle that transports longchain acyl-CoAs from the cytosol to the mitochondria for oxidation. Mice lacking ACC2 have elevated fatty acid oxidation and reduced body fat and body weight, establishing ACC2 as a target for anti-obesity, anti-diabetes, cardiovascular, metabolic and anti-infection agents.
The CT domain is the site of action of two different classes of widely-used commercial herbicides, as represented by haloxyfop (FOPs) and sethoxydim (DIMs) (FIG. 5A). These compounds are potent inhibitors of ACCs from sensitive plants and kill them by shutting down fatty acid biosynthesis. This confirms that an inhibitor of the CT domain is sufficient to block the function of ACC, and establishes this domain as a valid target for the development of inhibitors against these enzymes, especially the human ACCs.
However, the molecular mechanism for the inhibitory action of the herbicides was previously not known. Until recently, the herbicides were the only known potent inhibitors of the CT domain.
The present invention provides the crystal structures of the CT domain of yeast ACC in complex with two different FOP inhibitors, haloxyfop and diclofop, at up to 2.5 Å resolution. These are the first structures of inhibitor complexes of any CT domains. They demonstrate that the herbicides are active site inhibitors of the CT domain, and are located at the interface of the dimer. Surprisingly, a large conformational change in the active site of the enzyme is required for the binding of these compounds. Most of the residues in this binding site are strictly conserved among the various CT domains. Therefore, this binding site likely exists in the other CT domains as well, and the herbicides are expected to share a similar binding mode to these domains, especially those from human ACCs.
The crystal structure of the CT domain of yeast ACC in complex with haloxyfop has been determined at 2.8 Å resolution (Table E). The enzyme:inhibitor complex was prepared by soaking pre-formed free-enzyme crystals of the CT domain with the inhibitor. The crystals were very sensitive to the herbicide, and most soaking experiments destroyed the diffraction of the crystal. The current diffraction data set was collected on a crystal that had been soaked for 1 hour in a solution containing 1 mM haloxyfop. Prior kinetic experiments showed that haloxyfop has a Ki of about 0.5 mM against this CT domain. Nonetheless, the crystallographic analysis clearly revealed the presence of haloxyfop in the structure, with well-defined electron density (FIG. 5B).
To assess whether there are conformational changes in the enzyme upon inhibitor binding, the structure at 2.5 Å resolution of the free enzyme of the CT domain was determined (Table E). The free enzyme structure in Example 1 was based on a crystal that was grown in the presence of acetyl-CoA (Zhang et al., 2003). For the current structure, acetyl-CoA was not included in the crystallization solution. In addition, a new expression construct (yCT2ACC; SEQ ID NO:3) to prepare the protein samples for this crystal. This construct covers residues 1476-2233 of yeast ACC, removing about 50 residues at the N terminus (1429-1475) that were found to be completely disordered in the earlier structure (Zhang et al., 2003). This new protein sample readily produces large crystals of the CT domain.
The enzyme:diclofop complex was prepared by co-crystallization, using the new CT domain protein sample covering residues 1476-2233. These co-crystals are in a different crystal form compared to the crystals of the free enzyme and the haloxyfop complex, and the structure was determined by the molecular replacement method (Jogl, G., et al. (2001). COMO: A program for combined molecular replacement. Acta Cryst. D57, 1127-1134.) (Fable E).
Binding mode of haloxyfop. The haloxyfop herbicide is bound in the active site, at the interface between the two monomers of the dimer (FIG. 1D). Structural comparison with the CoA complex in Example 1 shows that the haloxyfop molecule in the active site will disrupt the binding of the acetyl- and malonyl-CoA substrates for catalysis (FIG. 5C, and see FIG. 7A for a detailed view), consistent with the kinetic observations suggesting that haloxyfop is a competitive inhibitor with respect to malonyl-CoA (Zhang et al., 2003). Previous studies with wheat ACC showed that the herbicides are nearly competitive with respect to the substrate acetyl-CoA (Rendina et al., 1990).
Haloxyfop is located in a groove between the N domain of one monomer and the C domain of the other monomer (FIG. 6A). The pyridyl ring of haloxyfop is sandwiched between the side chains of Tyr1738 and Phe1956′ (primed residue numbers indicate the C domain of the other monomer), showing π-π interactions (FIG. 6B). The chloro substituent on this ring is pointed towards the side chains of Leu1756 and Leu1968′, although the chlorine atom has relatively weaker electron density based on the crystallographic analysis (FIG. 5B). The trifluoromethyl group is positioned over the plane of the Trp1924′ side chain. It also has interactions with the side chains of Val1967′, Ile1974′, and Val2002′. The ring nitrogen of the pyridyl group and the two ether oxygen atoms of the inhibitor are not involved in hydrogen-bonding interactions with the enzyme. The phenyl ring in the center of the inhibitor is situated between the amide bonds linking residues Gly1734 to Ile1735, and Gly1997′ to Gly1998′ (FIG. 6B). For the carboxylate group of the inhibitor, one of its oxygen atoms is hydrogen-bonded to the main-chain amides of Ala1627 and Ile1735 (FIG. 6B), whereas the other oxygen atom is exposed to the solvent. The negative charge on the carboxylate is not formally balanced by a positively-charged side chain of the enzyme. The methyl group of the propionate has van der Waals interactions with the side chains of Ala1627 and Leu1705.
The structure of haloxyfop as modeled into the electron density is the R stereoisomer (FIG. 6A), in agreement with results from earlier kinetic studies (Gronwald, J. W. (1991). Lipid biosynthesis inhibitors. Weed Science 39, 435-449; Rendina, A. R., et al. (1990) Inhibition of acetyl-coenzyme A carboxylase by two classes of grass-selective herbicides. J Agric Food Chem 38, 1282-1287). The S stereoisomer cannot assume this binding mode as the methyl group would clash with one of the carboxylate oxygens (FIG. 6A), indicating the molecular mechanism for the stereoselectivity of the CT domain for this class of compounds.
The binding mode of haloxyfop can also explain earlier observations that the CoA ester of this herbicide is a more potent inhibitor of ACC. The CoA molecule could be linked to haloxyfop, as the thiol group of CoA is located close to the carboxylic oxygen that is exposed to the solvent (FIG. 7A). A conformational change for the pantotheine portion of the CoA molecule is needed to form the covalent link to haloxyfop, but the adenine nucleotide portion of CoA should be able to maintain its interaction with the enzyme (Zhang et al., 2003). The establishment of these additional interactions is likely the basis for the enhanced potency of the CoA ester of haloxyfop.
Large conformational changes in the enzyme for haloxyfop binding. Unexpectedly, significant conformational changes in the active site of the enzyme are needed for inhibitor binding. Most importantly, the side chains of Tyr1738 and Phe1956′ assume new positions in the inhibitor complex to become 1-stacked with the pyridyl ring of haloxyfop (FIG. 7A). These two side chains help cover the hydrophobic core of the dimer interface in the free enzyme and the CoA complex. Their positions in the free enzyme actually clash with the bound conformation of haloxyfop (FIG. 7A), and the inhibitor binding pocket does not exist in the free enzyme (FIG. 7B). With the conformational changes for these and other residues in the active site, a binding pocket is revealed on the surface of the CT domain and the trifluoro-pyridyl group of the inhibitor is inserted deep into the hydrophobic core of the dimer (FIG. 7C). It is unlikely that this hydrophobic pocket is used by the substrates (acetyl-CoA or biotin) during the catalysis by the enzyme (FIG. 7A).
Extensive structural changes are observed near the Phe1956′ residue (FIG. 7A), even though residues 1952′-1959′ are highly conserved among the CT domains (FIG. 7D). The side chain rotates by about 120° around its χ1 torsion angle. Moreover, the main chain also moves, by about 2 Å, such that the side chain does not clash with the inhibitor (FIG. 7A). This triggers a conformational change for an entire segment of the CT domain, residues 1955′-1967′ (FIG. 7A). Several residues in this segment (1959′-1964′) have no electron density and are likely disordered in the current structure. This region corresponds to the α4A helix in the free enzyme structure, and is weakly conserved among the CT domains (FIG. 7D). This helix is probably unwound in the inhibitor complex.
In comparison, the conformational change for Tyr1738 is mostly limited to its side chain (FIG. 7A), which rotates by about 70° around the χ1 and χ2 torsion angles. It interacts with the side chains of Ala1712, Leu1742 and Val1975′ in its new position, and its hydroxyl group forms a hydrogen-bond with the main chain carbonyl oxygen of Gly1971′.
Inhibitor binding at the dimer interface also causes a change in the organization of the dimer (FIG. 7A). With one monomer of the dimer in superposition, a rotation of about 2.5° is needed to bring the second monomer into overlap. The conformational changes in the monomer, and especially the change in dimer organization, may explain the detrimental effects of inhibitor binding on the diffraction quality of the crystals in the soaking experiments.
Diclofop has a similar binding mode. The binding mode of the herbicide as well as the conformational changes in the monomer and dimer of the CT domain are confirmed by the structure of the complex with diclofop (FIG. 5A), at 2.5 Å resolution (Table E). This complex was produced by cocrystallization, and the crystals are in a different space group as compared to the free enzyme and the haloxyfop complex. Nonetheless, the structure of the diclofop complex is essentially the same as that of the haloxyfop complex. This confirms that the structural changes observed for the haloxyfop complex is unlikely biased by crystal packing interactions.
The carboxyl groups of the two inhibitors essentially have the same binding mode (FIG. 6C). The aromatic rings of diclofop show small but recognizable differences in their positions as compared to those of haloxyfop, but the two chloro substituents in diclofop superimpose well with the substituents in haloxyfop (FIG. 6C). For the enzyme, the Phe1956′ side chain has a different conformation, which may be linked to the change in the position of the inhibitor (FIG. 6C). On the other hand, the Tyr1738 side chains show little structural differences, and the other residues in the binding site have essentially the same conformation in the two complexes. The α4A helix is disordered in the co-crystals with diclofop as well. Moreover, the dimer organization in the diclofop complex is the same as the haloxyfop complex, as it also has the 2.5° rotation of the second monomer relative to the first monomer.
This binding pocket is likely present in most CT domains. Most of the residues that interact with the herbicides are either strictly or highly conserved among all the CT domains (FIG. 1B, FIG. 4, FIG. 7D; and alignments with SEQ ID NO:1 or 2 with GenBank Nos. BAA11238; T30568; P32874; S60200; AAK16499; T30568; AAL02056; T02235; AAA81579; T09538; BAA07012; CAA54683; NP—776649; CAA56352; NP—071529; AAP94122; A29924; NP—446374; XP—132282; CAE01471; NP—610342; and NP—493922). Therefore, it may be expected that this binding site also exists in most other CT domains, and that haloxyfop, diclofop and other FOPs can share a similar binding mode to these domains. Structures of the herbicide complexes of the yeast CT domain should be directly relevant for the design and optimization of inhibitors against the human ACCs.
The formation of this binding site requires conformational variability for several residues in the active site of the enzyme (FIG. 7A). The structure of the CT domain as observed here in the inhibitor complex is unlikely to be stable on its own, because of the significant exposure of the hydrophobic core of the dimer. Factors that regulate the conformational dynamics of residues in this region may affect the inhibitor sensitivity of the CT domain. This could be one mechanism for the herbicide resistance mutations that have been observed against the plant ACCs (see below).
Residues that confer resistance to herbicides are in the binding pocket. Only two residues in the binding site show appreciable variation among the different CT domains, Leu1705 and Val1967′ (FIG. 7D). Remarkably, it is exactly the variation/mutation of these two residues that can confer resistance to the herbicides in plants. The residue that is equivalent to Leu1705 in the CT domains of wheat and other sensitive ACCs is Ile, and the Ile to Leu mutation, a subtle change in the side chain of this residue, renders the enzyme resistant to both haloxyfop and sethoxydim. The residue that is equivalent to Val1967 in sensitive plants is Ile, and the Ile to Asn mutation makes the plants resistant to the FOPs, but not the DIMs. The Ile to Val mutation may also confer resistance to haloxyfop, although it does not affect the sensitivity to clodinafop. The structural information herein would predict that there may be natural mutations in the other residues in this binding pocket (FIG. 6A) that can confer resistance to the herbicides, even though these residues are highly conserved.
To assess whether mutations of the Leu1705 and Val 967 residues have similar effects on inhibitor sensitivity by the yeast CT domain, we created the L1705UV19671 double mutant as well as the L1705I and V1967I single mutants of this domain. These mutants are still dimeric in solution based on light scattering experiments. Kinetic studies show, however, that the single and double mutations have only minimal effects on the sensitivity of the CT domain to haloxyfop (FIG. 7E), with Ki remaining in the 0.5 mM range. Interestingly, the IC50 values of herbicides against resistant plant ACCs are also in the 0.1 to 0.5 mM range. At the same time, the L1705I and V1967I mutants generally have 50-fold or more reduction in catalytic activity as compared to the wild-type CT domain, with roughly a 10- to 20-fold increase in the Km for the malonyl-CoA substrate.
These experiments demonstrate that the Leu1705 and Val1967 residues do not have a major contribution to herbicide sensitivity by the yeast CT domain. In the structure of the complex, these two residues make mostly peripheral contacts with the inhibitor (FIG. 6A), consistent with the kinetic observations. The apicoplast ACC enzyme from the parasite Toxoplasma gondii has a Leu residue at position 1705 (FIG. 7D), but it is still sensitive to the FOPs, although insensitive to the DIMs.
Large segments of the CT domain are disordered in the L1705I/V19671 double mutant. To reveal the impact of the mutations on the conformation of the CT domain, the crystal structure of the L17051/V19671 double mutant at 2.6 Å resolution was determined (Table E). Surprisingly, a significant portion of the mutant structure, residues 1632-1702 (β7A-β7D insertion in the N domain) and 2026-2099 (α6 and α6A-α6D insertion in the C domain), are disordered, even though the mutant crystal is isomorphous to the wild-type crystal. These two inserted segments have intimate contacts with each other in the wild-type dimer interface (Zhang et al., 2003) (FIG. 5C), which are now missing in the mutant dimer (FIG. 8A).
Besides the disordered segments, conformational changes near the Leu1705 mutation site cause partial unwinding of the beginning of the α4 helix (FIG. 8B), and the new Ile side chain at this position has weak electron density. Therefore, it is likely that the L1705I mutation produces conformational changes for residues near the mutation site, which in turn gives rise to the disordering of the inserted segment (1632-1702) just prior to it. The new Ile side chain at the 1967 position is well defined, and the extra methyl group is placed between the side chains of Pro1926 and Phe1956 (FIG. 8B). However, kinetic studies show that the V19671 mutation is also detrimental to the catalytic activity of the CT domain.
The structural observations herein provide a molecular explanation for the reduced catalytic activity of these mutants. In the structure of the L1705I/V1967I double mutant, the α6 helix in the C domain is disordered, significantly changing the molecular surface in the active site (FIG. 8C). In addition, there are conformational differences for residues 1629-1631, just prior to the disordered segment (1632-1702), between the wild-type and the mutant (FIG. 8B). The main chain amide of residue 1629 is hydrogen-bonded to the N1 atom of the adenine base in acetyl-CoA (Zhang et al., 2003). Therefore, the mutations may have indirectly disrupted the binding of CoA to the enzyme, consistent with the increase in the Km of the malonyl-CoA substrate.
Compounds that strongly inhibit both isoforms of human ACC have recently been reported, representing the first known potent inhibitors of the human enzymes. Kinetic studies suggest that they probably also function by interfering with the CT activity, confirming that the CT domain is a valid target for inhibiting the human ACCs. (Harwood Jr., et al. (2003) Isozyme-nonselective N-substituted bipiperidylcarboxamide acetyl-CoA carboxylase inhibitors reduce tissue malonyl-CoA concentrations, inhibit fatty acid synthesis, and increase fatty acid oxidation in cultured cells and in experimental animals. J Biol Chem 278, 37099-37111) Moreeover, these compounds can both inhibit de novo fatty acid biosynthesis as well as stimulate fatty acid oxidation, which may be clinically more efficacious (Harwood Jr. et al., 2003). The structures of the inhibitor complexes of the CT domain provided herein reveal a large conformational change in the active site of the enzyme, which produces a highly conserved and highly hydrophobic binding pocket that leads deep into the dimer interface.
Experimental Procedures
Protein production and crystallization. The cloning, expression, purification, and crystallization of the CT domain (residues 1429-2233(SEQ ID NO:2; yCTACC)) of yeast ACC followed protocols as described earlier (Zhang et al., 2003; Example 1). Based on that first crystal structure, additional bacterial expression constructs for this domain were designed, and it was found that the construct covering residues 1476-2233 (SEQ ID NO:3; yCT2ACC) produces a large amount of soluble protein in E. coli. This protein can be purified following the same protocol, and readily produces large crystals of the free enzyme. The reservoir solution contains 0.1 M sodium citrate (pH 5.5), 200 mM NaCl, 8% (w/v) PEG8000, and 10% (v/v) glycerol. The protein is at 10 mg/ml concentration. These free enzyme crystals were cryo-protected by the introduction of 25% (v/v) ethylene glycol and flash-frozen in liquid propane for data collection at 100K.
To prepare the haloxyfop complex, crystals of the free enzyme (covering residues 1429-2233) were soaked with various concentrations of the herbicide for different lengths of time. Noting the poor affinity of the inhibitor, initial attempts used high concentration of the compound (5 mM and higher), however this invariably led to dissolution of the crystal or loss of X-ray diffraction. Good quality diffraction was maintained after soaking a crystal for 1 hour at 1 mM concentration of haloxyfop. The crystal was flash-frozen in liquid propane.
To prepare the diclofop complex, CT domain (residues 1476-2233) was mixed with the reservoir solution containing 2 mM of the compound. The reservoir solution contains 0.1 M sodium citrate (pH 5.5), 200 mM NaCl, 8% (w/v) PEG8000, and 10% (v/v) glycerol.
Structure Determination. X-ray diffraction data were collected at the X4A beamline of the National Synchrotron Light Source (NSLS). The diffraction images were processed with the HKL package (Otwinowski and Minor, 1997). The wild-type free enzyme, the haloxyfop complex, and the L1705I/V1967I mutant crystals belong to space group C2 and are isomorphous with each other, as well as with that of the free enzyme structure in Example 1 (Zhang et al., 2003). The unit cell parameters for the free enzyme crystal are a=247 Å, b=125 Å, c=145 Å, and β=94 for SEQ ID NO:2; and the unit cell parameters for the free enzyme crystal are a=246 Å, b=124 Å, c=145 Å, and β=94 for SEQ ID NO:3. The structure refinement was carried out with the program CNS (Brunger et al., 1998). Clear electron density for the herbicides was observed from the crystallographic analysis. The atomic model was built with the program O (Jones, T. A. (1978) A graphics model building and refinement system for macromolecules. J Appl Cryst 11, 268-272.). The crystallographic information is summarized in Table E.
Crystals of the diclofop complex are in a new crystal form. They belong to space group P3221, with cell parameters of a=b=137 Å and c=244 Å. There is one dimer of the CT domain in the asymmetric unit. The structure was solved by the molecular replacement method with the program COMO (Jogl, G., Tao, X., Xu, Y., and Tong, L. (2001). COMO: A program for combined molecular replacement. Acta Cryst D57, 1127-1134.), using the structure of the haloxyfop complex as the search model.
Mutagenesis and kinetic assays. The L1705I and V1967I single-site mutants as well as the L1705I/V1967I double mutant were made with the QuikChange kit (Stratagene), from the expression construct that covers residues 1476-2233. The mutants were sequenced, expressed in E. coli, and purified following the same protocol as that for thewild-type CT domain. The catalytic activity of the CT domain was assayed following protocols described earlier (Guchhait, R. B. et al. (1974) Acetyl coenzyme A carboxylase system from Escherichia coli. Purification and properties of the biotin carboxylase, carboxyltransferase, and carboxyl carrier protein components. J Biol Chem 249, 6633-6645; Zhang et al., 2003). For the inhibition studies shown in FIG. 7E, the activity of the enzyme in the presence of 0, 0.5 or 2 mM haloxyfop was determined. The concentration of the malonyl-CoA substrate was kept close to the expected Km, 75 μM for the wild-type enzyme and 750 μM for the mutants. The wild-type enzyme was at 2.5 μM concentration, whereas the mutants were at 20 μM concentration.







TABLE E







Summary of Crystallographic Information













Haloxyfop
Diclofop



Structure
Free enzyme
complex
complex
L1705I/V1967I





Maximum resolution (Å)
2.5
2.8
2.5
2.6


Number of observations
420,147
285,486
584,662
315,564


Rmerge1 (%)
6.9 (31.4)
9.3 (28.8)
7.6 (31.7)
5.0 (25.6)


Resolution range for
27-2.5
27-2.8
27-2.5
27-2.6


refinement


Number of reflections
130,501
96,167
88,661
117,132


Completeness (%)
86 (64)
88 (74)
96 (89)
87 (69)


R factor2 (%)
21.9 (26.7)
21.8 (27.9)
23.7 (28.5)
21.2 (26.8)


Free R factor2 (%)
25.0 (29.0)
25.2 (30.9)
26.5 (31.6)
23.7 (28.5)


rms deviation in bond
0.007
0.009
0.009
0.008


lengths (Å)


rms deviation in bond angles
1.2
1.2
1.1
1.2


(°)














  
    
      
    
    1
  
  ⁢
  
    R
    merge
  
  =
  
    
      ∑
      h
    
    ⁢
    
      
        ∑
        i
      
      ⁢
      
        
          
          
            
              I
              hi
            
            -
            
              〈
              
                I
                h
              
              〉
            
          
          
        
        /
        
          
            ∑
            h
          
          ⁢
          
            
              ∑
              i
            
            ⁢
            
              I
              hi
            
          
        
      
    
  






 


The numbers in parentheses are for the highest resolution shell.


 






  
    
      
    
    2
  
  ⁢
  R
  =
  
    
      ∑
      h
    
    ⁢
    
      
        
        
          
            F
            h
            o
          
          -
          
            F
            h
            c
          
        
        
      
      /
      
        
          ∑
          h
        
        ⁢
        
          F
          h
          o
        
      
    
  










Example 3
Expression, Purification and Assay of the CT Domain of Mouse ACC2
Materials and Methods
Various constructs comprising the CT domain of M. musculus ACC2 were subcloned into the pET26b vector (Novagen) to produce the constructs listed in Table F, which were then over-expressed in E. coli and purified as described above in Example 1.
Kinetic assays of CT activity also were performed as described in Example 1, and the activity of the enzyme was assayed in the reverse direction, i.e. measuring the transfer of the carboxyl group from malonyl-CoA to biotin methyl ester, as previously described (Zhang et al., 2003, Science 299:2064-2067).
Results
The mouse CT domain is enzymatically active and the Vmax and Km, values have been determined using malonyl-CoA as a substrate. The Vmax is 50×105 AU/s, and the Km=120 μM, comparable to the kinetic parameters of the yeast CT domain







TABLE F







Constructs created and tested for production of


proteins comprising the CT domain of mouse ACC2











Row
1st residue*
Last residue*
Induced
Soluble














1
54
810
+
−


2
43
810
+
−


3
35
810
+
−


4
24
810
+
−


5
11
810
+
−


6
1
810
+
−


7
54
767
+
+


8
43
767
+
+


9
35
767
+
+


(mCTACC2)


10
24
767
+
−


11
11
767
+
−


12
1
767
+
−


13
54
713
+
−


14
43
713
+
−


15
35
713
+
−


16
24
713
+
−


17
11
713
+
−


18
1
713
+
−


19
54
695
+
−


20
43
695
+
−


21
35
695
+
−


22
24
695
+
−


23
11
695
+
−


24
1
695
+
−





*Residue numbering based on GenBank Entry No. AAH22940


†NA—Not applicable






Example 4
Determination of the Crystal Structure of the CT Domain of Yeast ACC Complexed With CP-640186
Free crystals of the yeast CT domain (SEQ ID NO:3) was prepared as in Example 2. To prepare the CP-640186 complex, crystals of the free enzyme (covering residues 1476-2233) were soaked with the CP compound.
Structure Determination. X-ray diffraction data were collected at the X4A beamline of the National Synchrotron Light Source (NSLS). The diffraction images were processed with the HKL package (Otwinowski and Minor, 1997). The unit cell parameters for the complex crystal are a=247 Å, b=125 Å, c=146 Å, and β=94, with a space group of C2. The structure refinement was carried out with the program CNS (Brunger et al., 1998). Clear electron density for the herbicides was observed from the crystallographic analysis. The atomic model was built with the program O (Jones, T. A. (1978) A graphics model building and refinement system for macromolecules. J Appl Cryst 11, 268-272.).
Results. The crytal structure of yeast CT in complex with CP-640186 was determined at 2.8 Å resolution. This compound was recently reported by Pfizer to be a potent inhibitor of mammalian ACC1 and ACC2, with IC50 values of about 55 nM (FIG. 23).
From the crystal structure, several salient features of the complex should be noted. For example, the inhibitor is bound in the active site (FIG. 23), at the interface between two monomers of the enzyme. This proves that the inhibitor functions at the active site of the CT domain. In contrast the studies with the herbicides (diclfop or haloxyfop), there are only small conformational changes in the enzyme upon binding of the CP compound. The binding site for the CP compound is distinct from that for CoA or for the herbicides, and this is consistent with kinetic studies showing that the CP compound is non-competitive with respect to malonyl-CoA. The structure suggests that this binding site (i.e., the binding site for the CP compound) may overlap with that for biotin.
The anthracene group of the CP compound is placed in the narrow channel between helices α6 and α6′, interacting with residues Ala1761, Lys1764, Met1765 on one face, and residues Leu2025′, Gln2026′ and Gly2029′ on the other. The carbonyl oxygen next to the anthracene group is hydrogen-bonded to the main-chain amide of Gln2028′. The remainder of the inhibitor (the two piperidine rings and the morpholine ring) is placed next to the peptide segment Arg1954′-Gly1959′. In addition, it has interactions with Val1923′, Thr1757 and Ile1762. One face of these rings is exposed to the solvent in the CT complex. The carbonyl oxygen next to the morpholine ring is hydrogen-bonded to the main chain amide of Gly1958′.
Kinetic studies show that the inhibitor is non-competitive versus the substrate malonyl-CoA. The Ki values are about 4 μM, however, this value must be considered in relation to the fact that about 3 μM of enzyme is in the reaction buffer.
Most of the residues that interact with the CP compound are strictly or highly conserved among the CT domains. Two exceptions are Met1765, which is Val in most mammalian ACCs, and Ile1762, which is Leu in most other ACCs. Additional residues may also be important for inhibitor binding. For example, Gly2032 is replaced by Glu in most other ACCs, and this Glu side chain could ion-pair with Lys1764, forming a lid over the anthracene group.
The structural information proves that yeast CT is a valid surrogate for defining the binding modes of inhibitors against human ACCs, and provides a basis for the design of modulators against human ACC and other enzymes.







TABLE G







CT Domain Corresponding Residues (The residues correspond by row)


















SEQ ID
SEQ ID
SEQ ID
SEQ ID


SEQ ID
SEQ ID
SEQ ID
SEQ ID
NO: 6
NO: 8
NO: 10
NO: 14


NO: 1
NO: 2
NO: 3
NO: 4
(mouse
(human
(human
(mouse


(yeast)
(yeast)
(yeast)
(yeast)
ACC2)
ACC1)
ACC2)
ACC1)





Met 1503
Met 75
Met 28
Met 28
Leu 30
Leu 46
Leu 87
Leu 64


Lys 1592
Lys 164
Lys 117
Lys 117
Gln 116
Arg 140
Arg 173
Arg 158


Ile 1593
Ile 165
Ile 118
Ile 118
Ile 117
Ile 141
Ile 174
Ile 159


Ser 1595
Ser 167
Ser 120
Ser 120
Ser 119
Ser 143
Ser 176
Ser 161


Phe 1596
Phe 168
Phe 121
Phe 121
Phe 120
Phe 144
Phe 177
Phe 162


Asn 1624
Asn 196
Asn 149
Asn 149
Asn 148
Asn 172
Asn 205
Asn 190


Ser 1625
Ser 197
Ser 150
Ser 150
Ser 149
Ser 173
Ser 206
Ser 191


Gly 1626
Gly 198
Gly 151
Gly 151
Gly 150
Gly 174
Gly 207
Gly 192


Ala 1627
Ala 199
Ala 152
Ala 152
Ala 151
Ala 175
Ala 208
Ala 193


Arg 1628
Arg 200
Arg 153
Arg 153
Arg 152
Arg 176
Arg 209
Arg 194


Ile 1629
Ile 201
Ile 154
Ile 154
Met 153
Ile 177
Ile 210
Ile 195


Gly 1630
Gly 202
Gly 155
Gly 155
Gly 154
Gly 178
Gly 211
Gly 196


Met 1631
Met 203
Met 156
Met 156
Leu 155
Leu 179
Met 212
Leu 197


Gly 1699
Gly 271
Gly 224
Gly 224
Asn 220
Gly 244
Gly 277
Gly 262


Gly 1701
Gly 273
Gly 226
Gly 226
Gly 222
Gly 246
Gly 279
Gly 264


Glu 1703
Glu 275
Glu 228
Glu 228
Glu 224
Glu 248
Glu 281
Glu 266


Cys 1704
Cys 276
Cys 229
Cys 229
Asn 225
Asn 249
Asn 282
Asn 267


Leu 1705
Leu 277
Leu 230
Ile 230
Leu 226
Leu 250
Leu 283
Leu 268


Ser 1708
Ser 280
Ser 233
Ser 233
Ser 229
Ser 253
Ser 286
Ser 271


Ala 1712
Ala 284
Ala 237
Ala 237
Ala 233
Ala 257
Ala 290
Ala 275


Arg 1731
Arg 303
Arg 256
Arg 256
Arg 252
Arg 276
Arg 309
Arg 294


Val 1733
Val 305
Val 258
Val 258
Leu 254
Ile 278
Ile 311
Ile 296


Gly 1734
Gly 306
Gly 259
Gly 259
Gly 255
Gly 279
Gly 312
Gly 297


Ile 1735
Ile 307
Ile 260
Ile 260
Ile 256
Ile 280
Ile 313
Ile 298


Gly 1736
Gly 308
Gly 261
Gly 261
Gly 257
Gly 281
Gly 314
Gly 299


Ala 1737
Ala 309
Ala 262
Ala 262
Ala 258
Ala 282
Ala 315
Ala 300


Tyr 1738
Tyr 310
Tyr 263
Tyr 263
Tyr 259
Tyr 283
Tyr 316
Tyr 301


Leu 1739
Leu 311
Leu 264
Leu 264
Leu 260
Leu 284
Leu 317
Leu 302


Arg 1741
Arg 313
Arg 266
Arg 266
Arg 262
Arg 286
Arg 319
Arg 304


Leu 1742
Leu 314
Leu 267
Leu 267
Leu 263
Leu 287
Leu 320
Leu 305


Pro 1753
Pro 325
Pro 278
Pro 278
His 274
His 298
His 331
His 316


Ile 1755
Ile 327
Ile 280
Ile 280
Ile 276
Ile 300
Ile 333
Ile 318


Leu 1756
Leu 328
Leu 281
Leu 281
Leu 277
Leu 301
Leu 334
Leu 319


Thr 1757
Thr 329
Thr 282
Thr 282
Thr 278
Thr 302
Thr 335
Thr 320


Gly 1758
Gly 330
Gly 283
Gly 283
Gly 279
Gly 303
Gly 336
Gly 321


Ala 1759
Ala 331
Ala 284
Ala 284
Ala 280
Ala 304
Ala 337
Ala 322


Pro 1760
Pro 332
Pro 285
Pro 285
Gly 281
Gly 305
Ser 338
Gly 323


Ala 1761
Ala 333
Ala 286
Ala 286
Ala 282
Ala 306
Ala 339
Ala 324


Ile 1762
Ile 334
Ile 287
Ile 287
Leu 283
Leu 307
Leu 340
Leu 325


Asn 1763
Asn 335
Asn 288
Asn 288
Asn 284
Asn 308
Asn 341
Asn 326


Lys 1764
Lys 336
Lys 289
Lys 289
Lys 285
Lys 309
Lys 342
Lys 327


Met 1765
Met 337
Met 290
Met 290
Val 286
Val 310
Val 343
Val 328


Leu 1766
Leu 338
Leu 291
Leu 291
Leu 287
Leu 311
Leu 344
Leu 329


Tyr 1771
Try 343
Tyr 296
Tyr 296
Tyr 292
Tyr 316
Tyr 349
Tyr 334


Asn 1774
Asn 346
Asn 299
Asn 299
Asn 295
Asn 319
Asn 352
Asn 337


Ala 1908
Ala 480
Ala 433
Ala 433
Ala 431
Ala 455
Ala 488
Ala 473


Pro 1920
Pro 492
Pro 445
Pro 445
Ala 443
Ala 467
Ala 500
Ala 485


Gly 1921
Gly 493
Gly 446
Gly 446
Gly 444
Gly 468
Gly 501
Gly 486


Gln 1922
Gln 494
Gln 447
Gln 447
Gln 445
Gln 469
Gln 502
Gln 487


Val 1923
Val 495
Val 448
Val 448
Val 446
Val 470
Val 503
Val 488


Trp 1924
Trp 496
Trp 449
Trp 449
Trp 447
Trp 471
Trp 504
Trp 489


His 1925
His 497
His 450
His 450
Phe 448
Phe 472
Phe 505
Phe 490


Pro 1926
Pro 498
Pro 451
Pro 451
Pro 449
Pro 473
Pro 506
Pro 491


Ser 1928
Ser 500
Ser 453
Ser 453
Ser 451
Ser 475
Ser 508
Ser 493


Ala 1929
Ala 501
Ala 454
Ala 454
Ala 452
Ala 476
Ala 509
Ala 494


Phe 1930
Phe 502
Phe 455
Phe 455
Tyr 453
Phe 477
Tyr 510
Phe 495


Trp 1953
Trp 525
Trp 478
Trp 478
Trp 475
Trp 499
Trp 532
Trp 517


Arg 1954
Arg 526
Arg 479
Arg 479
Arg 476
Arg 500
Arg 533
Arg 518


Gly 1955
Gly 527
Gly 480
Gly 480
Gly 477
Gly 501
Gly 534
Gly 519


Phe 1956
Phe 528
Phe 481
Phe 481
Phe 478
Phe 502
Phe 535
Phe 520


Ser 1957
Ser 529
Ser 482
Ser 482
Ser 479
Ser 503
Ser 536
Ser 521


Gly 1958
Gly 530
Gly 483
Gly 483
Gly 480
Gly 504
Gly 537
Gly 522


Gly 1959
Gly 531
Gly 484
Gly 484
Gly 481
Gly 505
Gly 538
Gly 523


Gln 1960
Gln 532
Gln 485
Gln 485
Met 482
Met 506
Met 539
Met 524


Arg 1961
Arg 533
Arg 486
Arg 486
Lys 483
Lys 507
Lys 540
Lys 525


Asp 1962
Asp 534
Asp 487
Asp 487
Asp 484
Asp 508
Asp 541
Asp 526


Met 1963
Met 535
Met 488
Met 488
Met 485
Met 509
Met 542
Met 527


Phe 1964
Phe 536
Phe 489
Phe 489
Tyr 486
Tyr 510
Tyr 543
Tyr 528


Asn 1965
Asn 537
Asn 490
Asn 490
Glu 487
Asp 511
Asp 544
Asp 529


Glu 1966
Glu 538
Glu 491
Glu 491
Gln 488
Gln 512
Gln 545
Gln 530


Val 1967
Val 539
Val 492
Ile 492
Met 489
Val 513
Val 546
Val 531


Leu 1968
Leu 540
Leu 493
Leu 493
Leu 490
Leu 514
Leu 547
Leu 532


Lys 1969
Lys 541
Lys 494
Lys 494
Lys 491
Lys 515
Lys 548
Lys 533


Tyr 1970
Tyr 542
Tyr 495
Tyr 495
Phe 492
Phe 516
Phe 549
Phe 534


Gly 1971
Gly 543
Gly 496
Gly 496
Gly 493
Gly 517
Gly 550
Gly 535


Ser 1972
Ser 544
Ser 497
Ser 497
Ala 494
Ala 518
Ala 551
Ala 536


Ile 1974
Ile 546
Ile 499
Ile 499
Ile 496
Ile 520
Ile 553
Ile 538


Val 1975
Val 547
Val 500
Val 500
Val 497
Val 521
Val 554
Val 539


Glu 1994
Glu 566
Glu 519
Glu 519
Glu 516
Glu 540
Glu 573
Glu 558


Arg 1996
Arg 568
Arg 521
Arg 521
Arg 518
Arg 542
Arg 575
Arg 560


Gly 1997
Gly 569
Gly 522
Gly 522
Gly 519
Gly 543
Gly 576
Gly 561


Gly 1998
Gly 570
Gly 523
Gly 523
Gly 520
Gly 544
Gly 577
Gly 562


Ser 1999
Ser 571
Ser 524
Ser 524
Ser 521
Ser 545
Ser 578
Ser 563


Trp 2000
Trp 572
Trp 525
Trp 525
Trp 522
Trp 546
Trp 579
Trp 564


Val 2001
Val 573
Val 526
Val 526
Val 523
Val 547
Val 580
Val 565


Val 2002
Val 574
Val 527
Val 527
Val 524
Val 548
Val 581
Val 566


Val 2003
Val 575
Val 528
Val 528
Leu 525
Ile 549
Ile 582
Ile 567


Arg 2021
Arg 593
Arg 546
Arg 546
Arg 543
Arg 567
Arg 600
Arg 585


Gly 2023
Gly 595
Gly 548
Gly 548
Gly 545
Ser 569
Gly 602
Ser 587


Val 2024
Val 596
Val 549
Val 549
Val 546
Val 570
Val 603
Val 588


Leu 2025
Leu 597
Leu 550
Leu 550
Leu 547
Leu 571
Leu 604
Leu 589


Glu 2026
Glu 598
Glu 551
Glu 551
Glu 548
Glu 572
Glu 605
Glu 590


Pro 2027
Pro 599
Pro 552
Pro 552
Pro 549
Pro 573
Pro 606
Pro 591


Gln 2028
Gln 600
Gln 553
Gln 553
Glu 550
Glu 574
Glu 607
Glu 592


Gly 2029
Gly 601
Gly 554
Gly 554
Gly 551
Gly 575
Gly 608
Gly 593


Met 2030
Met 602
Met 555
Met 555
Thr 552
Thr 576
Thr 609
Thr 594


Val 2031
Val 603
Val 556
Val 556
Val 553
Val 577
Val 610
Val 595


Gly 2032
Gly 604
Gly 557
Gly 557
Glu 554
Glu 578
Glu 611
Glu 596


Ile 2033
Ile 605
Ile 558
Ile 558
Ile 555
Ile 579
Ile 612
Ile 597


Lys 2034
Lys 606
Lys 559
Lys 559
Lys 556
Lys 580
Lys 613
Lys 598


Arg 2036
Arg 608
Arg 561
Arg 561
Arg 558
Arg 582
Arg 615
Arg 600


Asp 2098
Asp 670
Asp 623
Asp 623
Asp 620
Asp 644
Asp 677
Asp 662


Val 2108
Val 680
Val 633
Val 633
Ile 630
Ile 654
Val 687
Val 672


Leu 2189
Leu 761
Leu 714
Leu 714
N/A
N/A
N/A
N/A

## Claims

1. A composition comprising a non-crystalline polypeptide consisting of:
(a) the amino acid sequence of SEQ ID NO:2,
(b) the amino acid sequence of SEQ ID NO:3, or
(c) an amino acid sequence that is at least 95% identical to the amino acid sequence of (a) or (b) and wherein the polypeptide binds acetyl-CoA, haloxyfop, diclofop, or CP-640186.

2. The composition of claim 1, wherein the composition comprises one or more dimers of said non-crystalline polypeptide.

3. The composition of claim 2, wherein the non-crystalline polypeptide consists of an amino acid sequence that is at least 99% identical to the amino acid sequence of (a) or (b) of claim 1 and wherein the polypeptide binds acetyl-CoA, haloxyfop, diclofop, or CP-640186.

4. The composition of claim 2, wherein each polypeptide of the dimer consists of the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:3.

5. The composition of claim 1, wherein the polypeptide is complexed with a ligand, wherein the ligand is selected from the group consisting of haloxyfop, diclofop and CP-640186.

6. The composition of claim 1, wherein the polypeptide consists of the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:3.

7. A composition comprising a non-crystalline carboxyltransferase domain dimer of two polypeptides, wherein each polypeptide of the dimer is selected from the group consisting of:
a) the amino acid sequence of SEQ ID NO:3, and
b) an amino acid sequence that is at least 95% identical to the amino acid sequence of SEQ ID NO:3, wherein each polypeptide binds acetyl-CoA, haloxyfop, diclofop, or CP-640186 and wherein the following amino acid residues corresponding to SEQ ID NO:3 are conserved or conservatively substituted: Ile 499, Val 527, Gly 523, Val 526, Val 549, Leu 493, Phe 481, Trp 449, Tyr 263, Ser 233, Ala 152, Ile 260, Gly 259, and Leu 281.

8. A composition comprising a non-crystalline dimer of two polypeptides, wherein each polypeptide of the dimer consists of the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:3.

9. A composition comprising a non-crystalline dimer of two polypeptides, wherein each polypeptide of the dimer consists of:
(a) the amino acid sequence of SEQ ID NO:3, or an amino acid sequence that is at least 95% identical to the amino acid sequence of SEQ ID NO:3, wherein the polypeptide binds acetyl-CoA, haloxyfop, diclofop, or CP-640186 and wherein the following amino acid residues corresponding to SEQ ID NO:3 are conserved or conservatively substituted: Ala 286, Lys 289, Leu 550, Glu 551, and Gly 554, or
(b) the amino acid sequence of SEQ ID NO:2, or an amino acid sequence that is at least 95% identical to the amino acid sequence of SEQ ID NO:2, wherein the polypeptide binds acetyl-CoA, haloxyfop, diclofop, or CP-640186 and wherein the following amino acid residues corresponding to SEQ ID NO:2 are conserved or conservatively substituted: Ala 333, Lys 336, Leu 597, Glu 598, and Gly 601.

10. A composition comprising a non-crystalline dimer of two polypeptides, wherein each polypeptide of the dimer consists of:
(a) the amino acid sequence of SEQ ID NO:3, or an amino acid sequence that is at least 95% identical to the amino acid sequence of SEQ ID NO:3, wherein the polypeptide binds acetyl-CoA, haloxyfop, diclofop, or CP-640186 and wherein the following amino acid residues corresponding to SEQ ID NO:3 are conserved or conservatively substituted: Ile 118, Ser 120, Phe 121, Asn 149, Ser 150, Gly 151, Ala 152, Arg 153, Ile 154, Gly 155, Gly 224, Leu 230, Arg 256, Gly 259, Ile 260, Tyr 263, Ile 280, Leu 281, Thr 282, Gly 283, Ala 284, Ala 286, Asn 299, Gly 480, Phe 481, Arg 521, Gly 522, Gly 523, Ser 524, Val 526, Val 549, Leu 550, Gly 554, Ile 558, Lys 559, and Arg 561, or
(b) the amino acid sequence of SEQ ID NO:2, or an amino acid sequence that is at least 95% identical to the amino acid sequence of SEQ ID NO:2, wherein the polypeptide binds acetyl-CoA, haloxyfop, diclofop, or CP-640186 and wherein the following amino acid residues corresponding to SEQ ID NO:2 are conserved or conservatively substituted: Ile 165, Ser 167, Phe 168, Asn 196, Ser 197, Gly 198, Ala 199, Arg 200, Ile 201, Gly 202, Gly 271, Leu 277, Arg 303, Gly 306, Ile 307, Tyr 310, Ile 327, Leu 328, Thr 329, Gly 330, Ala 331, Ala 333, Asn 346, Gly 527, Phe 528, Arg 568, Gly 569, Gly 570, Ser 571, Val 573, Val 596, Leu 597, Gly 601, Ile 605, Lys 606, and Arg 608.

11. A composition comprising a non-crystalline dimer of two polypeptides, wherein each polypeptide of the dimer consists of:
(a) the amino acid sequence of SEQ ID NO:3, or an amino acid sequence that is at least 95% identical to the amino acid sequence of SEQ ID NO:3, wherein the polypeptide binds acetyl-CoA, haloxyfop, diclofop, or CP-640186 and wherein the following amino acid residues corresponding to SEQ ID NO:3 are conserved: Ile 154, Leu 281, Thr 282, Gly 283, Ala 286, Asn 288, Lys 289, Leu 291, Tyr 296, Ala 433, Gin 447, Val 448, Trp 449, Trp 478, Arg 479, Gly 480, Phe 481, Ser 482, Gly 483, Gly 484, Asp 487, Arg 521, Gly 522, Ser 524, Val 549, Leu 550, Glu 551, Pro 552, Gly 554, Val 556, and Ile 558, or
(b) the amino acid sequence of SEQ ID NO:2, or an amino acid sequence that is at least 95% identical to the amino acid sequence of SEQ ID NO:2, wherein the polypeptide binds acetyl-CoA, haloxyfop, diclofop, or CP-640186 and wherein the following amino acid residues corresponding to SEQ ID NO:2 are conserved: Ile 201, Leu 328, Thr 329, Gly 330, Ala 333, Asn 335, Lys 336, Leu 338, Tyr 343, Ala 480, Gin 494, Val 495, Trp 496, Trp 525, Arg 526, Gly 527, Phe 528, Ser 529, Gly 530, Gly 531, Asp 534, Arg 568, Gly 569, Ser 571, Val 596, Leu 597, Glu 598, Pro 599, Gly 601, Val 603, and Ile 605.

12. A composition comprising a non-crystalline dimer of two polypeptides, wherein each polypeptide of the dimer consists of:
(a) the amino acid sequence of SEQ ID NO:3, or an amino acid sequence that is at least 95% identical to the amino acid sequence of SEQ ID NO:3, wherein the polypeptide binds acetyl-CoA, haioxyfop, diciofop, or CP-640186 and wherein the following amino acid residues corresponding to SEQ ID NO:3 are conserved: Phe 121, Ser 150, Gly 151, Ala 152, Arg 153, Ile 154, Leu 230, Ser 233, Ala 237, Gly 259, Ile 260, Gly 261, Ala 262, Tyr 263, Leu 264, Arg 266, Leu 267, Ile 280, Leu 281, Thr 282, Val 448, Trp 449, Pro 451, Ser 453, Ala 454, Trp 478, Gly 480, Phe 481, Ser 482, Val 492, Leu 493, Lys 494, Gly 496, Ile 499, Arg 521, Gly 522, Gly 523, Ser 524, Trp 525, Val 526, Val 527, Val 549, and Leu 550, or
(b) the amino acid sequence of SEQ ID NO:2, or an amino acid sequence that is at least 95% identical to the amino acid sequence of SEQ ID NO:2, wherein the polypeptide binds acetyl-CoA, haloxyfop, diclofop, or CP-640186 and wherein the following amino acid residues corresponding to SEQ ID NO:2 are conserved: Phe 168, Ser 197, Gly 198, Ala 199, Arg 200, Ile 201, Leu 277, Ser 280, Ala 284, Gly 306, Ile 307, Gly 308, Ala 309, Tyr 310, Leu 311, Arg 313, Leu 314, Ile 327, Leu 328, Thr 329, Val 495, Trp 496, Pro 498, Ser 500, Ala 501, Trp 525, Gly 527, Phe 528, Ser 529, Val 539, Leu 540, Lys 541, Gly 543, Ile 546, Arg 568, Gly 569, Gly 570, Ser 571, Trp 572, Val 573, Val 574, Val 596, and Leu 597.

13. A composition comprising a non-crystalline dimer, wherein each polypeptide of the dimer consists of:
(a) the amino acid sequence of SEQ ID NO:2,
(b) the amino acid sequence of SEQ ID NO:3, or
(c) an amino acid sequence that is at least 95% identical to the amino acid sequence of (a) or (b) and wherein the polypeptide binds acetyl-CoA, haloxyfop, diclofop, or CP-640186.

14. A crystal comprising a dimer of a carboxyltransferase (CT) domain of an acetyl-CoA carboxylase, wherein the CT domain consists of the amino acid sequence of SEQ ID NO:3;
(a) wherein the CT domain is unliganded and the crystal has unit cell dimensions of a=247±2 Å; b=125±2 Å; c=145±2 Å; α=90°; β+94±2°; Υ=90°; and space group C2;
(b) wherein the CT domain is unliganded and the crystal has unit cell dimensions of a=255±2 Å; b=113±2 Å; c=135±2 Å; α=90°; β=101±2°; Υ=90°;and space group C2;
(c) wherein the CT domain is unliganded and the crystal has unit cell dimensions of a=246±2 Å; b=124±2 Å; c=145±2 Å; α=90°; β=94±2°; Υ=90°; and space group C2;
(d) wherein the CT domain is complexed with diclofop and the crystal has unit cell dimensions of a=137±2 Å; b=137±2 Å; c=244±2 Å; α=90°; μ=90°; Υ=120°; and space group P3221; or
(e) wherein the CT domain is complexed with CP-640186 or haloxyfop and the crystal has unit cell dimensions of a=247±2 Å; b=125±2 Å; c=146±2 Å; α=90°; β=94±2°; Υ=90°; and space group C2.

15. The crystal of claim 14, wherein the CT domain is unliganded and the crystal has unit cell dimensions of : a=246±2 Å; b=124±2 Å; c=145±2 Å; α=90°; β=94±2°; Υ=90°; and space group C2.

16. The crystal of claim 14, wherein the CT domain is complexed with haloxyfop and the crystal has unit cell dimensions of a=247±2 Å; b=125±2 Å; c=146±2 Å; α=90°; β=94±2°; Υ=90°; and space group C2.

17. The crystal of claim 16, wherein the CT domain of the crystal comprises a three-dimensional structure having the atomic coordinates of Table 3.

18. The crystal of claim 14, wherein the CT domain is complexed with diclofop and the crystal has unit cell dimensions of a=137±2 Å; b=137±2 Å; c=244 ±2 Å; α=90°; β=90°; Υ=120°; and space group P3221.

19. The crystal of claim 18, wherein the CT domain of the crystal comprises a three-dimensional structure having the atomic coordinates of Table 4.

20. The crystal of claim 14, wherein the CT domain is complexed with CP-640186 and the crystal has unit cell dimensions of a=247±2 Å; b=125±2 Å; c =146±2 Å; α=90°; β=94±2°; Υ=90°; and space group C2.

21. The crystal of claim 20, wherein the CT domain of the crystal comprises a three-dimensional structure having the atomic coordinates of Table 5.

22. A crystal comprising a dimer of a carboxyltransferase (CT) domain of an acetyl-CoA carboxylase, wherein the CT domain consists of the amino acid sequence of SEQ ID NO:2 and is complexed with acetyl-CoA and wherein the crystal has unit cell dimensions of: a=93±2 Å; b=138±2 Å; c=101±2 Å; α=90°; β=114±2°; Υ=90°; and space group P21.

23. The crystal of claim 22, wherein the CT domain of the crystal comprises a three-dimensional structure having the atomic coordinates of Table 2.