# Patent

## Title
Glutamate 2,3-aminomutases and methods of use thereof

## Abstract

There are provided nucleic acids, including isolated DNA molecules, which encode glutamate 2,3-aminomutase enzymes, polypeptides produced from such nucleic acids and methods of making the nucleic acids and polypeptides. There are further provided methods of producing β-glutamate from glutamate using glutamate 2,3-aminomutase.

## Background
CROSS REFERENCES TO RELATED APPLICATIONS
This application claims priority to U.S. Provisional Application Ser. No. 60/725,350, filed Oct. 11, 2005, the entire contents of which is incorporated herein by reference and for all purposes.


GOVERNMENT RIGHTS
Part of the work performed during development of this invention utilized U.S. Government Funds, specifically the National Institute of Diabetes and Digestive and Kidney Diseases, Grant No. DK 28607. Therefore, the U.S. Government has certain rights in this invention.


FIELD OF THE INVENTION
The present invention relates to novel 2,3-aminomutases, such as glutamate 2,3-aminomutases, and include nucleic acids encoding for polypeptides having glutamate 2,3-aminomutase activity and methods of making the same. This invention further relates to methods of using glutamate 2,3-aminomutases to produce β-glutamate.
BACKGROUND/RELATED ART
Although less abundant than the corresponding α-amino acids, β-amino acids occur in nature in both free forms and in peptides. Cardillo and Tomasini, Chem. Soc. Rev. 25:77 (1996); Sewald, Amino Acids 11:397 (1996). Since β-amino acids are stronger bases and weaker acids than α-amino acid counterparts, peptides that contain a β-amino acid in place of an α-amino acid, have a different skeleton atom pattern, resulting in new properties. For example, various peptides are protease inhibitors because the presence of the β-amino-α-hydroxy acid motif acts as a transition state mimic of peptide hydrolysis.
β-Amino acids are of particular interest in the preparation of medicaments, such as β-lactams. Well-known β-lactam antimicrobial agents include penicillins, cephalosporins, carbapenems, and monobactams. Other examples of medically useful molecules that contain β-amino-α-hydroxy acids include the anti-tumor agent taxol, the anti-bacterial agent, dideoxykanamicin A, bestatin, an immunological response modifier, the kynostatins, which are highly potent human immunodeficiency virus-1 protease inhibitors, and microginin, a tetrapeptide which has anti-hypertensive properties. Accordingly, enantiomerically pure β-amino-α-hydroxy acids are of considerable importance as crucial components of pharmacologically active compounds. Additionally, enantiomerically pure β-amino acids are useful as precursors for preparing various industrial chemicals. Thus, it is desirable to develop new methods for the synthesis of β-amino acids.
Previously, lysine 2,3-aminomutase has been reported to catalyze the conversion of not only lysine but other α-amino acids to the corresponding β-amino acid (see Frey and Ruzicka, U.S. Patent Publication Nos. 2003/0113882 and 2002/0173637, the entire disclosures of which are incorporated herein by reference). By contrast, it is believed that an enzyme which specifically possesses glutamate 2,3-aminomutase activity has not previously been reported.
SUMMARY OF THE INVENTION
It has been discovered for the first time that a gene exists that expresses glutamate 2,3-aminomutase activity, and that the gene product produces β-glutamate from L-glutamate in a reaction requiring S-(5′-adenosyl)-L-methionine, pyridoxal 5′-phosphate and an iron-sulfur cluster. The chemical equation for the transformation of L-glutamate into β-glutamate is:

HOOC—CH2—CH2—CH(NH2)—COOH→HOOC—CH2—CH(NH2)—CH2—COOH

Thus, the present invention provides nucleic acids, including isolated DNA molecules, which encode glutamate 2,3-aminomutase enzymes, polypeptides produced from such nucleic acids and methods of making the nucleic acids and polypeptides. There are further provided methods of producing β-glutamate from glutamate.
Thus, in accordance with one aspect, the invention provides an isolated DNA molecule encoding a polypeptide having glutamate 2,3-aminomutase activity, wherein the DNA molecule comprises a sequence selected from the group consisting of a) a DNA sequence encoding a polypeptide having at least 50% or 60% sequence identity to the amino acid sequence of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, or 18 as defined herein; b) a DNA sequence comprising SEQ. ID NO: 1, 3, 5, 7, 9, 11, 13, 15, or 17 as defined herein; and c) a DNA sequence which is degenerate to the sequence of (a) or (b) due to the genetic code. In some embodiments, the DNA sequence encoding a polypeptide has at least 70%, at least 80%, at least 90% or at least 95% sequence identity to the amino acid sequence of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, or 18 as defined herein. In other embodiments, there are provided expression vectors comprising the DNA molecule encoding a polypeptide having glutamate 2,3-aminomutase activity. The DNA molecule may be operably linked to one or more control sequences which direct the production of the polypeptide in a host cell.
In another aspect, the invention provides recombinant host cells comprising a DNA molecule as described herein. The recombinant host cell may include the expression vector as described herein. In some embodiments, the recombinant host cells of the invention are prokaryotic cells such as bacterial cells (e.g., E. coli).
In still another aspect, the invention provides methods of producing a polypeptide having glutamate 2,3-aminomutase activity comprising culturing a recombinant host cell as described herein. Such methods may further include isolating the polypeptide produced from the recombinant host cell.
In some aspects, the invention provides isolated, recombinant, or isolated and recombinant polypeptides having glutamate 2,3-aminomutase activity and comprising an amino acid sequence selected from the group consisting of (a) SEQ ID NO: 2; (b) SEQ ID NO: 4; (c) SEQ ID NO: 6; (d) SEQ ID NO: 8; (e) SEQ ID NO: 10; (f) SEQ ID NO: 12; (g) SEQ ID NO: 14; (h) SEQ ID NO: 16; (i) SEQ ID NO: 18; (j) a variant having at least 50% or 60% sequence identity to any one of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, or 18 as described herein; and (g) a functional fragment having at least 50% or at least 60% sequence identity to any one of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, or 18 as described herein. In other embodiments, there are provided isolated, recombinant, or isolated and recombinant polypeptides having glutamate 2,3-aminomutase activity and comprising an iron-sulfur cluster, S-(5′-adenosyl)-L-methionine, and pyridoxal 5′-phosphate. Such polypeptides may have a molecular weight of from about 35 kDa to about 65 kDa, and in some embodiments, from about 40 kDa to about 60 kDa, or about 45 kDa to about 55 kDa.
In another aspect, the invention provides methods of producing β-glutamic acid. The methods include (a) catalyzing the conversion of α-glutamic acid to β-glutamic acid by utilizing a glutamate 2,3-aminomutase as described herein as the catalyst, wherein the glutamate 2,3-aminomutase is isolated, recombinant, or isolated and recombinant; and (b) isolating the β-glutamic acid. Typically, the α-glutamic acid is L-glutamic acid. The method may further include separating the β-glutamic acid from α-glutamic acid by any suitable technique such as by using high performance chromatography. In some embodiments, the method is a continuous process. In others, the glutamate 2,3-aminomutase comprises the following amino acid sequences: CXXXCRXCXR (SEQ ID NO: 19); S(T)GGD(E) (SEQ ID NO: 20), GXXXPXXXXXXXXXXXK (SEQ ID NO: 21), PXYXXXXKXXXG (SEQ ID NO: 22), and PXXXXNXXXXXXK (SEQ ID NO: 23).
In some embodiments of methods of producing β-glutamic acid, step (a) further comprises culturing a host cell comprising an expression vector that encodes glutamate 2,3-aminomutase in the presence of α-glutamic acid, wherein the cultured host cell expresses glutamate 2,3-aminomutase; and/or wherein (b) further comprises isolating the β-glutamic acid from the cultured host cells. Thus, the expression vector can include a DNA molecule encoding a polypeptide having glutamate 2,3-aminomutase activity, wherein the DNA molecule comprises a sequence selected from the group consisting of (i) a DNA sequence encoding a polypeptide having at least 50% or at least 60% sequence identity to the amino acid sequence of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, or 18 as defined herein; (ii) a DNA sequence comprising SEQ. ID NO: 1, 3, 5, 7, 9, 11, 13, 15, or 17 as defined herein; and (iii) a DNA molecule which is degenerate to the sequence of (i) or (ii). In some embodiments, the DNA sequence encodes a polypeptide having at least 70%, at least 80%, at least 90%, or at least 95% sequence identity to the amino acid sequence of SEQ ID NOs 2, 4, 6, 8, 10, 12, 14, 16, or 18 as defined herein.
In other methods of producing β-glutamic acid, step (a) further comprises incubating glutamic acid in a solution containing purified glutamate 2,3-aminomutase and added cofactors required for glutamate 2,3-aminomutase activity; and/or wherein (b) further comprises isolating β-glutamic acid from the incubation solution. Suitable added cofactors include: (i) at least one of ferrous sulfate or ferric ammonium sulfate; (ii) pyridoxal phosphate; (iii) at least one of cysteine, dehydrolipoic acid, glutathione or dithiothreitol; (iv) S-adenosylmethionine; and (v) sodium dithionite.
In still other methods of producing β-glutamic acid, step (a) further comprises: (i) immobilizing glutamate 2,3-aminomutase on a suitable support; and (ii) activating the glutamate 2,3-aminomutase with cofactors required for glutamate 2,3-aminomutase activity; and (iii) contacting glutamic acid with the immobilized glutamate 2,3-aminomutase to produce the corresponding β-glutamic acid.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 SDS Polyacrylamide Gel Electrophoresis of Recombinant Produced C. difficile Glutamate 2,3-aminomutase in E. coli Cell Extract and Purified Form. Lane 1—Protein standards (Benchmark Protein Ladder, Invitrogen) 1 μg each protein, Lane 2—E. coli cell extract 30 μg, Lane 3—Purified recombinant C. difficile glutamate 2,3-aminomutase 4 μg. Arrow indicates marker for 50,000 MW protein standard.
FIG. 2. Interconversion of L-glutamate and β-glutamate by C. difficile glutamate 2,3-aminomutase. Separation and identification by HPLC. Assay conditions as described in the Examples: A. L-glutamate as substrate. Initial conditions: L-glutamate—5 mM, enzyme 3.7 μM (subunit). B. β-glutamate as substrate. Initial conditions: β-glutamate—5 mM, enzyme 3.7 μM (subunit).
FIG. 3. Effect of Sodium Dithionite Concentration on the Activity of Purified C. difficile Glutamate 2,3-aminomutase. Assay conditions as described in the Examples except the following: L-glutamate, 50 mM; S-(5′-adenosyl)-L-methionine, 250 μM; enzyme, 3.7 μM; and sodium dithionite concentrations: ♦ - - - ♦, 3.3 mM; Δ - - - Δ, 0.67 mM; □— - —□, 0.17 mM; ●—●, 0.067 mM.
FIG. 4. Protein Concentration vs. Glutamate 2,3-Aminomutase Activity. Purified glutamate 2,3-aminomutase was used as isolated. Assay conditions as described in the Examples except the following: L-glutamate 50 mM, S-(5′-adenosyl)-L-methionine 250 μM, and sodium dithionite 0.067 mM.
FIG. 5. Glutamate 2,3-aminomutase Activity vs. L-Glutamate Concentration. Enzyme kinetic parameters were determined by varying the concentration of L-glutamate (0.6-20 mM) following assay conditions described in the Examples. Enzyme concentration was 0.15 μM. Initial velocities were measured, and curve fitting was done by the nonlinear least squares curve fitting method of Cleland (25). Insert: double reciprocal (Lineweaver Burk) plot of saturation data.
FIG. 6. Electron Paramagnetic Resonance (EPR) spectroscopy of C. difficile Glutamate 2,3-aminomutase. See Example 2 for description of sample preparation. A) L-glutamate 50 mM, B) β-glutamate 50 mM, C) (2-13C)-DL-glutamate 100 mM; D) (2,3,3,4,4-d5)-L-glutamate 50 mM, E) L-glutamate 50 mM S-(5′-adenosyl)-L-methionine omitted, F) L-glutamate 50 mM, sodium dithionite omitted.
FIG. 7. UV-Visible Spectrophotometry of C. difficile Glutamate 2,3-aminomutase. Purified enzyme as isolated (0.45 mg/ml) in 0.02M sodium EPPS pH 8.0 buffer was evaluated anaerobically with a Hewlett-Packard Diode Array Spectrophotometer (Model 8452A).
FIG. 8. The likely chemical mechanism for the action of glutamate 2,3-aminomutase.



DETAILED DESCRIPTION OF THE INVENTION
1. Definitions and Abbreviations
In the description that follows, a number of terms are utilized extensively. Definitions are herein provided to facilitate understanding of the invention.
Cloning vector. A DNA molecule, such as a plasmid, cosmid, phagemid, or bacteriophage, which has the capability of replicating autonomously in a host cell and which is used to transform cells for gene manipulation. Cloning vectors typically contain one or a small number of restriction endonuclease recognition sites at which foreign DNA sequences may be inserted in a determinable fashion without loss of an essential biological function of the vector, as well as a marker gene which is suitable for use in the identification and selection of cells transformed with the cloning vector. Marker genes typically include genes that provide tetracycline resistance or ampicillin resistance.
Complementary DNA (cDNA). Complementary DNA is a single-stranded DNA molecule that is formed from an mRNA template by the enzyme reverse transcriptase. Typically, a primer complementary to portions of mRNA is employed for the initiation of reverse transcription. Those skilled in the art also use the term “cDNA” to refer to a double-stranded DNA molecule derived from a single mRNA molecule.
Enhancer. A promoter element. An enhancer can increase the efficiency with which a particular gene is transcribed into mRNA irrespective of the distance or orientation of the enhancer relative to the start site of transcription.
Expression. Expression is the process by which a polypeptide is produced from a structural gene. The process involves transcription of the gene into mRNA and the translation of such mRNA into polypeptide(s).
Expression vector. A DNA molecule comprising a cloned structural gene encoding a foreign protein which provides the expression of the foreign protein in a recombinant host. Typically, the expression of the cloned gene is placed under the control of (i.e., operably linked to) certain regulatory sequences such as promoter and enhancer sequences. Promoter sequences may be either constitutive or inducible.
Lysine 2,3-aminomutase. An enzyme that catalyzes the interconversion of lysine and β-lysine, typically L-lysine to L-β-lysine.
Glutamate 2,3-aminomutase. An enzyme that catalyzes the interconversion of glutamic acid and β-glutamic acid, typically L-glutamic acid to β-glutamic acid.
Promoter. A DNA sequence which directs the transcription of a structural gene to produce mRNA. Typically, a promoter is located in the 5′ region of a gene, proximal to the start codon of a structural gene. If a promoter is an inducible promoter, then the rate of transcription increases in response to an inducing agent. In contrast, the rate of transcription is not regulated by an inducing agent if the promoter is a constitutive promoter.
Recombinant host. A recombinant host may be any prokaryotic or eukaryotic cell which contains either a cloning vector or expression vector. This term is also meant to include those prokaryotic or eukaryotic cells that have been genetically engineered to contain the cloned gene(s) in the chromosome or genome of the host cell. For examples of suitable hosts, see Sambrook et al., MOLECULAR CLONING: A LABORATORY MANUAL, Second Edition, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989) [“Sambrook”].
Structural gene. A DNA sequence that is transcribed into messenger RNA (mRNA) which is then translated into a sequence of amino acids characteristic of a specific polypeptide (protein).
As used herein, a substantially pure protein means that the desired purified protein is essentially free from contaminating cellular components, as evidenced by a single band following polyacrylamide-sodium dodecyl sulfate gel electrophoresis (SDS-PAGE). The term “substantially pure” is further meant to describe a molecule which is homogeneous by one or more purity or homogeneity characteristics used by those of skill in the art at the present time. For example, a substantially pure glutamate 2,3-aminomutase will show constant and reproducible characteristics within standard experimental deviations for parameters such as the following: molecular weight, chromatographic migration, amino acid composition, amino acid sequence, blocked or unblocked N-terminus, HPLC elution profile, biological activity such as Vmax, and other such parameters. In some embodiments, a substantially pure protein of the invention will be at least 90% pure as judged by SDS-PAGE and/or other parameters. The term, however, is not meant to exclude artificial or synthetic mixtures of glutamate 2,3-aminomutase with other compounds. In addition, the term is not meant to exclude glutamate 2,3-aminomutase fusion proteins isolated from a recombinant host.
Abbreviations: EPPS, N-[2-hydroxyethyl-piperazine-N′-(3-propanesulfonic acid)]; dNTP, a 2′-deoxyribonucleotide-5′-triphosphate; DTT, dithiothreitol; EDTA, ethylenediamine tetraacetic acid; EPR, electron paramagnetic resonance; HPLC, high performance liquid chromatography; IPTG, isopropyl-β-D-thiogalactopyranoside; PCR, polymerase chain reaction; PITC, phenylisothiocyanate; PMSF, phenylmethanesulfonyl fluoride; Tris, tris(hydroxymethyl)aminomethane.
2. Isolation of a DNA Molecule that Encodes the Clostridium Glutamate 2,3-Aminomutase
Although the existence of the clostridial lysine 2,3-aminomutase has been known for over 35 years, there is no report in the scientific literature on the isolation of the gene encoding glutamate 2,3-aminomutase. Now, for the first time and as described herein, DNA molecules encoding the clostridial glutamate 2,3-aminomutase gene have been isolated from the chromosomal DNA of Clostridium difficile. The nucleotide and predicted amino acid sequences of clostridial glutamate 2,3-aminomutase (SEQ ID NOs: 1 and 2) isolated from the genomic database are:









SEQ ID NO:1




ATGAATGAACAAACTAGAATATCCTTAGAGAGAGCTGCTGAATTAAAATCAAAAATTGAT
60


 


GATTATATTCAGGCTAGAAAAACGATTAACAGAGGTCTTGAAAAAGAAGAAGAGATAAAT
120


 


AAACGAAAACAGAAAATATTAAGTATCTTAAATGGAACTGAAGAGGATTGGAATAACTAC
180


 


AAATGGCAATTATCAAATAGAATAACAGATGTAGATACTTTATCAAAAATTATAACTCTA
240


 


ACTAAAAAAGAAAAAGAATATATAAAAGAGGTTGGTACTCAATTTAGATGGGCAATATCT
300


 


CCATATTATTTGAGTCTTATAGACCCAGAAGATATATGTGACCCAATAAAATTACTGTCT
360


 


ATACCAACACATATAGAGTTGGAAGATGAACAAGAAGATTTGGACCCAATGGGAGAAGAG
420


 


TATACAAACCCAGCAGGATGTATAACTAGAAGATACCCGGATAGATTAATAATAAATGTA
480


 


ACAAATGAGTGTGCTATGTATTGTAGACACTGTCAGAGAAGAAGAAATATTGGACAACAA
540


 


GATTCTCATAAGTCAAAAGCTATTATCCAAGAATCTATAGACTATATCAGAGAAAATGAA
600


 


GAAATAAGAGATGTACTAGTAACTGGTGGAGATGCTCTTACATTAAAAGATGATTATTTA
660


 


GAGTGGATTCTTAGCCAACTTAAAGAGATACCACATGTTGATTATGTTAGATTAGGTACT
720


 


AGGACTCTTGTTACAATGCCACAAAGAATTACAGATGAATTTTGCAATATGCTAAAAAAA
780


 


TATCACCCTATATATATAAATACTCATTTTAATCATCCAATGGAAATAACTAAGGAATCT
840


 


AAAGAAGCTTGTGAAAAGTTAGCAAATGCAGGAGTTCCATTAGGAAATCAGGCAGTATTA
900


 


TTAAATGGAATAAATAATGATAAATTTGTAATGAGATGTTTAAATCAAGAATTACTGAAA
960


 


ATAAGAGTAAAACCTTATTATATATTCCAAAGTAAACATGTAAAGGGAACAAAACATTTC
1020


 


AATACATCAGTAGATGATGGTCTTGAAATCATGGAGTATTTAAGAGGATATACATCAGGA
1080


 


ATGGCTATACCAACATATATAGTAAATGCTCCAAAAGGAGGAGGAAAGACTCCTTTGCTT
1140


 


CCTCAATACCTTGTATCAAAAGGAACAGATTACGTTATGCTTAGAACATGGGAAGGAAAA
1200


 


GTTATAAAAATGGAAGATGAACCTGCTGTAGATATAAAGAAACTTATAAAAGAACAAGCA
1260


 


CAGGATTAA
1269














SEQ ID NO:2



MNEQTRISLE RAAELKSKID DYIQARKTIN RGLEKEEEIN
50


KRKQKILSIL


 


NGTEEDWNNY KWQLSNRITD VDTLSKIITL TKKEKEYIKE
100


VGTQFRWAIS


 


PYYLSLIDPE DICDPIKLLS IPTHIELEDE QEDLDPMGEE
150


YTNPAGCITR


 


RYPDRLIINV TNECAMYCRH CQRRRNIGQQ DSHKSKAIIQ
200


ESIDYIRENE


 


EIRDVLVTGG DALTLKDDYL EWILSQLKEI PHVDYVRLGT
250


RTLVTMPQRI


 


TDEFCNMLKK YHPIYINTHF NHPMEITKES KEACEKLANA
300


GVPLGNQAVL


 


LNGINNDKFV MRCLNQELLK IRVKPYYIFQ SKHVKGTKHF
350


NTSVDDGLEI


 


MEYLRGYTSG MAIPTYIVNA PKGGGKTPLL PQYLVSKGTD
400


YVMLRTWEGK


 


VIKMEDEPAV DIKKLIKEQA QD
422






DNA molecules encoding the clostridial glutamate 2,3-aminomutase gene can be obtained by screening cDNA or genomic libraries with polynucleotide probes having nucleotide sequences based upon SEQ ID NO:1. For example, a suitable library can be prepared by obtaining genomic DNA from Clostridium difficile and constructing a library according to standard methods. See, for example, Ausubel et al. (eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, 5th Edition, pages 2-1 to 2-13 and 5-1 to 5-6 (John Wiley & Sons, Inc. 2002).
Alternatively, the clostridial glutamate 2,3-aminomutase gene can be obtained by synthesizing DNA molecules using mutually priming long oligonucleotides. See, for example, Ausubel et al., (eds.), CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, pages 8.2.8 to 8.2.13 (1990) [“Ausubel”]. Also, see Wosnick et al., Gene 60:115 (1987); and Ausubel et al. (eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, 5th Edition, John Wiley & Sons, Inc. (2002). Established techniques using the polyrnerase chain reaction provide the ability to synthesize DNA molecules at least 2 kilobases in length. Adang et al., Plant Molec. Biol. 21:1131 (1993); Bambot et al., PCR Methods and Applications 2:266 (1993); Dillon et al., “Use of the Polymerase Chain Reaction for the Rapid Construction of Synthetic Genes,” in METHODS IN MOLECULAR BIOLOGY, Vol. 15: PCR PROTOCOLS: CURRENT METHODS AND APPLICATIONS, White (ed.), pages 263-268, (Humana Press, Inc. 1993); Holowachuk et al., PCR Methods Appl. 4:299 (1995).
Included in the invention are also DNA molecules in which the nucleotide sequences are degenerate, because of the genetic code, to the nucleotide sequences shown as SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, and 17. A sequential grouping of three nucleotides, a “codon”, codes for one amino acid. Since there are 64 possible codons, but only 20 natural amino acids, most amino acids are coded for by more than one codon. This natural “degeneracy”, or “redundancy”, of the genetic code is well known in the art. It will thus be appreciated that the DNA sequences described herein and shown in the Sequence Listing are only examples within a large but definite group of DNA sequences which will encode the polypeptides described herein. Exemplary degenerate DNA sequences include but are not limited to SEQ ID NOs: 28, 29, 30, and 31, which are presented in Example 3 and are degenerate to SEQ ID NOs: 3, 5, 7, and 9, respectively.
Variants of glutamate 2,3-aminomutase can be produced that contain one or more conservative or non-conservative amino acid changes, compared with the native enzyme, so long as glutamate 2,3-aminomutase activity is retained. Typically variants have at least 50%, at least 60%, at least 70%, at least 80%, or at least 90% amino acid sequence identity compared to the original sequences such as any one of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, or 18. In some embodiments, high sequence identity variants are provided in which the amino acid sequence identity of the variant to the glutamate 2,3-aminomutase is at least 95%, at least 96%, at least 97%, at least 98% or even at least 99%. In other embodiments, glutamate 2,3-aminomutase variants include 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more conservative or nonconservative amino acid substitutions such as 15, 20, 25, 30, or even 40 amino acid substitutions so long as glutamate 2,3-aminomutase activity is retained. The ability of variants of glutamate 2,3-aminomutase to convert L-glutamate to β-glutamate can be determined using a standard enzyme activity assay, such as the assay described herein.
Conservative variants can be obtained that contain one or more amino acid substitutions of, e.g., SEQ ID NO:2, in which an alkyl amino acid is substituted for an alkyl amino acid in the glutamate 2,3-aminomutase amino acid sequence, an aromatic amino acid is substituted for an aromatic amino acid in glutamate 2,3-aminomutase amino acid sequence, a sulfur-containing amino acid is substituted for a sulfur-containing amino acid in the glutamate 2,3-aminomutase amino acid sequence, a hydroxy-containing amino acid is substituted for a hydroxy-containing amino acid in the glutamate 2,3-aminomutase amino acid sequence, an acidic amino acid is substituted for an acidic amino acid in the glutamate 2,3-aminomutase amino acid sequence, a basic amino acid is substituted for a basic amino acid in the glutamate 2,3-aminomutase amino acid sequence, or a dibasic monocarboxylic amino acid is substituted for a dibasic monocarboxylic amino acid in the glutamate 2,3-aminomutase amino acid sequence.
Among the common amino acids, for example, a “conservative amino acid substitution” is illustrated by a substitution among amino acids within each of the following groups: (1) glycine, alanine, (2) valine, leucine, and isoleucine, (3) phenylalanine, tyrosine, and tryptophan, (4) cysteine and methionine, (5) serine and threonine, (6) aspartate and glutamate, (7) glutamine and asparagine, and (8) lysine, arginine and histidine.
Conservative amino acid changes in, e.g., the clostridial glutamate 2,3-aminomutase, can be introduced by substituting appropriate nucleotides for the nucleotides recited in SEQ ID NO:1. Such “conservative amino acid” variants can be obtained, for example, by oligonucleotide-directed mutagenesis, linker-scanning mutagenesis, mutagenesis using the polymerase chain reaction, and the like. Ausubel et al., supra; Ausubel et al. (eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, 5th Edition, John Wiley & Sons, Inc. (2002). Also see generally, McPherson (ed.), DIRECTED MUTAGENESIS: A PRACTICAL APPROACH, IRL Press (1991). Similarly, conservative amino acid changes may be made in the glutamate 2,3-aminomutase from other species by substituting appropriate nucleotides in the sequences recited in SEQ ID NOs:3, 5, 7, 9, 11, 13, 15, and 17.
Glutamate 2, 3-aminomutase variants that contain one or more non-conservative amino acid substitutions, such as those based on glutamate 2,3-aminomutase having any one of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, or 18, and that retain the ability to produce β-glutamic acid from α-glutamic acid can also be produced and used as disclosed herein. Non-conservative amino acid substitutions are known in the art and include, without limitation, leucine for aspartate or valine for threonine. Non-conservative variants can also include amino acid insertions as compared to the native sequence such as, without limitation, insertion of methionine. As will be appreciated by the skilled artisan, the same methods used for generating conservative variants may be adapted and used to produce nonconservative variants.
In addition, routine deletion analyses of DNA molecules can be performed to obtain “functional fragments” of the clostridial glutamate 2,3-aminomutase or other glutamate 2,3-aminomutases. As an illustration, DNA molecules having the nucleotide sequence of SEQ ID NO:1 can be digested with Bal31 nuclease to obtain a series of nested deletions. The fragments are then inserted into expression vectors in proper reading frame, and the expressed polypeptides are isolated and tested for glutamate 2,3-aminomutase enzyme activity. One alternative to exonuclease digestion is to use oligonucleotide-directed mutagenesis to introduce deletions or stop codons to specify production of a desired fragment. Alternatively, particular fragments of the clostridial glutamate 2,3-aminomutase gene can be synthesized using the polymerase chain reaction. Standard techniques for functional analysis of proteins are described by, for example, Treuter et al., Molec. Gen. Genet. 240:113 (1993); Content et al., “Expression and preliminary deletion analysis of the 42 kDa 2-5A synthetase induced by human interferon,” in BIOLOGICAL INTERFERON SYSTEMS, PROCEEDINGS OF ISIR-TNO MEETING ON INTERFERON SYSTEMS, Cantell (ed.), pages 65-72 (Nijhoff 1987); Herschman, “The EGF Receptor,” in CONTROL OF ANIMAL CELL PROLIFERATION, Vol. 1, Boynton et al., (eds.) pages 169-199 (Academic Press 1985); Coumailleau et al., J. Biol. Chem. 270:29270 (1995); Fukunaga et al., .J Biol. Chem. 270:25291 (1995); Yamaguchi et al., Biochem. Pharmacol. 50:1295 (1995); and Meisel et al., Plant Molec. Biol. 30:1 (1996). Similar deletions may be carried out on SEQ ID NOs: 3, 5, 7, 9, 11, 13, 15, and 17. In some embodiments the functional fragment retains at least 50% or at least 60% of the amino acids of the native sequence. In others the functional fragment retains at least 70%, at least 80%, at least 90%, at least 95%, at least 98% or at least 99% of the amino acids of the native sequence.
The present invention also contemplates functional fragments of glutamate 2,3-aminomutases having the sequences disclosed herein that have conservative and non-conservative amino acid changes.
3. Expression of Cloned Glutamate 2,3-Aminomutase
To express the polypeptide encoded by a glutamate 2,3-aminomutase gene, the DNA sequence encoding the enzyme must be operably linked to regulatory sequences that control transcriptional expression in an expression vector and then, introduced into either a prokaryotic or eukaryotic host cell. In addition to transcriptional regulatory sequences, such as promoters and enhancers, expression vectors can include translational regulatory sequences and a marker gene which is suitable for selection of cells that carry the expression vector.
Suitable promoters for expression in a prokaryotic host can be repressible, constitutive, or inducible. Suitable promoters are well-known to those of skill in the art and include promoters capable of recognizing the T4, T3, Sp6 and T7 polymerases, the PR and PL promoters of bacteriophage lambda, the trp, recA, heat shock, lacUV5, tac, lpp-lacλpr, phoA, gal, trc and lacZ promoters of E. coli, the α-amylase and the σ28-specific promoters of B. subtilis, the promoters of the bacteriophages of Bacillus, Streptomyces promoters, the int promoter of bacteriophage lambda, the bla promoter of the β-lactamase gene of pBR322, and the CAT promoter of the chloramphenicol acetyl transferase gene. Prokaryotic promoters are reviewed by Glick, J. Ind. Microbiol. 1:277 (1987); Watson et al., MOLECULAR BIOLOGY OF THE GENE, 4th Ed., Benjamin Cummins (1987); Ausubel et al., supra, and Sambrook et al., supra.
Preferred prokaryotic hosts include E. coli, Clostridium, and Haemophilus. Suitable strains of E. coli include DH1, DH4α, DH5, DH5α, DH5αF′, DH5αMCR, DH10B, DH10B/p3, DH11S, C600, HB101, JM101, JM105, JM109, JM110, K38, RR1, Y1088, Y1089, CSH18, ER1451, BL21(DE3), BL21(DE3)plysS, BLR(DE3), BLR(DE3)plysS, and ER1647 (see, for example, Brown (Ed.), MOLECULAR BIOLOGY LABFAX, Academic Press (1991)). Suitable Clostridia include Clostridium subterminale SB4 (ATCC No. 29748) and Clostridium acetobutylicum (ATCC No. 824), while a suitable Haemophilus host is Haemophilus influenza (ATCC No. 33391).
An alternative host is Bacillus subtilus, including such strains as BR151, YB886, MI119, MI120, and B170. See, for example, Hardy, “Bacillus Cloning Methods,” in DNA CLONING: A PRACTICAL APPROACH, Glover (Ed.), IRL Press (1985).
Methods for expressing proteins in prokaryotic hosts are well-known to those of skill in the art. See, for example, Williams et al., “Expression of foreign proteins in E. coli using plasmid vectors and purification of specific polyclonal antibodies,” in DNA CLONING 2: EXPRESSION SYSTEMS, 2nd Edition, Glover et al. (eds.), pages 15-58 (Oxford University Press 1995). Also see, Ward et al., “Genetic Manipulation and Expression of Antibodies,” in MONOCLONAL ANTIBODIES: PRINCIPLES AND APPLICATIONS, pages 137-185 (Wiley-Liss, Inc. 1995); and Georgiou, “Expression of Proteins in Bacteria,” in PROTEIN ENGINEERING: PRINCIPLES AND PRACTICE, Cleland et al. (eds.), pages 101-127 (John Wiley & Sons, Inc. 1996).
An expression vector can be introduced into bacterial host cells using a variety of techniques including calcium chloride transformation, electroporation, and the like. See, for example, Ausubel et al. (eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, 3rd Edition, pages 1-1 to 1-24 (John Wiley & Sons, Inc. 1995).
To maximize recovery of functional glutamate 2,3-aminomutase from recombinant hosts, transformed cells should be cultured under anaerobic conditions or under air without oxygen enrichment. Methods for culturing recombinant clostridia are well-known to those of skill in the art. See, for example, Mermelstein et al., Ann. N.Y. Acad. Sci. 721:54 (1994); Walter et al., Ann. N.Y. Acad. Sci. 721:69. (1994). Additionally, anaerobic culturing of bacteria is well known in the art. See, for example, Smith and Neidhardt, J. Bacteriol. 154:336 (1983).
4. Isolation of Cloned Glutamate 2,3-Aminomutase and Production of Anti-Glutamate 2,3-Aminomutase Antibodies
A. Isolation of Recombinant Glutamate 2,3-Aminomutase
General methods for recovering protein produced by a bacterial system are provided by, for example, Grisshammer et al., “Purification of over-produced proteins from E. coli cells,” in DNA CLONING 2: EXPRESSION SYSTEMS, 2nd Edition, Glover et al. (eds.), pages 59-92 (Oxford University Press 1995); Georgiou, “Expression of Proteins in Bacteria,” in PROTEIN ENGINEERING: PRINCIPLES AND PRACTICE, Cleland et al. (eds.), pages 101-127 (Wiley-Liss, Inc. 1996).
Recombinant glutamate 2,3-aminomutases can be purified from bacteria using standard methods similar to those that have been used to purify Clostridium subterminale SB4 lysine 2,3-aminomutase. In general, several precautions can be taken to ensure high enzyme activity of the purified protein. As discussed above, for example, enzyme activity will generally be maximal when host cells are cultured under anaerobic conditions or conditions which restrict the presence of oxygen, Frey and Reed, Adv. Enzymol. 66:1 (1993), although rigid anaerobic conditions are not required in culturing host cells and culture conditions in air have been successful. Oxygen should also be excluded during all purification steps. Purification under anaerobic conditions protects metal cofactors from being irreversibly degraded and allows maximal activity to be attained upon activation with S-adenosylmethionine. However, variants of glutamate 2,3-aminomutase may be stable in air and even function under aerobic conditions.
Lysine 2,3-aminomutase activity can be determined as detailed in the examples.
B. Preparation of Anti-Glutamate 2,3-Aminomutase Antibodies and Fragments Thereof
Antibodies to glutamate 2,3-aminomutase can be obtained, for example, using the product of an expression vector as an antigen. Polyclonal antibodies to recombinant enzyme can be prepared using methods well-known to those of skill in the art. See, for example, Green et al., “Production of Polyclonal Antisera,” in IMMUNOCHEMICAL PROTOCOLS (Manson, ed.), pages 1-5 (Humana Press 1992). Also see, Williams et al., “Expression of foreign proteins in E. coli using plasmid vectors and purification of specific polyclonal antibodies,” in DNA CLONING 2: EXPRESSION SYSTEMS, 2nd Edition, Glover et al. (eds.), pages 15-58 (Oxford University Press 1995).
Alternatively, an anti-glutamate 2,3-aminomutase antibody can be derived from a rodent monoclonal antibody (MAb). Rodent monoclonal antibodies to specific antigens may be obtained by methods known to those skilled in the art. See, for example, Kohler et al., Nature 256:495 (1975), and Coligan et al (eds.), CURRENT PROTOCOLS IN IMMUNOLOGY, VOL. 1, pages 2.5.1-2.6.7 (John Wiley & Sons 1991) [“Coligan”]. Also see, Picksley et al., “Production of monoclonal antibodies against proteins expressed in E. coli,” in DNA CLONING 2: EXPRESSION SYSTEMS, 2nd Edition, Glover et al. (eds.), pages 93-122 (Oxford University Press 1995).
Briefly, monoclonal antibodies (MAbs) can be obtained by injecting mice with a composition comprising an antigen, verifying the presence of antibody production by removing a serum sample, removing the spleen to obtain B-lymphocytes, fusing the B-lymphocytes with myeloma cells to produce hybridomas, cloning the hybridomas, selecting positive clones which produce antibodies to the antigen, culturing the clones that produce antibodies to the antigen, and isolating the antibodies from the hybridoma cultures.
MAbs can be isolated and purified from hybridoma cultures by a variety of well-established techniques. Such isolation techniques include affinity chromatography with Protein-A Sepharose, size-exclusion chromatography, and ion-exchange chromatography. See, for example, Coligan at pages 2.7.1-2.7.12 and pages 2.9.1-2.9.3. Also, see Baines et al., “Purification of Immunoglobulin G (IgG),” in METHODS IN MOLECULAR BIOLOGY, VOL. 10, pages 79-104 (The Humana Press, Inc. 1992).
For particular uses, it may be desirable to prepare fragments of anti-glutamate 2,3-aminomutase antibodies. Such antibody fragments can be obtained, for example, by proteolytic hydrolysis of the antibody. Antibody fragments can be obtained by pepsin or papain digestion of whole antibodies by conventional methods. As an illustration, antibody fragments can be produced by enzymatic cleavage of antibodies with pepsin to provide a 5S fragment denoted F(ab′)2. This fragment can be further cleaved using a thiol reducing agent to produce 3.5S Fab′ monovalent fragments. Optionally, the cleavage reaction can be performed using a blocking group for the sulfhydryl groups that result from cleavage of disulfide linkages. As an alternative, an enzymatic cleavage using pepsin produces two monovalent Fab fragments and an Fc fragment directly. These methods are described, for example, by Goldenberg, U.S. Pat. Nos. 4,036,945 and 4,331,647 and references contained therein. Also, see Nisonoff et al., Arch Biochem. Biophys. 89:230 (1960); Porter, Biochem. J. 73:119 (1959), Edelman et al., in METHODS IN ENZYMOLOGY VOL. 1, page 422 (Academic Press 1967), and Coligan at pages 2.8.1-2.8.10 and 2.10.-2.10.4.
Other methods of cleaving antibodies, such as separation of heavy chains to form monovalent light-heavy chain fragments, further cleavage of fragments, or other enzymatic, chemical or genetic techniques may also be used, so long as the fragments bind to the antigen that is recognized by the intact antibody.
For example, Fv fragments comprise an association of VH and VL chains. This association can be noncovalent, as described in Inbar et al., Proc. Nat'l Acad. Sci. USA 69:2659 (1972). Alternatively, the variable chains can be linked by an intermolecular disulfide bond or cross-linked by chemicals such as glutaraldehyde. See, for example, Sandhu, Crit. Rev. Biotech. 12:437 (1992).
Preferably, the Fv fragments comprise VH and VL chains which are connected by a peptide linker. These single-chain antigen binding proteins (sFv) are prepared by constructing a structural gene comprising DNA sequences encoding the VH and VL domains which are connected by an oligonucleotide. The structural gene is inserted into an expression vector which is subsequently introduced into a host cell, such as E. coli. The recombinant host cells synthesize a single polypeptide chain with a linker peptide bridging the two V domains. Methods for producing sFvs are described, for example, by Whitlow et al., Methods: A Companion to Methods in Enzymology 2:97 (1991). Also see Bird et al., Science 242:423 (1988), Ladner et al., U.S. Pat. No. 4,946,778, Pack et al., Bio/Technology 11:1271 (1993), and Sandhu, supra.
Another form of an antibody fragment is a peptide coding for a single complementarity-determining region (CDR). CDR peptides (“minimal recognition units”) can be obtained by constructing genes encoding the CDR of an antibody of interest. Such genes are prepared, for example, by using the polymerase chain reaction to synthesize the variable region from RNA of antibody-producing cells. See, for example, Larrick et al., Methods: A Companion to Methods in Enzymology 2:106 (1991); Courtenay-Luck, “Genetic Manipulation of Monoclonal Antibodies,” in MONOCLONAL ANTIBODIES: PRODUCTION, ENGINEERING AND CLINICAL APPLICATION, Ritter et al. (eds.), pages 166-179 (Cambridge University Press 1995); and Ward et al., “Genetic Manipulation and Expression of Antibodies,” in MONOCLONAL ANTIBODIES: PRINCIPLES AND APPLICATIONS, Birch et al., (eds.), pages 137-185 (Wiley-Liss, Inc. 1995).
5. Isolation of Additional Glutamate 2,3-Aminomutase Genes
The nucleotide sequences of the clostridial glutamate 2,3-aminomutase gene and antibodies to the enzyme provide a means to isolate additional glutamate 2,3-aminomutase genes. Such genes can encode enzymes from various organisms, including but not limited to Thermoanaerobacter tengcongensis, Desulfitobacterium hafniense DCB-2, Moorella thermoacetica, Syntrophomonas wolfei (str. Goettingen), Alkaliphilus metalliredigenes QYMF, Caldicellulosiruptor saccharolyticus DSM 8903, Desulfotomaculum reducens MI-1, and Carboxydothermus hydrogenoformans Z-2901.
For example, the amino acid sequence of the clostridial glutamate 2,3-aminomutase was used to identify related enzymes in various bacteria. Sequence analyses revealed a sequence identity of about 50-60% between the amino acid sequence of the clostridial enzyme and the gene products of SEQ ID NOs: 3, 5, 7, 9, 11, 13, 15, and 17.
The nucleotide and amino acid sequences (SEQ ID NOs:3 and 4) of the Thermoanaerobacter tengcongensis polypeptide are:









1
atgagcagca cgggttcact cacagtggag gaaaaaagga aaatagcact ccaaagagcg



 


61
gaagagttaa aaaagaagat agagccatac ttgagagcat ctgaaaaaat agagacgggc


 


121
tttaagttat cagaaaaatt tagagaaaac aaggagaaaa ttaaaaactt atttggagca


 


181
acagaagagg aatggaatga ttggcgatgg cagataagaa atcgtataag tgatgttgaa


 


241
actctcaaaa agattgtaaa cctttctgag gaggaaattg aaaacataaa gagggtaagt


 


301
actcgctaca gatgggcaat ttcaccatac tatgcttctt taatggatcc ggataatcct


 


361
ttctgtccta ttcgaatgag agctatccca agtattaagg aacttacaga taaatatgga


 


421
gttccagacc cgatggcaga agaatatact tctcccgctc ctttaataac acgtcgttat


 


481
cctgatcgac tgattataaa cgtaacaaat caatgtggca tgttctgtag acattgtcag


 


541
aggagacgca acataggaga agtggattat cctgcaaaac acgaagacat agaagcggca


 


601
ttagaatata ttcgaaataa tccagaaatt agagatgtgc tgataacagg gggagaccct


 


661
ctcactcttg aggatgaaaa aatcgactgg attttgtcag aattagataa aattccacat


 


721
gtagaaataa aacgaatagg gacggctgcc ccagtgactt ttccacagag aattaccgat


 


781
gaattatgca agattttaac aaaacatctg cctctgtaca ttaataccca gtttaatcat


 


841
ccaaaagaag ttactgaaga agcaaaagag gcttgcttta aattagcaag agctggggtg


 


901
gcattaggaa atcaagcagt gcttttaaaa gggataaata atgaccctca tgttatgaaa


 


961
aagttaaacc acgaattact tagaattatg gttaaacctt actacatttt ccatgcgaaa


 


1021
tctgttcaag ggactaccca ttttgttact acagttcaag atggattaga gattatggaa


 


1081
caacttcgcg gttatacttc agggcttgcc attccgtggt atataatcaa tgcacctgaa


 


1141
gggcatggga agactcctat tgtgcctcag tatctcctta tggttgggaa agaatatgtt


 


1201
cttataagaa attgggaagg aaaagttttt gaatatccga atggcttccc tgacgattaa


 


1
msstgsltve ekrkialqra eelkkkiepy lrasekietg fklsekfren kekiknlfga


 


61
teeewndwrw qirnrisdve tlkkivnlse eeienikrvs tryrwaispy yaslmdpdnp


 


121
fcpirmraip sikeltdkyg vpdpmaeeyt spaplitrry pdrliinvtn qcgmfcrhcq


 


181
rrrnigevdy pakhedieaa leyirnnpei rdvlitggdp ltledekidw ilseldkiph


 


241
veikrigtaa pvtfpqritd elckiltkhl plyintqfnh pkevteeake acfklaragv


 


301
algnqavllk ginndphvmk klnhellrim vkpyyifhak svqgtthfvt tvqdgleime


 


361
qlrgytsgla ipwyiinape ghgktpivpq yllmvgkeyv lirnwegkvf eypngfpdd






The nucleotide and amino acid sequences (SEQ ID NOs:5 and 6) of the Desulfitobacterium hafniense DCB-2 polypeptide are:









1
atggcaatag aatttctacc ccctaaccca agacaggctt cacaagcaag agctttggaa



 


61
ttaaaacaaa aagttcaatc ctacaacaaa cgcaaagaaa cgattccctg cggccttgcc


 


121
ttaagcgaag aatttaatga aaaccgagac tttatactgg atcagttaga tgctgacctg


 


181
gagcattggc aggattggaa gtggcagctt aaaaaccgta ttcaggatgc tgaaaacttg


 


241
agcaccctgc ttcccctgac ccccaagcaa agacatgaaa tcaacgaggt gggcaaggct


 


301
taccgttggg ctgtttcacc ctattattta agcctgatcg ataaagatga tcctcaggat


 


361
cccatccgtc tgcaaagtct cccctctgtg gaagagatcc tcgacgattc cggagaagca


 


421
gatcccatgg gagaagagta tacatcccct gcgccttgca tcacacgtcg ttacccggat


 


481
cgcctcatta ttaatgtaac caatttgtgt gctatgtatt gcaggcactg ccaacgccga


 


541
cggaatatcg gggaaattga cctccatgaa acccgtgcta acctggaggc cgccctggat


 


601
tatatacgct ccaatccaga gattcgggat gtgctagtca ccggtggcga tgctctcctt


 


661
ctcagcgatc aaatgctgga ctggttattg ggagaattgc atgaaattaa gcatgtggag


 


721
atcaaacgta tcggcacccg ggttcccgtc actctgccca tgcgcattac cgatgagctc


 


781
tgcgctattc ttgaaaaata tccacccctt tatatcaata ctcaattcaa tcatccccaa


 


841
gaggtgaccg aggagaccaa gaaagctgct gatcgcttaa tcaaagcggg agtcatctta


 


901
ggcaaccaag cagttcttct taaaggaatc aatgaccaac cagagattat gaaacgcctt


 


961
aaccaagaac ttcttaaaat tcgcgttcgc ccctactata ttttccatgc caaaaatgtt


 


1021
aaaggcacga gccactttat tccccgcatt caggacgggt taaggattat ggaaaacttg


 


1081
cgcggctaca cctctggttt ggccattccg acctatatta ttaatgcccc gggaggcggt


 


1141
ggcaaaaccc ccatcttacc acagtacctt atttccctaa acgatgaaga agcagtcatc


 


1201
agaacctggg aaggtaaggt tgtgcattat cctaatcatt aa


 


1
maieflppnp rqasqarale lkqkvqsynk rketipcgla lseefnenrd fildqldadl


 


61
ehwqdwkwql knriqdaenl stllpltpkq rheinevgka yrwavspyyl slidkddpqd


 


121
pirlqslpsv eeilddsgea dpmgeeytsp apcitrrypd rliinvtnlc amycrhcqrr


 


181
rnigeidlhe tranleaald yirsnpeird vlvtggdall lsdqmldwll gelheikhve


 


241
ikrigtrvpv tlpmritdel cailekyppl yintqfnhpq evteetkkaa drlikagvil


 


301
gnqavllkgi ndqpeimkrl nqellkirvr pyyifhaknv kgtshfipri qdglrimenl


 


361
rgytsglaip tyiinapggg gktpilpqyl islndeeavi rtwegkvvhy pnh






The nucleotide and amino acid sequences (SEQ ID NOs:7 and 8) of the Moorella thermoacetica polypeptide (ATCC 39073) are:









1
atgggaaggg aagctaaaag ggaaattgct cttgaccggg cagccgaatt gaaagccagg



 


61
attgtcgatt acctggaaga aagggagaag atcgccagcg gcctggaggc ggcagccgag


 


121
atcgaagcca gcaagcaacg tatcctggct tactttggcg ccggggaagc cgagtggcag


 


181
gactggcgct ggcagttgac ccaccgtatc acctcggtgg caaccctggc ggaactgatt


 


241
cccctgacag aagctgaaaa ggaagccata ctaaaggtag aacgtaccta tcgctgggcg


 


301
gtttctcctt actacctgag cctgatggga ccggaacctg attgccccat ccggcgccag


 


361
gctctgccca gtgccgccga actggaggat aaccatggcg tcctggaccc catggatgaa


 


421
gagttgacct ccccggcgcc ggctattacc cgccgttatc cggatcgttt gattatcaac


 


481
gtaaccaacc agtgtgctat gtactgtcgt cactgccagc ggcgtcgcaa tatcggtgaa


 


541
gtcgaccgca gtcgcagccg ccgggaactg gagcaggccc tccagtatat ccgccagaat


 


601
gaagagatcc gcgatgtcct gatcactggc ggtgacgccc tgatgctcag cgatgccatg


 


661
atcgactggt tgttgacgga actcgataat atcccccacg tagaaattaa gcgcctgggc


 


721
accagggtgc cggtcactat gccccagcgg attaccccgg agctgtgccg ggttctggcc


 


781
aagcacccgc ccatctatct caatacccag ttcaaccacc cccgggaggt taccgcggcc


 


841
gccaaagaag cctgcgatcg cctggtccag gccggggtgg tcctcggcaa ccaggcggtt


 


901
ttgttaaagg gcgtcaacaa ccatcccttt gtgatgcgta aattaaacca ggaactcttg


 


961
aaaataaggg tacggcccta ctatatcttc cacgccaagc cggtgaaggg gaccacccac


 


1021
tttattacct ccattgagga gggcgtggag atcatggata agctccgggg ctatacctcc


 


1081
ggcctggccg tgcctaccta tataatcaat gccccccacg gtctgggcaa gacccccatc


 


1141
ttgccacagt atgtaatcgc ccgtaatgat caccaggtga tcctgaggac ctgggagaag


 


1201
cggattattt tttactccaa cctgggacgc cagaaggaac aggcctaa


 


1
mgreakreia ldraaelkar ivdyleerek iasgleaaae ieaskqrila yfgageaewq


 


61
dwrwqlthri tsvatlaeli plteaekeai lkvertyrwa vspyylslmg pepdcpirrq


 


121
alpsaaeled nhgvldpmde eltspapait rrypdrliin vtnqcamycr hcqrrrnige


 


181
vdrsrsrrel eqalqyirqn eeirdvlitg gdalmlsdam idwllteldn iphveikrlg


 


241
trvpvtmpqr itpelcrvla khppiylntq fnhprevtaa akeacdrlvq agvvlgnqav


 


301
llkgvnnhpf vmrklnqell kirvrpyyif hakpvkgtth fitsieegve imdklrgyts


 


361
glavptyiin aphglgktpi lpqyviarnd hqvilrtwek riifysnlgr qkeqa






The nucleotide and amino acid sequences (SEQ ID NOs:9 and 10) of the Syntrophomonas wolfei (str. Goettingen) polypeptide are:









1
ttgttgttaa gagaagattt gataaacgaa gaaattcggg agatgaaacg cgaagtatct



 


61
ttacgtaggg cggatgagct caaacaggaa atttctgact atcttgatat cgaatctact


 


121
attgaaacgg gaatgcgatt acatgaacgt aatctgcaca ataaggaaca tatcctgaaa


 


181
tactttgagg tcagcgagaa tgattgggat aattgggcct ggcaaatgag gaatcgcatc


 


241
aatgatggaa atgtgctggc ttccattctg ggcttaaatg aattcgaagt gcagacaatt


 


301
aaaagggttt ccaaaaaagt ccgctgggct atttctccct attatcttag tttaatcgat


 


361
tttgaaaatt acgcggcgtc acccatttac aagcagtctg tccccagtct gcatgaaata


 


421
atagaatgta agggtgagga tgaccccatg ggagaagaga tgagtagtcc tgctccccgt


 


481
attacacgtc gttatcccga ccgacttata atcaatgtta ccaatcaatg tgctatgtac


 


541
tgccgccatt gtcagcgccg tagaaatttc ggtgaaactg ataaccatgc cgcccataaa


 


601
gacctggaag ctgccctgca gtacattaaa aacaattctg aaatacggga tgttcttatt


 


661
accggtgggg atgctctaat gcttagcgat cgtacacttg actggttact gggagaactc


 


721
gatgccattt cacatgttga aattaagcgt attggtacca ggacaccggt aacacttcca


 


781
caaagaataa ccgccaatct ttgtgcagtg ctaaaaaggc atacacccat atatattaat


 


841
acccaattta attcaccgct ggaagttact ccggaagcca aacaggcctg tgatcggctt


 


901
attgaagcag gagtagtatt gggtaaccag gctgttctgc taaagggaat caacgataat


 


961
gtccatgtta tgaaaaaact taaccaggag ttgctgaaaa tccgggttcg cccctactat


 


1021
ttattccagg ccaaagaggt aaaaggaact acccatttta ttagcccggt caataccggc


 


1081
ctggatatta tgaagcattt acggggctat acttctggcc tggccatccc cacttatgtt


 


1141
atcaacgcac caggaggtta cggtaaaact ccagttaacc cggaatatgt actggatatt


 


1201
aatgaaaatg aagttataat tagtacctgg cagggtaaaa cttttaacta tccccatcgt


 


1261
aacaattag


 


1
mllredline eiremkrevs lrradelkqe isdyldiest ietgmrlher nlhnkehilk


 


61
yfevsendwd nwawqmrnri ndgnvlasil glnefevqti krvskkvrwa ispyylslid


 


121
fenyaaspiy kqsvpslhei ieckgeddpm geemsspapr itrrypdrli invtnqcamy


 


181
crhcqrrrnf getdnhaahk dleaalqyik nnseirdvli tggdalmlsd rtldwllgel


 


241
daishveikr igtrtpvtlp qritanlcav lkrhtpiyin tqfnsplevt peakqacdrl


 


301
ieagvvlgnq avllkgindn vhvmkklnqe llkirvrpyy lfqakevkgt thfispvntg


 


361
ldimkhlrgy tsglaiptyv inapggygkt pvnpeyvldi neneviistw qgktfnyphr


 


421
nn






The nucleotide and amino acid sequences (SEQ ID NOs:11 and 12) of the Alkaliphilus metalliredigenes QYMF polypeptide are:









1
gtgaatcata ccgatacaac aaacagtcgt caaatttcaa tcgatcgagc taagcatcta



 


61
aaattaacca tacaggatta cttagagata aaagacctca ttcccaaagg attatctcgt


 


121
caagtggaaa tcgaagcgaa aaagcaaaaa atcctatccc attttggtgc tactgaagat


 


181
aattggaatg attggcaatg gcaattaagc aatcgaatat ctgatgttga taccttaaca


 


241
aaaataatta agttagatga taaagaaatt gaagatataa aaaaagtagg acaagaattt


 


301
agatggtcag tatcacctta ttacaccact ctaattgatg acaataataa gtattgtcca


 


361
attaaactta tggctatacc ccatggctac gaaattgcca ataccaaagg agatacagat


 


421
ccaatggcag aagagttcac gaatcctgct ggatcaatta cacgccgcta tcccgatcga


 


481
ttaattatta atgtaaccaa tgaatgtgca atgtactgta gacattgtca acgaagaaga


 


541
aacataggaa ctaatgatct ccatacatcc cgagaggttt tacaagaatc gattgattat


 


601
attcgtgata atcctgaaat ccgggatgta ttaattactg gtggcgacgc attgaccctt


 


661
tctaatagta tgcttgattg gttattggga gaattacatg caattccatc cgtagactat


 


721
attagattgg gctctcgtac attggtcact atgccccaaa gaatcacaga taagttgatc


 


781
aatattctta aaaagtaccc acctattttt attaataccc actttaatca ccccatggag


 


841
attacagaag agtccaaggc agcatgtgat agattatcca atgcgggcat tccattaggt


 


901
aaccaagcag ttctccttaa tggcattaat aataataagt ttgtcatgag attacttaat


 


961
cacgaactat taaaatgtcg tgttcgtcct tactatatat tccatgcgaa acatgttatt


 


1021
ggcactagtc attttaacac gtctgttgat gatggcatcg aaatcatgga gtacttaaga


 


1081
ggctacacat ctggtatggc aattccaacc tatatcatta atgcccctgg cggaaaagga


 


1141
aaaactccta tacttccaca atatctaatt tctagaggct ctcattctat taaaattaga


 


1201
acttgggatg gtgaagtgat tgattatcca aatcacccta caattccaat tgaagaaaca


 


1261
ctaaagtaa


 


1
mnhtdttnsr qisidrakhl kltiqdylei kdlipkglsr qveieakkqk ilshfgated


 


61
nwndwqwqls nrisdvdtlt kiiklddkei edikkvgqef rwsvspyytt liddnnkycp


 


121
iklmaiphgy eiantkgdtd pmaeeftnpa gsitrrypdr liinvtneca mycrhcqrrr


 


181
nigtndlhts revlqesidy irdnpeirdv litggdaltl snsmldwllg elhaipsvdy


 


241
irlgsrtlvt mpqritdkli nilkkyppif inthfnhpme iteeskaacd rlsnagiplg


 


301
nqavllngin nnkfvmrlln hellkcrvrp yyifhakhvi gtshfntsvd dgieimeylr


 


361
gytsgmaipt yiinapggkg ktpilpqyli srgshsikir twdgevidyp nhptipieet


 


421
lk






The nucleotide and amino acid sequences (SEQ ID NOs:13 and 14) of the Caldicellulosiruptor saccharolyticus DSM 8903 polypeptide are:









1
atggaaaagt tagatgttat taacaacaga gaaagattcg aaaagttaaa agaagctatt



 


61
aaagactact tagaggtcaa agacacaatc aaaactggca tagatgatga ggaaaagatt


 


121
gaatatcaaa aaagaaagat tctttcctac tttggtgcaa gcgaaaagga ctgggaaaat


 


181
tataagtggc agctgaaaaa tagaattacc tcggccaaaa tattaaaaga acttttaaac


 


241
cttgatgaaa aagaagcaca gcaaatagaa gaagtagcca aaatttaccg ttttgcaatc


 


301
tcaccttact atctctcttt gattgaccca agtgatcctc actgtccaat aaagaagcaa


 


361
tcagtcccaa gctcatttga gcttatagaa aaaggtgagc ttgacccaat ggacgaagag


 


421
catacatccc ctacaaagat tattacacag cgctatcctg acaggctcat aataaaagtt


 


481
acaaacatat gtgggatgtt ttgcagattc tgtcaaagaa gaagacttat tggtgagact


 


541
gacacacacg catcgctgga tgatattacg gatgcaattg aatatgtagc acaaaatcca


 


601
aatatcagag atgttctcat cacaggtggc gatgccctga tgctctctga tgagattttg


 


661
gagtggattt taaggtcgct aaggcaaata cctcatgttg agataatcag aattggaaca


 


721
agagcacctg tgacgttgcc acaaaggatt acaaaagagc ttgttgatat gctaaaaaag


 


781
tatcacccta tttatgtaaa cacccacttt aaccacccac gtgagataac aaaagaatca


 


841
aaaagagctt gtgagatgct tgcagatggc ggcattccgc ttggcaacca gatggttttg


 


901
ttaaatgggg tcaacaacga caaatacgtt gtgagaaggc tcaatcaaca gcttttaaaa


 


961
atccgagtaa agccatatta tatctttcat ccaaaaaggg taaaaggtac atcgcacttt


 


1021
tgggtgacaa ttgaagaggg tatggagatt attgaaagcc tcagaggaag aacctcaggc


 


1081
atggcaattc ccacatacat cataaatgct ccaaaaggca aaggaaaaac accaattatg


 


1141
ccaaattatc ttctttactt tggtaaaggc aaggtagttt ttagaaactg ggaaggtgag


 


1201
gtttttgagg ttgagaatgg gtaa


 


1
mekldvinnr erfeklkeai kdylevkdti ktgiddeeki eyqkrkilsy fgasekdwen


 


61
ykwqlknrit sakilkelln ldekeaqqie evakiyrfai spyylslidp sdphcpikkq


 


121
svpssfelie kgeldpmdee htsptkiitq rypdrliikv tnicgmfcrf cqrrrliget


 


181
dthaslddit daieyvaqnp nirdvlitgg dalmlsdeil ewilrslrqi phveiirigt


 


241
rapvtlpqri tkelvdmlkk yhpiyvnthf nhpreitkes kracemladg giplgnqmvl


 


301
lngvnndkyv vrrlnqqllk irvkpyyifh pkrvkgtshf wvtieegmei ieslrgrtsg


 


361
maiptyiina pkgkgktpim pnyllyfgkg kvvfrnwege vfeveng






The nucleotide and amino acid sequences (SEQ ID NOs:15 and 16) of the Desulfotomaculum reducens MI-1 polypeptide are:









1
atgtctgttc atttaaagca agaagagttc cggctaagac aagaaaaacg aaaaattgct



 


61
ctaaaaaggg caaaggagtt aaaagctcgt atcactgatt atcttgagaa caaggatcaa


 


121
attaaaaatg gttttgaggt gcaagaacag tacaatcggg caaaacaaac tttactaaat


 


181
ttttttaatg cagataatga gcagtgggaa aattggcact ggcaaatggc aaatcgtatt


 


241
aaagatgtta aagtaataag ccagttaata gatctttccc cggctgaaaa agaggccatt


 


301
gaaaaagtgg ggcgccagta ccgttgggcg gtatcaccct attatatggc tctggcaatg


 


361
gtaagtggtt ccggtggccc tgtttggtta caggctatac cctgtataga agaagtaaag


 


421
gatcgttacg gtgtagaaga tcccatggga gaagaataca cttcacctgt ggaaggggta


 


481
acaagacgct acccagaccg tttgattatt aatgtaacaa atcaatgtgc tatgtattgt


 


541
cgccactgcc aacgacgtag aaatatcggg gaaattgatg ttcacaaatc acgtaaggtt


 


601
ttagaaggtg ccctgcagta tattagggaa aataaggaga taagggatgt attaataact


 


661
ggtggggatg ctttattgtt atcagaccga caaattgaat ggctgctgac tgaattagat


 


721
aatattcctc atgtggaaat taagagattg ggaacacgta ctccggttac tatgccccaa


 


781
agaattacac cggagttatg taagatttta gagaaccatc caccgattta tatcaacacc


 


841
cagtttaatc atcctttgga agttacacca gaagcaaaaa aggcctgtga tatgttggta


 


901
aaagcaggtg ttgttctagg taatcaagct gtactactaa aaaatataaa taaccaaccg


 


961
gatgttatga agaggttaaa ccaaagtctc ctaaccattc gagttcgccc ttactatata


 


1021
ttccatgcta aagccgtaaa aggaaccaga cattttatca ctggagtaga tgacggcatt


 


1081
gctattatgg aacaattaag aggctatacc tcaggacttg ctgttcctac gtatatcatt


 


1141
aatgccccca atggttatgg taaaactcct gtacttcccc agtatattat tgagaataaa


 


1201
aatgatcaag ttacccttag aacctgggaa aagaggatta ttccctataa tattagcgga


 


1261
aaacattag


 


1
msvhlkqeef rlrqekrkia lkrakelkar itdylenkdq ikngfevqeq ynrakqtlln


 


61
ffnadneqwe nwhwqmanri kdvkvisqli dlspaekeai ekvgrqyrwa vspyymalam


 


121
vsgsggpvwl qaipcieevk drygvedpmg eeytspvegv trrypdrlii nvtnqcamyc


 


181
rhcqrrrnig eidvhksrkv legalgyire nkeirdvlit ggdalllsdr qiewllteld


 


241
niphveikrl gtrtpvtmpq ritpelckil enhppiyint qfnhplevtp eakkacdmlv


 


301
kagvvlgnqa vllkninnqp dvmkrlnqsl ltirvrpyyi fhakavkgtr hfitgvddgi


 


361
aimeqlrgyt sglavptyii napngygktp vlpqyiienk ndqvtlrtwe kriipynisg


 


421
kh






The nucleotide and amino acid sequences (SEQ ID NOs: 17 and 18) of the Carboxydothermus hydrogenoformans Z-2901 polypeptide are:









1
atgaatagag caagaatttc gcagaaagat gaaggattga aacggcaaag agagcttacc



 


61
cggattggtc gtagtaggtt aagggaaaga aaaaaggttt tatcgggatt tgaagcctgg


 


121
gaaaaaattt taaaacaaaa agagaagatt ttaaaggtat taggtggaac ggaagaagac


 


181
tggcaggatt ggcgctggca gttgaaaaat cggataacaa cgccggaagt tttacgaaaa


 


241
attttgcctt taagcgacca ggtcctctgg gaacttgagg aggtcagtaa ggtttatcgc


 


301
tttgccattt cgccttatta tttgagcttg attgatcccg atgatcccga ttgcggtatt


 


361
aagaaacagt cgattccttc cattttggag gttttagatg ataccggtga acttgacccg


 


421
atgaatgaag cggggacttc gccggtggcg gcggttaccc ggcgttatcc ggaccgctta


 


481
ataattaatg ttaccaatat gtgcgggatg tattgccgtc actgtcagcg gcgaagaaat


 


541
atcggtgagg ttgaccggaa aactcccagg gagcagataa aagaagccct tctttacatc


 


601
cgggagcata aagaaatccg ggatgtttta attaccggtg gggatgcact tctcttatcc


 


661
gatttggagc tggactggat attaaaagaa ctttccgaaa taccccatgt agaaattaaa


 


721
aggattggta cccgggtacc ggtgaccttg ccgcaaaggg ttaccgataa tctggttaaa


 


781
atattaaaaa aatacccgcc gatatatatc aatacccagt ttaaccatcc ccgggaggta


 


841
actcctgagg ccaaaaaagc ggtggataaa ttaattgaag cgggggtggt attaggtaat


 


901
caggcggtgc ttttaaaagg ggtaaatgac aatcccgtaa ttatggagaa attgaaccat


 


961
gagcttttaa aaattcgggt acggccgtac tatatcttcc aggcgaagag ggtacgggga


 


1021
acgatgcatt ttgttcccaa gattgaagac ggattaagga taatggaaag cttgcggggc


 


1081
tatacctcgg gactggcagt gccgtattat atcgtcaacg cgcctggagg ctttgggaaa


 


1141
attccgcttt taccccagta tttaattgaa ctctcggaag aagaagcagt tttacgcaac


 


1201
tgggaaggcc ggataattag atatccgaat aattaa


 


1
mnrarisqkd eglkrqrelt rigrsrlrer kkvlsgfeaw ekilkqkeki lkvlggteed


 


61
wqdwrwqlkn rittpevlrk ilplsdqvlw eleevskvyr faispyylsl idpddpdcgi


 


121
kkqsipsile vlddtgeldp mneagtspva avtrrypdrl iinvtnmcgm ycrhcqrrrn


 


181
igevdrktpr eqikeallyi rehkeirdvl itggdallls dleldwilke lseiphveik


 


241
rigtrvpvtl pqrvtdnlvk ilkkyppiyi ntqfnhprev tpeakkavdk lieagvvlgn


 


301
qavllkgvnd npvimeklnh ellkirvrpy yifqakrvrg tmhfvpkied glrimeslrg


 


361
ytsglavpyy ivnapggfgk ipllpqylie lseeeavlrn wegriirypn n






Thus, the present invention contemplates the use of clostridial enzyme sequences to identify glutamate 2,3-aminomutase from other species. The present invention further contemplates variants of such glutamate 2,3-aminomutases, and the use of such enzymes to preparre β-glutamate.
In one screening approach, polynucleotide molecules having nucleotide sequences disclosed herein can be used to screen genomic or cDNA libraries. Screening can be performed with clostridial glutamate 2,3-aminomutase polynucleotides that are either DNA or RNA molecules, using standard techniques. See, for example, Ausubel et al. (eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, pages 6-1 to 6-11 (John Wiley & Sons, Inc. 1995). Genomic and cDNA libraries can be prepared using well-known methods. See, for example, Ausubel et al. (eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, pages 5-1 to 5-6 (John Wiley & Sons, Inc. 1995).
Additional glutamate 2,3-aminomutase genes can also be obtained using the polymerase chain reaction (PCR) with oligonucleotide primers having nucleotide sequences that are based upon the nucleotide sequences of the glutamate 2,3-aminomutase genes of Clostridium, Thermoanaerobacter, Desulfitobacterium, Moorella, Syntrophomonas, as described herein. General methods for screening libraries with PCR are provided by, for example, Yu et al., “Use of the Polymerase Chain Reaction to Screen Phage Libraries,” in METHODS IN MOLECULAR BIOLOGY, Vol. 15: PCR PROTOCOLS: CURRENT METHODS AND APPLICATIONS, White (ed.), pages 211-215 (Humana Press, Inc. 1993). Moreover, techniques for using PCR to isolate related genes are described by, for example, Preston, “Use of Degenerate Oligonucleotide Primers and the Polymerase Chain Reaction to Clone Gene Family Members,” in METHODS IN MOLECULAR BIOLOGY, Vol. 15: PCR PROTOCOLS: CURRENT METHODS AND APPLICATIONS, White (ed.), pages 317-337 (Humana Press, Inc. 1993).
Anti-glutamate 2,3-aminomutase antibodies can also be used to isolate DNA sequences that encode enzymes from cDNA libraries. For example, the antibodies can be used to screen λgt11 expression libraries, or the antibodies can be used for immunoscreening following hybrid selection and translation. See, for example, Ausubel et al. (eds.), SHORT PROTOCOLS IN MOLECULAR BIOLOGY, 3rd Edition, pages 6-12 to 6-16 (John Wiley & Sons, Inc. 1995); and Margolis et al., “Screening λ expression libraries with antibody and protein probes,” in DNA CLONING 2: EXPRESSION SYSTEMS, 2nd Edition, Glover et al. (eds.), pages 1-14 (Oxford University Press 1995).
Furthermore, the identification of glutamate 2,3-aminomutases is simplified by using known conserved regions in the DNA sequences of genes encoding the enzymes. By matching the conserved sequences with potential glutamate 2,3-aminomutases, positive identification can be achieved. These conserved sequences include CXXXCRXCXR (SEQ ID NO: 19)—the iron sulfur center residues; S(T)GGD(E) (SEQ ID NO: 20)—S-adenosyl-L-methionine binding domain, and GXXXPXXXXXXXXXXXK (SEQ ID NO: 21)—pyridoxal 5′-phosphate binding domain. (The standard one-letter codes are used to represent the various amino acids of the conserved sequences; X may be any of the 20 naturally occurring amino acids.) In addition, conserved active site residues (in glutamate 2,3-aminomutase from Cl. difficile) important for binding to glutamate include 325 PXYXXXXKXXXG 336 (SEQ ID NO: 22) and 364 PXXXXNXXXXXXK 376 (SEQ ID NO: 23). In contrast, the corresponding sequences of lysine 2,3-aminomutase from C. subterminale SB4 are respectively: 286 PXYXXXXDXXXG 297 (SEQ ID NO: 24)and 325 PXXXXDXXXXXXK 337 (SEQ ID NO: 25). As glutamate 2,3-aminomutase does not catalyze the conversion of L-lysine to β-lysine, it is believed that the change of K for D and N for D in the active site of glutamate 2,3-aminomutase is responsible in large part for the change in substrate specificity compared to lysine 2,3-aminomutase. In variants of glutamate 2,3-aminomutase as described above include each of these conserved sequence motifs.
6. The Use of glutamate 2,3-Aminomutase to Produce β-glutamic acid
A. Production of β-Glutamate Using Purified Enzyme
Recombinant glutamate 2,3-aminomutase can be purified from host cells as described above, and used to prepare β-glutamic acid. β-glutamic acid can be prepared in batchwise reactors using soluble glutamate 2,3-aminomutase. The glutamate 2,3-aminomutase can then be mixed with the cofactors including, but not limited to: (1) ferrous sulfate or ferric ammonium sulfate; (2) pyridoxal phosphate; (3) dehydrolipoic acid, glutathione, or dithiothreitol; (4) S-adenosylmethionine; and (5) sodium dithionite, and α-glutamic acid at an appropriate pH at a temperature between 25° C. to 37° C., until the production of β-glutamic acid is at equilibrium.
Alternatively, enantiomerically pure β-glutamic acid can be obtained by continuous processing using immobilized glutamate 2,3-aminomutase. Glutamate 2,3-aminomutase can be packed in a column and activated by the addition of cofactors and a solution containing α-glutamic acid at an appropriate pH can be passed through the column at a rate that allows completion of the reaction during contact with the enzyme. The effluent from the column will contain the β-glutamic acid.
Both of the above methods will produce an equilibrium mixture of α-amino acid and β-amino acid in which the predominant species is β-amino acid. If higher purity β-glutamic acid is desired, the L-glutamic acid can be separated from the β-glutamic acid by any number of means well known in the art, including high performance chromatography procedures, such as ion exchange chromatography at an appropriate pH to take advantage of the differences in acidities of the carboxylic acid groups and the α- and β-ammonium groups.
B. Production of β-Amino Acid Using Recombinant Host Cells
In an alternative approach, β-glutamate is produced by fermentation using recombinant host cells that over-express cloned glutamate 2,3-aminomutase. General methods for high level production of amino acids from cultured bacteria are well-known to those of skill in the art. See, for example, Daugulis, Curr. Opin. Biotechnol. 5:192 (1994); Lee, TIBTECH 14:98 (1996).
The gene for glutamate 2,3-aminomutase can be incorporated into an E. coli plasmid that carries necessary markers and E. coli regulatory elements for overexpression of genes. When codon usage for the glutamate 2,3-aminomutase gene cloned from Clostridia is inappropriate for expression in E. coli, the host cells can be cotransformed with vectors that encode species of tRNA that are rare in E. coli but are frequently used by Clostridia. For example, cotransfection of the gene dnaY, encoding tRNAArgAGA/AGG, a rare species of tRNA in E. coli, can lead to high-level expression of heterologous genes in E. coli. Brinkmann et al., Gene 85:109 (1989) and Kane, Curr. Opin. Biotechnol. 6:494 (1995). Heterologous host cells expressing glutamate 2,3-aminomutase can be cultured with favorable energy, carbon and nitrogen sources under conditions in which α-amino acid in the medium is absorbed by the cells and converted intracellularly into β-amino acid by glutamate 2,3-aminomutase. Unused β-amino acid will be excreted into the growth medium. β-amino acid can then be purified from the medium by any methods well known in the art, including high performance chromatography procedures previously described.
The present invention, thus generally described, will be understood more readily by reference to the following examples, which are provided by way of illustration and are not intended to be limiting of the present invention.
EXAMPLES
Example 1
Cloning and Expression of Recombinant Clostridium difficile glutamate 2,3-aminomutase
The DNA and translated amino acid sequ containing significant sequence identity (>60%) to the amino acid sequence of lysine 2,3-aminomutase from Clostridium subterminale SB4 (U.S. Pat. No. 6,248,874 B1) was obtained from the Sanger Institute genomic database (reverse complement of Clostridium difficile Strain 630 nucleotide sequence—Positions 2610029-2608761) following a search and subsequent sequence alignment study. C. difficile chromosomal DNA (obtained from American Tissue Type Cell Collection # 9689D) was used to clone the gene using PCR techniques. Genomic DNA was dissolved in TE buffer (10 mM Tris-HCl, with 1 mM EDTA) buffer at pH 8.0 to a concentration of 0.5 μg/μl. The PCR reaction mixture (100 μl total volume) contained: C. difficile chromosomal DNA—1 μg; cloned Pfu DNA polymerase reaction buffer (Stratagene, La Jolla, Calif.); dNTPs—0.2 mM each; oligonucleotide primers (Primer A-5′-ACACATATGAATGAACAAACTAGAATATCCTTAG (SEQ ID NO: 26) and Primer B-5′-TGACTCGAGTTAATCCTGTGCTTGTTCTTTTATAAG (SEQ ID NO: 27)) 25 pmoles each; cloned Pfu DNA polymerase (Stratagene, La Jolla, Calif.)—5 units. All samples were overlayered with mineral oil and subjected to 30 cycles of 1 min. at 94° C., 30 sec. at 37° C., 15 sec. at 50° C., and 2 min. at 72° C. After thermocycling, DNA formed during the PCR process was further purified by agarose electrophoresis (2% agarose, Promega Corp., Madison, Wis.) in TAE buffer (0.04 M Tris-acetate at pH 8.0 with 1 mM EDTA). Following identification and excision of the appropriately sized (1272 base pairs) ethidium bromide stained band, DNA was extracted from the agarose using the GenElute Minus EtBr spin column (Sigma #5-6501, St. Louis, Mo.), concentrated by precipitation with ethanol, and resuspended in TE buffer at pH 8.0.
The purified PCR product was blunt-end ligated to PCR Blunt II TOPO vector (Invitrogen #K2800, Carlsbad, Calif.) using 0.5 μl PCR insert product to 1 μl vector according to manufacturer's specifications. The ligated DNA was used to transform TOP10 One Shot E. coli cells (Invitrogen) which were subsequently plated on LB+kanamycin (50 μg/ml) plates and cultured overnight. Individual colonies were chosen and subcloned in LB+kanamycin (Fisher #BP906-5) (50 μg/ml) media for plasmid purification. Plasmid DNA was purified using Qiagen Plasmid mini kit (Qiagen, Inc., Santa Clarita, Calif.). To confirm the nucleotide sequence, the inserted gene was sequenced in entirety in four colonies by the automated ABI Prism Dye Terminator Cycle sequencing procedure (Perkin-Elmer, Norwalk, Conn.) by the University of Wisconsin Biotechnology Center (Madison, Wis.).
Purified PCR Blunt II TOPO+gene insert plasmid was subjected to restriction digestion. For the gene insert, 10 μg of plasmid DNA was cut with NdeI (New England Biolabs, Beverly, Mass.)—20 units and XhoI (Promega Corp., Madison, Wis.)—10 units in a total volume of 100 μl for 1 hour. at 37° C. The insert DNA was separated from the plasmid DNA by agarose gel electrophoresis (2% agarose in TAE buffer) and purified and concentrated as previously described. The expression vector, pET23a(+) (Novagen, Madison, Wis.) was similarly cut with NdeI and XhoI, dephosphorylated at the 5′ end with calf-intestine alkaline phosphatase (Promega Corp.)—1 unit for 30 min. at 37° C., purified by agarose gel electrophoresis, and concentrated by ethanol precipitation (as previously described). The pET-23a(+) insert and the pET-23a(+) cut vector were ligated with T4 DNA ligase. To 3 ng of insert DNA were added 10 ng of cut vector in T4 DNA ligase buffer (Promega Corp.)+T4 DNA ligase (Promega Corp.)—3 units in a total volume of 10 μl and incubated for 16 hours. at 14° C. Competent E. coli (Epicurian coli XL2-Blue MRF′, Stratagene) were transformed with 2 μl ligation mix and plated on LB+carbenicillin (Sigma #C1389) (100 μg/ml) plates and plasmid DNA isolated as described previously. The pET23a(+) gene insert was sequenced in entirety including both regions of the start and stop codon to confirm the correctness of the construct.
For protein expression, the pET23a(+) gene insert expression vector was transformed into competent E.coli BL21(DE3) CodonPlus RILP cells (Stratagene, La Jolla, Calif.). This cell line is a λDE3 lysogen carrying the gene for T7 RNA polymerase under control of IPTG. For transformation, 100 μl of competent cells were treated with 54 ng of plasmid DNA Cells were heat shocked for 20 sec. at 42° C. After transformation, 10 μl of cells were plated on LB+carbenicillin (100 μg/ml)+chloramphenicol (Sigma #C-0378) (34 μ/ml) plates and grown overnight at 37° C. Individual colonies were subcultured in LB media containing carbenicillin (100 μg/ml) and chloramphenicol (34 μ/ml) to prepare frozen stocks. Cells from frozen stocks were subsequently used to streak LB plates containing carbenicillin (100 μg/ml) and chloramphenicol (34 μg/ml). Individual colonies were selected, grown in LB media containing carbenicillin (100 μg/ml) and chloramphenicol (34 μg/ml) for approximately 6 hours at 37° C., and used to inoculate 2 liter shake flasks each containing 1 liter of LB medium with ampicillin (Fisher #BP1760-25) (100 μg/ml) and chloramphenicol (34 μg/ml) and supplemented with 100 μM FeCl3. Cells were cultured overnight (16 hours) at 37° C. with slow shaking (100 RPM). After 16 hours IPTG (Inalco, San Louis Obispo, Calif. #1758-1400) was added to a concentration of 1 mM, and culturing was continued for an additional 4 hours at 37° C. prior to harvesting by centrifugation. Cells were harvested by centrifugation at 6,000×gav for 10 min., and small portions were frozen in liquid nitrogen and stored at −70° C. until used for enzyme purification. Approximately 40 grams (wet weight) of cells were harvested from 10 liters of growth medium.
For purification of glutamate 2,3-aminomutase, all steps except centrifugation were conducted in an anaerobic chamber (Coy, Grass Lake, Mich.) at room temperature. To prevent oxygen contamination, liquid suspensions were sealed into centrifuge bottles inside the anaerobic chamber before centrifugation at 4° C. outside the chamber. Cells were thawed in 70 ml standard buffer (SB) [0.03 M sodium EPPS (Sigma #E9502) at pH 8.0, 40 μM FeSO4 (J T Baker #2070-1), 40 μM pyridoxal-5′-phosphate (Sigma #P9255), 1 mM L-glutamate, 1 mM DTT (Inalco #1758-9030), and 1 mM PMSF (Sigma #P7626)] prior to sonication using the standard tip of the Sonic Dismembrator (Misonix, Farmingdale, N.Y., Model #3000) (setting 8 for six 30 sec. intervals at 4-8° C.). Following sonication, cells were centrifuged at 20,000×gav for 30 min. The supernatant fluid was subjected sequentially first to streptomycin sulfate (Sigma #S6501) treatment (3% at 4° C.) to remove nucleic acids, and then to ammonium sulfate treatment (70% saturation at 4° C.) to precipitate proteins. Each precipitation was followed by centrifugation at 20,000×gav for 20 min at 4° C.
The protein pellet after ammonium sulfate precipitation was dissolved in SB+1 M ammonium sulfate and applied to a phenyl-Sepharose 6 Fast Flow (high substitution) (Amersham Biosciences, Piscataway, N.J.) column (2.5×25 cm) previously equilibrated with the same buffer. The enzyme was adsorbed to the column and was eluted with a linear gradient formed from two liters each of 1.) SB+1 M ammonium sulfate and 2.) SB. The gradient starting at 1 M ammonium sulfate and decreasing linearly was operated at a flow rate of 2.5 ml/min. Glutamate 2,3-aminomutase emerged toward the end of the gradient as a yellow-brown band of protein. The desired fractions were identified and pooled, and the protein was precipitated by addition of solid ammonium sulfate (70% saturation 4° C.) and centrifugation as previously described. The precipitated protein was redissolved in 750 ml of SB and applied to a Q-Sepharose Fast Flow (Amersham Biosciences) column (2.5×25 cm) column previously equilibrated with SB buffer. Bound protein was eluted with a linear gradient composed of two liters each of 1.) SB and 2.) SB+0.5 M NaCl and operated at a flow rate of 2.5 ml/min. Glutamate 2,3-aminomutase emerged in the latter half of the gradient as a yellow-brown protein band that was collected and concentrated by ammonium sulfate precipitation (70% saturation at 4° C.) and centrifugation at 20,000×gav for 20 min. The protein pellet was dissolved in 6 ml of SB buffer and passed through a Sephacryl S200 HR (Amersham Biosciences) column (2.5×25 cm) equilibrated with SB at a flow rate of 2 ml/min. The protein band was collected and concentrated using Centricon YM10 (Amicon, Bedford, Mass.) spin concentrators to a protein concentration of 20 mg/ml, frozen as droplets in liquid nitrogen, and stored in liquid nitrogen until used for analysis.
Example 2
Quantitative Analysis of Purified Glutamate 2,3-aminomutase
The gene product of the C. difficile gene prepared according to Example 1 was analyzed using the following procedures.
SDS PAGE electrophoresis. SDS polyacrylamide gel electrophoresis was conducted according to the method of Laemmli (24) using Tris-glycine buffer {0.025M Tris, 0.19 M glycine, 0.1% SDS (sodium dodecyl sulfate)} and 10-20% polyacrylamide gels (Ready Gel #161-1106, Bio-Rad, Hercules, Calif.).
Measurement of Protein Concentration by Amino Acid Analysis: Method. The protein concentration of the purified C. difficile glutamate 2,3-aminomutase was measured by amino acid analysis following complete hydrolysis in 6 N HCl at 110° C. Protein (5 μl) was added to hydrolysis tubes (Pierce Chemical Co., Rockford, Ill.) containing 700 μl 6N HCl. To one half the tubes, 25 μl of amino acid standard solution (2.5 mM each amino acid—Pierce Chemical Co—#20088) was added in addition to protein. Tubes were sealed in vacuo and heated for 24, 48, and 72 hours at 110° C. Following hydrolysis, samples were transferred to 2 ml microcentrifuge tubes and concentrated to dryness by vacuum centrifugation. The dried samples and amino acid standards were derivatized with PITC (Pierce Chemical Co., Rockford, Ill.) and separated by HPLC according to the method of Heinrikson and Meredith (20). Dried samples were dissolved in 100 μl of coupling buffer, concentrated to dryness by vacuum centrifugation, redissolved in 100 μl coupling buffer plus 10 microliters of PITC, allowed to react for 30 min at room temperature, concentrated to dryness as above, and dissolved in 1 ml water prior to injection and separation by HPLC using a Beckman Gold HPLC. The PITC derivative of each amino acid was separated by HPLC chromatography using a C18 reverse phase column (Phenomenex Gemini 5μ, 4.6 mm×25 cm, #G-4435-EO), flow rate 1 ml/min, room temperature, sample injection volume 50 μl. The eluted compounds were detected by spectrophotometry at a wavelength of 254 nm. The PITC-amino acids were separated with a complex linear gradient starting with 0.05 M ammonium acetate in water (buffer A) and 0.10 M ammonium acetate in 44% water, 46% acetonitrile, and 10% methanol (buffer B). The gradient established was 0% Buffer B in 5 min, 0-10% Buffer B in 40 min, 10-35% Buffer B in 35 min, 35-55% Buffer B in 35 min, 55-100% Buffer B in 10 min. The PITC derivatives of the amino acids emerged from the column at the following retention times in minutes: Asx—13, Glx—18, Ser—36, Gly—39, His—54, Thr—56, Ala—58, Arg—60, Pro—62, Tyr—84, Val—85, Met—89, Ile—98, Leu—99, Phe—108 and Lys—117.
Cofactor analysis. Iron content was measured by the method of Kennedy et al (21). Sulfide analysis was conducted by the method of Beinert (22). Pyridoxal 5′-phosphate was measured by the method of Wada and Snell (23).
Glutamate 2,3-aminomutase Activity Measurements. Enzyme assays were conducted in an anaerobic chamber (Coy, Grass Lake, Mich.) at 37° C. Recombinantly produced glutamate 2,3-aminomutase (0.15 μM—subunit) was mixed with the following components: A) EPPS, 60 mM pH 8.0, Na salt; B) S-(5′-adenosyl)-L-methionine (Sigma) 250 μM; sodium hydrosulfite (Sigma #G-1251; also known as sodium dithionite) 65 μM; C) L-glutamate (Sigma #G1251) or β-glutamate (Sigma #G-1763) 20 mM. At various time intervals (0-3 min), 45 μl of reaction mix was added to 15 μl of 2N perchloric acid to stop the reaction. Samples were centrifuged at 14,000×g for 10 min. The supernatant fluids were treated with PITC according to the method of Heinrikson and Meredith (20). Samples were dissolved in 100 μl of coupling buffer, concentrated to dryness by vacuum centrifugation, redissolved in 400 μl coupling buffer plus 20 μl of PITC, allowed to react for 30 min at room temperature, concentrated to dryness as above, and dissolved in either 0.5 or 1.0 ml water prior to injection (50 or 100 μl). The PITC derivative of L-glutamate was separated from the β-glutamate derivative by HPLC chromatography (20) using a C18 reverse phase column (Phenomenex Gemini 5μ, 4.6 mm×25 cm, #G-4435-E0), flow rate 1 ml/min, room temperature. The PITC-amino acids were separated with a linear gradient composed of 0.05 M ammonium acetate in water (buffer A) and 0.1 M ammonium acetate in 44% water, 46% acetonitrile, and 10% methanol (buffer B). The gradient established was 0-10% Buffer B in 20 min, 10-100% Buffer B in 10 min. The PITC derivative of L-glutamate emerged at a retention time of 14.8-15.0 min whereas the PITC derivative of β-glutamate emerged at 15.5-15.7 min. Concentrations of L-glutamate or β-glutamate were measured using an amino acid standard solution (Pierce Chemical Co., #20088). For enzyme activity measurements at selected time points, the peak area of either L-glutamate or β-glutamate was divided by the total peak area (L-glutamate+β-glutamate) and multiplied by the starting concentration of either L-glutamate or β-glutamate to obtain molar concentrations. Enzyme kinetic parameters were determined by varying the concentration of L-glutamate (0.6-20 mM). Two separate analyses were conducted at two concentrations of enzyme (0.75 and 0.15 μM—subunit) with remaining conditions as stated above. Initial velocities were measured and used to calculate kinetic parameters (Vmax and Km) by the nonlinear least squares curve fitting method of Cleland (25).
Measurement of the Equilibrium Constant for Conversion of L-Glutamate into β-Glutamate Catalyzed by Glutamate 2,3-aminomutase. Assays were conducted as previously described (see activity measurements above) except at 24° C. Initial concentrations of either L-glutamate or β-glutamate were set at 0.6 to 20 mM. Initial enzyme concentrations were either 0.75 μM or 0.15 μM. After approximately 4 hours at 24° C., an additional aliquot of enzyme was added to make the final enzyme concentration either 1.5 μM or 0.3 μM, and the reaction was allowed to proceed for an additional 16 hours at 24° C. The reaction was stopped with 0.55 N perchloric acid, and the amino acids were derivatized with PITC as previously described. Following HPLC separation of the PITC derivatized L-glutamate and β-glutamate, the simple ratio of the peak areas of the two compounds was calculated based on the equivalent extinction coefficient of the two compounds (20).
Electron Paramagnetic Resonance (EPR) spectroscopy of C. difficile Glutamate 2,3-aminomutase. Enzyme as isolated (180 μM-subunit) was quickly mixed at 24° C. and frozen at −150° C. (total time <30 sec) with the following components: Tris (Sigma #252859) (Tris-sulfate) at 80 mM and pH 8.0; S-(5′-adenosyl)-L-methionine, 1 mM; sodium dithionite, 1 mM. In addition, each solution contained one of the following: A) L-glutamate at 50 mM; B) β-glutamate at 50 mM; C) (2-13C)-DL-glutamate (Aldrich, Milwaukee, Wis., #48,657-4) at 100 mM; D) (2,3,3,4,4-d5)-L-glutamate (Aldrich-Isotech #616281) at 50 mM; E) L-glutamate 50 mM with S-(5′-adenosyl)-L-methionine omitted; F) L-Glutamate at 50 mM with sodium dithionite omitted. Following freezing, samples were evaluated at 77° K by EPR using a Varian model E3 spectrometer with the following settings: Field center 3260 Gauss; Scan width 200 Gauss; Microwave frequency 9.1 GHz; Microwave power 5 milliWatts; Modulation frequency 100 kHz; Modulation amplitude 2.0 Gauss; Time constant 0.3 sec; Scan time 240 sec. Gain 80,000 (A,B,E, F), 320,000 (C), 40,000 (D).
UV-Visible Spectrophotometry of Cl. difficile Glutamate 2,3-aminomutase. The UV-Visible absorption spectrum of the purified enzyme (0.45 mg/ml) in 0.02M sodium EPPS buffer at pH 8.0 was measured anaerobically with a Hewlett-Packard Diode Array Spectrophotometer (Model 8452A).
Cloning the C. difficile gene with a suitable plasmid expression vector, pET23a(+) (Novagen) clearly demonstrated high expression in E. coli cells (FIG. 1). As shown in column 2, SDS polyacrylamide gel electrophoresis (PAGE) of a cellular extract isolated from E. coli cells disrupted by sonication following induction of recombinant protein synthesis indicated one predominant band at approximately 50 KDa with many minor bands from other cellular proteins. The size of the major protein is comparable to the calculated molecular weight of 48.9 KDa for the gene product based on amino acid content. Purification of the recombinant protein by conventional column chromatography yielded approximately 200 mg of purified protein from 40 gms (wet weight) of E. coli cells. As shown in lane 3 of FIG. 1, the purification procedure produces a highly purified protein with less than 5% contaminating protein. The high purity of the recombinant protein shown by SDS PAGE, estimated to be  ̃95%, is supported by the results of amino acid analysis of the purified protein (Table 1). The data on amino acid content data agree with the expected number of each amino acid measured from the predicted amino acid sequence (SEQ ID #2).







TABLE 1







Estimation of Protein Concentration by Amino Acid Analysis









Protein Concentration (mM) - Subunit











Amino Acid
No
24 hours
48 hours
72 hours














GLY
21
0.41
0.42
0.49


HIS
9
0.44
0.44
0.44


ALA
16
0.44
0.47
0.47


ARG
23
0.44
0.47
0.46


PRO
18
0.41
0.42
0.40


GLX
56
0.45
0.48
0.50


TYR
20
0.46
0.46
0.46


VAL
19
0.43
0.43
0.45


MET
11
0.44
0.43
0.42


ILE
41
0.44
0.46
0.42


LEU
38
0.44
0.45
0.47


PHE
6
0.45
0.44
0.45


LYS
37
0.41
0.41
0.40







Protein Concentration (Mean ± SD, n = 39) 440 ± 24 μM











SER
17
0.42
0.39
0.37


THR
27
0.40
0.35
0.32


ASX
50
0.54
0.71
0.69


CYS
8
NA*
NA*
NA


TRP
5
NA*
NA*
NA





*NA Not available






Amino acid analysis also allowed for an accurate measurement of protein concentration of the recombinant protein (Table 1). All amino acids with the exception of Ser, Thr, Asx, Cys, and Trp were used to measure protein concentration following complete acid hydrolysis and amino acid analysis by HPLC procedure. Ser and Thr were found to decrease with extended hydrolysis as expected (26). Asx (Asp+Asn) increased at 48 and 72 hours hydrolysis due to the conversion of cysteine to cysteic acid. In the HPLC separation, the PITC derivative of cysteic acid has the same retention time as the PITC derivative of aspartic acid. Cys and Trp were destroyed by acid hydrolysis and could not be measured by this procedure. Based on this protein analysis, the cofactor content of the purified recombinant protein is: 2.9±0.14 Fe/subunit; 2.5±0.13 S2−/subunit; and 1.1±0.05 pyridoxal-5′-phosphate/subunit.
As shown in FIGS. 2A and 2B, the recombinant protein displays L-glutamate 2,3-aminomutase activity. PITC-derivatized L-glutamate and β-glutamate are separable by HPLC. FIG. 2A shows HPLC chromatograms that demonstrate conversion of L-glutamate to β-glutamate within minutes at 37° C. in solutions containing purified recombinant protein. Similarly, FIG. 2B shows that the enzyme catalyzes the reverse reaction from β-glutamate to L-glutamate. The products of both the forward and reverse reactions were identified by addition of increasing amounts of L-glutamate and β-glutamate standards to the unknowns. Co-chromatography produced a single symmetrical peak in each case. Both reactions starting with different substrates led to the same end point, equilibrium in which β-Glu is favored to L-glutamate by a ratio of approximately 16 to 1 (Table 2).







TABLE 2







Measurement of the Equilibrium Constant for L-Glutamate:


β-Glutamate Catalyzed by C. difficile Glutamate


2,3-aminomutase at 24° C.












[L-Glutamate] mM

[β-Glutamate] mM




(start)
Keq
(start)
Keq











[Enzyme] = 1.5 μM (subunit)












22.9
15.3
22.9
15.9



12.4
15.6
12.3
16.4



6.6
15.6
6.2
16.4



3.1
16.0
3.1
16.3



1.4
15.2
1.4
15.8



0.6
14.2
0.6
15.3







[Enzyme] = 0.30 μM (subunit)












22.1
15.5
24.3
16.1



12.9
16.3
12.3
16.6



6.4
15.9
6.2
15.7



3.2
15.9
3.1
16.2



1.6
15.7
1.4
15.6



0.8
14.8
0.6
15.6







Keq [β-Glutamate]/[L-Glutamate] = 15.7 ± 0.5 Mean ± SD (n = 24)









Properties of the enzyme catalyzed reaction are shown in Table 3A. Enzyme activity measured at 20 mM for either substrate indicates very significant rates in the forward and reverse directions: 20 mM L-glutamate reacts to produce β-glutamate at a rate of 5.9 μmoles min−1· (mg protein)−1, and 20 mM β-glutamate reacts to produce L-glutamate at a rate of 2.3 μmoles min−1· (mg protein)−1. The in vitro reaction depends on the addition of S-(5′-adenosyl)-L-methionine as a cofactor and sodium dithionite as a reducing agent. Although dithionite is necessary for this reaction, an excess can be inhibitory (FIG. 3). A progressive loss over time of enzyme activity was observed at higher levels of dithionite (>70 μM) A slight increase (20%) in enzyme activity was observed when purified enzyme was subjected to reductive incubation, a reductive process utilizing a thiol agent, L-cysteine and iron to restore full activity lost during purification (Table 3). Activity was found to be proportional to enzyme concentration (FIG. 4).







TABLE 3





Activity and Kinetic Parameters of Purified C. difficile


Glutamate 2,3-aminomutase at 37° C.







A. Enzyme Activity













Specific Activity


Substrate
SAM
Dithionite
(μmoles · min−1 · mg−1 Protein





L-Glutamate*
+
+
5.9


L-Glutamate*
+
−
0.16


L-Glutamate*
−
+
<0.01


β-Glutamate*
+
+
2.3





*Concentration of substrates - 20 mM







B. Kinetic Parameters














Km







(L-Glutamate)

kcat
kcat/Km4




mM
Vmax*
s−1
M−1 · s−1







Assay 1
2.2 ± 0.16
7.5 ± 0.18
6.2
2840



Assay 2
2.3 ± 0.18
7.3 ± 0.19
6.0
2550







*μmoles · β-Glutamate min−1 (mg protein)−1






Kinetic parameters in the forward direction were measured (Table 3B). The Michaelis constant (Km) for L-glutamate is 2 mM, and the maximum velocity at 37° C. is 7 μmoles of β-glutamate min−1· (mg protein)−1. The value of kcat is 6 s−1 and that of kcat/Km is 2500 M−1·s−1 under the conditions of Table 3, indicating efficient enzymatic catalysis. These values are within the same order of magnitude to those reported for C. subterminale SB4 lysine 2,3-aminomutase (27).
The purified recombinant enzyme (FIG. 7) exhibits spectroscopic properties resembling lysine 2,3-aminomutase from C. subterminale SB4. The UV-Visible absorption spectrum of the purified enzyme displays two prominent peaks at 280 and 420 nm typical of absorption due to amino acid components (Phe and Tyr) at 280 nm and the internal aldimine of pyridoxal-5′-phosphate at 420 nm. Furthermore a broad overlapping absorption band is observed decreasing from 300 nm to 700 nm representative of iron-sulfur cluster absorption.
EPR spectroscopy of the purified enzyme in the presence of either L-glutamate or β-glutamate and S-(5′-adenosyl)-L-methionine and reduced by dithionite (FIG. 6A, B) reveals the presence of a radical species analogous to the product-related radical reported for the reaction of C. subterminale SB4 lysine 2,3-aminomutase with L-lysine (13). The splittings in the EPR signal result from nuclear hyperfine coupling of the C2-hydrogen atom with the unpaired electron on C2. FIG. 6D shows that when deuterium labeled [2,3,3,4,4-d5]-L-glutamate was used, the signal collapses into a single, broadened line. This results from the 6-fold smaller splitting constant for deuterium relative to hydrogen. The spectrum shown in FIG. 6C proves that the EPR signal originates from a radical with the unpaired electron centered on C2 of β-glutamate. FIG. 6C shows significant signal broadening and changes in the splitting pattern when L-[2-13C]glutamate is substituted for L-glutamate. As in enzyme activity measurements, no EPR signal can be observed when either S-(5′-adenosyl)-L-methionine or dithionite are omitted (FIG. 6E, F).
Glutamate 2,3-aminomutase expressed by E. coli in aerobic shake flasks is active inside the E. coli cell. This is known by the fact that analysis of the protein-free cell extract from E. coli expressing the enzyme shows the presence of both L-glutamate and β-glutamate, predominantly β-glutamate. PITC-derivatization of the cell extract and HPLC analysis clearly shows the PITC-derivatives of both amino acids, with PITC-β-glutamate as the dominant species. The predominance of β-glutamate also shows that the reaction in vivo is near equilibrium, in accord with the equilibrium constant in Table
The coenzyme requirements of glutamate 2,3-aminomutase are the same as those of lysine 2,3-aminomutase, and the amino acid sequences of the two enzymes are similar. While not wishing to be bound by theory, on this basis, it is believed that the two enzymes are likely to act by similar chemical mechanisms, while displaying different substrate specificities. In support of this proposition, the free radical observed by EPR spectroscopy in the steady state of the reaction of glutamate 2,3-aminomutase is analogous to that observed in the reaction of lysine 2,3-aminomutase. The two free radicals display spin on C2 of the carbon skeletons of the two respective substrates. The two free radicals are the product-related radicals in the radical isomerization mechanism established for the action of lysine 2,3-aminomutase. This mechanism is adapted to the reaction of glutamate 2,3-aminomutase in FIG. 8. The mechanism is the same as that for lysine 2,3-aminomutase, with the substitution of a carboxymethyl group (−OOC—CH2—) in L-glutamate for the aminopropyl group (+H3N—CH2CH2CH2—) in L-lysine. The EPR spectrum of the free radical observed in the steady state of the reaction of glutamate 2,3-aminomutase in FIG. 6 is radical 3 in FIG. 8.
Thus, again while not wishing to be bound by theory, it is believed that the chemical mechanism in FIG. 8 is initiated by the reversible cleavage of S-(5′-adenosyl)-L-methionine into the 5-deoxyadenosyl radical and methionine at the active site of glutamate 2,3-aminomutase. This is likely brought about by electron transfer from the [4Fe-4S]1+ cluster by the same mechanism as in the action of lysine 2,3-aminomutase (10,11,15-17).
Example 3
Cloning, Expression and Analysis of Glutamate 2,3-aminomutase from Other Species
Based on the nucleic acid sequences obtained from the genomic database (SEQ ID NOs: 3,5,7,9), synthetic genes optimized for expression in E. coli hosts were obtained from Genscript Corp., Piscataway, N.J. Each of these genes was supplied ligated to the pUC57 plasmid containing NdeI and XhoI restriction sites for future cloning in the appropriate E. coli expression vector. The synthetic genes had the following nucleic acid sequences, each of which codes for the identical protein indicated in SEQ ID Nos: 4, 6, 8, and 10, respectively:







Thermoanaerobacter tengcongensis (SEQ ID NO: 28)









1
ATGAGCTCCA CCGGTAGCCT GACTGTGGAA GAAAAACGTA AAATTGCCCT GCAGCGCGCA



 


61
GAGGAGCTGA AAAAGAAAAT CGAACCATAC CTGCGTGCCA GCGAGAAAAT CGAAACAGGA


 


121
TTTAAACTGA GCGAAAAGTT TCGTGAAAAC AAAGAAAAGA TCAAGAACCT GTTTGGCGCA


 


181
ACTGAAGAAG AATGGAACGA TTGGCGCTGG CAGATCCGCA ACCGCATTTC AGATGTGGAG


 


241
ACCCTGAAGA AAATTGTTAA CCTGAGCGAA GAAGAAATTG AAAACATTAA GCGCGTCAGT


 


301
ACTCGCTATC GTTGGGCAAT TTCGCCGTAT TATGCATCGC TGATGGACCC GGATAACCCT


 


361
TTTTGCCCGA TTCGCATGCG CGCAATCCCG TCTATCAAAG AACTGACAGA TAAATATGGC


 


421
GTGCCAGATC CGATGGCGGA GGAATATACG TCCCCGGCGC CGCTGATTAC TCGCCGTTAT


 


481
CCGGATCGTC TGATTATCAA CGTGACCAAT CAATGTGGCA TGTTTTGCCG TCACTGTCAG


 


541
CGTCGCCGCA ATATCGGCGA AGTGGACTAC CCGGCGAAAC ATGAAGATAT TGAAGCGGCG


 


601
CTGGAATATA TCCGTAATAA TCCAGAGATC CGTGATGTTC TGATCACGGG CGGCGATCCA


 


661
CTGACCCTGG AAGACGAAAA GATTGACTGG ATTCTGAGCG AACTGGATAA AATTCCGCAC


 


721
GTGGAAATTA AGCGCATCGG TACCGCGGCT CCAGTGACGT TCCCGCAACG TATTACCGAC


 


781
GAACTGTGTA AAATTCTGAC GAAACATCTG CCGCTGTATA TCAACACACA ATTTAACCAT


 


841
CCGAAAGAGG TTACCGAAGA GGCGAAAGAA GCCTGTTTTA AACTGGCGCG TGCGGGTGTG


 


901
GCTCTGGGCA ATCAGGCGGT ACTGCTGAAA GGCATCAATA ACGATCCACA TGTCATGAAG


 


961
AAACTGAATC ATGAACTGCT GCGCATCATG GTCAAACCTT ATTATATTTT CCACGCGAAA


 


1021
TCTGTGCAAG GTACTACACA TTTTGTGACC ACCGTTCAGG ATGGCCTGGA AATTATGGAG


 


1081
CAGCTGCGCG GTTATACTAG TGGTCTGGCG ATCCCGTGGT ATATCATTAA CGCACCGGAA


 


1141
GGTCATGGTA AAACTCCGAT CGTTCCGCAG TACCTGCTGA TGGTAGGAAA GGAATACGTT


 


1201
CTGATCCGCA ATTGGGAAGG TAAAGTGTTT GAATATCCGA ACGGTTTCCC GGATGATTAA


 







Desulfitobacterium hafniense DCB-2


(SEQ ID NO: 29)









1
ATGGCGATTG AATTTCTGCC GCCGAATCCG CGTCAGGCGA GCCAGGCGCG CGCGCTGGAA



 


61
CTGAAACAGA AAGTGCAGAG CTATAATAAA CGTAAAGAAA CCATTCCGTG CGGCCTGGCG


 


121
CTGAGCGAAG AATTTAACGA AAACCGTGAT TTTATTCTGG ATCAGCTGGA TGCGGATCTG


 


181
GAACATTGGC AGGATTGGAA ATGGCAGCTG AAAAACCGCA TTCAGGATGC GGAAAATCTG


 


241
AGCACCCTGC TGCCGCTGAC CCCGAAACAG CGCCATGAAA TTAATGAAGT GGGCAAAGCG


 


301
TATCGTTGGG CGGTGAGCCC GTATTATCTG AGCCTGATTG ATAAAGATGA TCCGCAGGAT


 


361
CCGATTCGCC TGCAGAGCCT GCCGAGCGTG GAAGAAATTC TGGATGATAG CGGTGAAGCG


 


421
GATCCGATGG GCGAAGAATA TACCAGCCCG GCGCCGTGCA TTACCCGCCG CTATCCGGAT


 


481
CGCCTGATTA TTAATGTTAC CAACCTGTGC GCGATGTATT GCCGTCATTG CCAGCGCCGC


 


541
CGTAATATTG GCGAAATTGA TCTGCATGAA ACCCGTGCGA ACCTGGAAGC GGCGCTGGAT


 


601
TATATTCGTA GCAACCCGGA AATTCGCGAT GTGCTGGTGA CCGGTGGCGA TGCGCTGCTG


 


661
CTGAGCGATC AGATGCTGGA TTGGCTGCTG GGCGAACTGC ATGAAATTAA ACATGTGGAA


 


721
ATTAAACGCA TTGGCACCCG TGTGCCGGTG ACCCTGCCGA TGCGCATTAC CGATGAACTG


 


781
TGTGCGATTC TGGAAAAATA TCCGCCGCTG TATATTAACA CCCAGTTTAA CCATCCGCAG


 


841
GAAGTGACCG AAGAAACCAA AAAAGCGGCG GATCGCCTGA TTAAAGCGGG CGTTATTCTG


 


901
GGCAATCAGG CGGTTCTGCT GAAAGGCATT AACGATCAGC CGGAAATTAT GAAACGTCTG


 


961
AACCAGGAAC TGCTGAAAAT TCGTGTGCGC CCGTATTATA TTTTTCATGC GAAAAACGTG


 


1021
AAAGGCACCA GCCATTTTAT TCCGCGTATT CAGGATGGCC TGCGCATTAT GGAAAACCTG


 


1081
CGTGGTTATA CCAGCGGTCT GGCGATTCCG ACCTATATTA TTAACGCGCC GGGTGGTGGC


 


1141
GGCAAAACCC CGATTCTGCC GCAGTATCTG ATTAGCCTGA ACGATGAAGA AGCGGTGATT


 


1201
CGTACCTGGG AAGGCAAAGT GGTGCATTAT CCGAATCATT AA


 







Moorella thermoacetica (ATCC 39073)


(SEQ ID NO: 30)









1
ATGGGTCGTG AAGCGAAACG CGAAATTGCG CTGGATCGTG CGGCGGAACT GAAAGCGCGT



 


61
ATTGTGGATT ATCTGGAAGA ACGTGAAAAA ATTGCGAGCG GCCTGGAAGC GGCCGCGGAA


 


121
ATCGAAGCCA GCAAACAGCG CATCCTGGCC TATTTTGGTG CGGGCGAAGC CGAATGGCAG


 


181
GATTGGCGTT GGCAGCTGAC CCATCGCATT ACCAGCGTGG CGACCCTGGC GGAACTGATT


 


241
CCGCTGACCG AAGCCGAAAA AGAAGCCATT CTGAAAGTTG AACGTACCTA TCGCTGGGCG


 


301
GTGAGCCCGT ATTATCTGAG CCTGATGGGC CCGGAACCGG ATTGTCCGAT CCGTCGTCAG


 


361
GCGCTGCCGA GCGCCGCGGA ACTGGAAGAT AACCATGGCG TGCTGGATCC GATGGATGAA


 


421
GAACTGACCA GCCCGGCGCC GGCCATTACC CGTCGTTATC CGGATCGCCT GATTATTAAC


 


481
GTGACCAACC AGTGTGCGAT GTATTGCCGC CATTGCCAGC GTCGCCGTAA TATCGGTGAA


 


541
GTGGATCGTA GCCGTAGCCG TCGTGAACTG GAACAGGCCC TGCAGTATAT TCGTCAGAAT


 


601
GAAGAAATTC GTGATGTTCT GATTACCGGT GGTGATGCGC TGATGCTGAG CGATGCGATG


 


661
ATTGATTGGC TGCTGACCGA ACTGGATAAC ATTCCGCATG TTGAAATCAA ACGCCTGGGT


 


721
ACCCGTGTGC CGGTGACCAT GCCGCAGCGT ATCACCCCGG AACTGTGCCG TGTTCTGGCC


 


781
AAACATCCGC CGATCTATCT GAATACCCAG TTTAATCATC CGCGCGAAGT TACCGCGGCG


 


841
GCGAAAGAAG CGTGTGATCG CCTGGTGCAG GCGGGCGTGG TTCTGGGTAA CCAGGCGGTT


 


901
CTGCTGAAAG GCGTGAATAA CCATCCGTTT GTGATGCGTA AACTGAATCA GGAACTGCTG


 


961
AAAATCCGTG TTCGCCCGTA TTATATCTTT CATGCGAAAC CGGTGAAAGG CACCACCCAT


 


1021
TTCATTACCA GCATTGAAGA AGGTGTGGAA ATTATGGATA AACTGCGTGG CTATACCAGC


 


1081
GGTCTGGCGG TGCCGACCTA TATCATTAAT GCGCCGCATG GTCTGGGCAA AACCCCGATC


 


1141
CTGCCGCAGT ATGTTATCGC GCGTAACGAT CACCAGGTGA TTCTGCGTAC CTGGGAAAAA


 


1201
CGCATTATCT TCTATAGCAA CCTGGGCCGC CAGAAAGAAC AGGCGTAA


 







Syntrophomonas wolfei (str. Goettingen)


(SEQ ID NO: 31)









1
ATGCTGCTGC GCGAAGATCT GATTAACGAA GAAATTCGCG AAATGAAACG CGAAGTGAGC



 


61
CTGCGTCGTG CGGATGAACT GAAACAGGAA ATTAGCGATT ATCTGGATAT TGAAAGCACC


 


121
ATTGAAACCG GTATGCGTCT GCATGAACGC AACCTGCATA ACAAAGAACA TATTCTGAAA


 


181
TATTTTGAAG TGAGCGAAAA CGATTGGGAT AACTGGGCGT GGCAGATGCG TAACCGTATT


 


241
AATGATGGTA ACGTGCTGGC GAGCATTCTG GGCCTGAATG AATTTGAAGT TCAGACCATT


 


301
AAACGTGTGA GCAAAAAAGT GCGTTGGGCG ATTAGCCCGT ATTATCTGAG CCTGATTGAT


 


361
TTTGAAAATT ATGCGGCGAG CCCGATTTAT AAACAGAGCG TGCCGAGCCT GCATGAAATT


 


421
ATTGAATGCA AAGGTGAAGA TGATCCGATG GGTGAAGAAA TGAGCAGCCC GGCGCCGCGT


 


481
ATTACCCGTC GTTATCCGGA TCGTCTGATT ATTAATGTTA CCAATCAGTG CGCGATGTAT


 


541
TGCCGCCATT GTCAGCGCCG CCGTAATTTT GGTGAAACCG ATAACCATGC GGCGCATAAA


 


601
GATCTGGAAG CGGCGCTGCA GTATATTAAA AATAATAGCG AAATTCGTGA TGTGCTGATT


 


661
ACCGGCGGTG ATGCGCTGAT GCTGAGCGAT CGCACCCTGG ATTGGCTGCT GGGTGAACTG


 


721
GATGCGATTA GCCATGTGGA AATTAAACGC ATTGGCACCC GTACCCCGGT GACCCTGCCG


 


781
CAGCGTATTA CCGCGAACCT GTGCGCGGTG CTGAAACGCC ATACCCCGAT TTATATTAAT


 


841
ACCCAGTTTA ACAGCCCGCT GGAAGTGACC CCGGAAGCGA AACAGGCGTG CGATCGCCTG


 


901
ATTGAAGCGG GCGTGGTTCT GGGTAATCAG GCGGTGCTGC TGAAAGGCAT TAACGATAAC


 


961
GTGCATGTGA TGAAAAAACT GAATCAGGAA CTGCTGAAAA TTCGTGTGCG TCCGTATTAT


 


1021
CTGTTTCAGG CGAAAGAAGT GAAAGGCACC ACCCATTTTA TTAGCCCGGT TAACACCGGT


 


1081
CTGGATATTA TGAAACATCT GCGTGGTTAT ACCAGCGGCC TGGCGATTCC GACCTATGTT


 


1141
ATTAATGCGC CGGGTGGTTA TGGTAAAACC CCGGTGAATC CGGAATATGT GCTGGATATT


 


1201
AATGAAAATG AAGTGATTAT TAGCACCTGG CAGGGTAAAA CCTTTAACTA TCCGCATCGT


 


1261
AACAACTAA






pUC57 plasmids containing the synthetic genes were subjected to restriction digestion. For each gene insert, 10 μg of plasmid DNA was cut with NdeI (New England Biolabs, Beverly, Mass.)—20 units and XhoI (Promega Corp., Madison, Wis.)—10 units in a total volume of 100 μl for 1 hour. at 37° C. The insert DNA was separated from the plasmid DNA by agarose gel electrophoresis (2% agarose in TAE buffer). Following identification and excision of the appropriately sized ethidium bromide stained band (approximately 1200 bp), DNA was extracted from the agarose using the GenElute Minus EtBr spin column (Sigma #5-6501, St. Louis, Mo.), concentrated by precipitation with ethanol, and resuspended in TE buffer at pH 8.0. The expression vector, pET21a(+) (Novagen, Madison, Wis.) was similarly cut with NdeI and XhoI, dephosphorylated at the 5′ end with calf-intestine alkaline phosphatase (Promega Corp.)—1 unit for 30 min. at 37° C., purified by agarose gel electrophoresis, and concentrated by ethanol precipitation (as previously described). The pET-21a(+) insert and the pET-21a(+) cut vector were ligated with T4 DNA ligase. To 3 ng of insert DNA were added 10 ng of cut vector in T4 DNA ligase buffer (Promega Corp.)+T4 DNA ligase (Promega Corp.)—3 units in a total volume of 10 μl and incubated for 16 hours. at 14° C. Competent E. coli (Epicurian coli XL2-Blue MRF′, Stratagene) were transformed with 2 μl ligation mix and plated on LB+carbenicillin (Sigma #C1389) (100 μg/ml) plates and cultured overnight. Individual colonies were chosen and subcloned in LB+carbenicillin (100 μg/ml) media for plasmid purification. Plasmid DNA was purified using Qiagen Plasmid mini kit (Qiagen, Inc., Santa Clarita, Calif.). The pET21a(+) synthetic gene inserts were sequenced in entirety including both regions of the start and stop codon to confirm the correctness of the constructs. The pET21a(+) gene insert expression vectors and pET21a(+) vector without recombinant gene (Control) were transformed into competent E.coli BL21(DE3) (Gold) cells (Stratagene, La Jolla, Calif.). 100 μl of competent cells were treated with 25 ng of plasmid DNA. Cells were heat shocked for 20 sec. at 42° C. After transformation, 10 μl of cells were plated on LB+carbenicillin (100 μg/ml) plates and grown overnight at 37° C. Individual colonies were subcultured in LB media containing carbenicillin (100 μg/ml) to prepare frozen stocks.
For protein expression, cells from frozen stocks were subsequently used to streak LB plates containing carbenicillin (100 μg/ml). Individual colonies were selected, grown in LB media containing carbenicillin (100 μg/ml) for approximately 6 hours at 37° C., and used to inoculate 2 liter shake flasks each containing 1 liter of LB medium with ampicillin (Fisher #BP1760-25) (100 μg/ml) and supplemented with 100 μM FeCl3. Cells were cultured overnight (16 hours) at 37° C. with slow shaking (100 RPM). After 16 hours IPTG (Inalco, San Louis Obispo, Calif. #1758-1400) was added to a concentration of 1 mM, and culturing was continued for an additional 4 hours at 37° C. prior to harvesting by centrifugation. Cells were harvested by centrifugation at 6,000×gav for 10 min., and small portions were frozen in liquid nitrogen and stored at −70° C. until used for enzyme purification. Approximately 40 grams (wet weight) of cells were harvested from 10 liters of growth medium.
For preparation of cell extracts, all steps except centrifugation were conducted in an anaerobic chamber (Coy, Grass Lake, Mich.) at room temperature. To prevent oxygen contamination, liquid suspensions were sealed into centrifuge bottles inside the anaerobic chamber before centrifugation at 4° C. outside the chamber. Cells were thawed in 50 ml standard buffer (SB) [0.03 M sodium EPPS (Sigma #E9502) at pH 8.0, 40 μM FeSO4 (J T Baker #2070-1), 40 μM pyridoxal-5′-phosphate (Sigma #P9255), 1 mM DTT (Inalco #1758-9030), and 1 mM PMSF (Sigma #P7626)] prior to sonication using the standard tip of the Sonic Dismembrator (Misonix, Farmingdale, N.Y., Model #3000) (setting 8 for six 30 sec. intervals at 4-8° C.). Following sonication, cells were centrifuged at 20,000×gav for 30 min. The supernatant fluids of each cell extract were snap frozen in liquid nitrogen and stored in liquid nitrogen until used for enzyme assay.
Glutamate 2,3-aminomutase Activity Measurements of Cell Extracts. Enzyme assays for cell extracts of homologous glutamate 2,3-aminomutase proteins were conducted in an anaerobic chamber (Coy, Grass Lake, Mich.) at 37° C. or 65° C. Cell extracts were mixed with the following components: A) EPPS, 60 mM pH 8.0, Na salt; B) S-(5′-adenosyl)-L-methionine (Sigma) 150 μM; sodium hydrosulfite (Sigma #G-1251) 200 μM; C) L-glutamate (Sigma #G1251) 50 mM. At various time intervals (0-15 min), 35 μl of reaction mix was added to 15 μl of 2 N perchloric acid to stop the reaction. Samples were centrifuged at 14,000×g for 10 min. The supernatant fluids were treated with PITC and subjected to HPLC analysis as described in Example 2.
Glutamate 2,3-aminomutase activity was measured in extracts of E. coli cells containing plasmid expression vectors with homologous recombinant genes from Desulfitobacterium hafniense, eSyntrophomonas wolfei, Thermoanaerobacter tengcongensis, and Moorella thermoacetica (Table 4). No glutamate 2,3-aminomutase activity was measured in E. coli cell extracts containing the pET21a(+) expression vector without the above recombinant genes. Therefore the above homologous genes code for glutamate 2,3-aminomutase proteins. The different activities measured are a reflection of the kinetic properties and the amount of protein expression of each enzyme in the cell extracts.







TABLE. 4







E. coli plasmid vector-based expression of homologous glutamate


2,3-aminomutase genes. Glutamate 2,3-aminomutase activity in E. coli


cell extracts.









Specific Acitivity


Bacterial source
nmoles β-Glu min−1 mg−1 Protein





Desulfitobacterium hafniense
2.5*


Syntrophomonas wolfei
 0.62*


Thermoanaerobacter tengcongensis
31.4+  


Moorella thermoacetica
18.5+  


Control (Plasmid without gene)
0  





*Assay temperature - 37 deg C.


+Assay temperature - 65 deg C.






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All publications, patent applications, issued patents, and other documents referred to in this specification are herein incorporated by reference as if each individual publication, patent application, issued patent, or other document was specifically and individually indicated to be incorporated by reference in its entirety. Definitions that are contained in text incorporated by reference are excluded to the extent that they contradict definitions in this disclosure.
Although the foregoing refers to particular preferred embodiments, it will be understood that the present invention is not so limited. It will occur to those of ordinary skill in the art that various modifications may be made to the disclosed embodiments and that such modifications are intended to be within the scope of the present invention, which is defined by the following claims.

## Claims

1. An isolated DNA molecule encoding a polypeptide having glutamate 2,3-aminomutase activity, wherein the DNA molecule comprises a sequence selected from the group consisting of
a) a DNA sequence encoding a polypeptide having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 2, wherein the polypeptide comprises the following amino acid sequences: CXXXCRXCXR (SEQ ID NO: 19), S/(T)GGE/(D) (SEQ ID NO: 20), GXXXPXXXXXXXXXXXK (SEQ ID NO: 21), PXYXXXXKXXXG (SEQ ID NO: 22), and PXXXXNXXXXXXK (SEQ ID NO: 23);
b) a DNA sequence comprising SEQ ID NO: 1; and
c) a DNA sequence which is degenerate to the sequence of (b) due to the genetic code.

2. An expression vector comprising the DNA molecule of claim 1.

3. The expression vector of claim 2 wherein the DNA molecule is operably linked to one or more control sequences which direct the production of the polypeptide in a host cell.

4. A recombinant host cell comprising the DNA molecule of claim 1.

5. A recombinant host cell comprising the expression vector of claim 2.

6. The recombinant host cell of claim 5 wherein the recombinant host cell is a prokaryotic cell.

7. The recombinant host cell of claim 6 wherein the cell is a bacterial cell.

8. The recombinant host cell of claim 6 wherein the cell is an E. coli cell.

9. A method of producing a polypeptide having glutamate 2,3-aminomutase activity comprising culturing the recombinant host cell of claim 6.

10. The method of claim 9 further comprising isolating the polypeptide produced from the recombinant host cell.

11. The isolated DNA molecule of claim 1 wherein the DNA sequence encoding the polypeptide has at least 95% sequence identity to the amino acid sequence of SEQ ID NO: 2.

12. An isolated DNA molecule encoding a polypeptide having glutamate 2,3-aminomutase activity, wherein the DNA molecule comprises a sequence encoding a polypeptide having at least 95% sequence identity to the amino acid sequence of SEQ ID NO: 2.

13. A recombinant host cell comprising the DNA molecule of claim 12.

14. An expression vector comprising the DNA molecule of claim 12.

15. The expression vector of claim 14 wherein the DNA molecule is operably linked to one or more control sequences which direct the production of the polypeptide in a host cell.

16. A recombinant host cell comprising the expression vector of claim 15.

17. The recombinant host cell of claim 16 wherein the recombinant host cell is a prokaryotic cell.

18. The recombinant host cell of claim 17 wherein the cell is a bacterial cell.

19. The recombinant host cell of claim 18 wherein the cell is an E. coli cell.

20. A method of producing a polypeptide having glutamate 2,3-aminomutase activity comprising culturing the recombinant host cell of claim 16.

21. The method of claim 20 further comprising isolating the polypeptide produced from the recombinant host cell.