MURD PROTEIN AND GENE OF STAPHYLOCOCCUS AUREUS

Abstract: This invention provides the murD gene of Staphylococcus aureus. Purified and isolated MurD recombinant proteins are also provided. Nucleic acid sequences which encode functionally active MurD proteins are described. Assays for the identification of modulators of the expression of murD and inhibitors of the activity of MurD, are also provided.

Description: TITLE OF THE INVENTION MURD PROTEIN AND GENE OF STAPHYLOCOCCUS AUREUS CROSS-REFERENCE TO RELATED APPLICATIONS This application claims the benefit of U.S. Provisional Application No. 60/064,183, filed November 4, 1997, the contents of which are incorporated herein by reference in their entirety. STATEMENT REGARDING FEDERALLY-SPONSORED R&D Not applicable. REFERENCE TO MICROFICHE APPENDDX Not applicable. FIELD OF THE INVENTION This invention relates to the genes and enzymes involved in cell wall synthesis in bacteria, and particularly to the inhibition of such enzymes. BACKGROUND OF THE INVENTION The molecular target of many naturally- occurring antibiotics, including fosfomycin, cycloserine and b-lactams, is the synthesis of the bacterial cell wall. The frequency with which these types of antibiotics arose in evolution indicates that the pathway of cell wall biosynthesis is a particularly effective point of attack against bacteria. Genetic studies confirm the soundness of this process as a target, as temperature- sensitive alleles of the intracellular pathway genes are lytic, and therefore lethal. Since the building blocks of the cell wall are highly conserved structures in both Gram-positive and Gram- negative bacteria, but are unique to the eubacteria, novel inhibitors of cell wall formation are expected to be both broad spectrum and safe antibiotics. The bacterial cell wall is a polymer - a single molecule composed of peptidoglycan — that defines the boundary and shape of the cell. Assembled by crosslinking glycan chains with short peptide bridges (Rogers, H. J., H. R. Perkins, and J. B. Ward, 1980, Biosynthesis of peptidoglycan. p. 239-297. In Microbial cell walls and membranes. Chapman & Hall Ltd. London), the completed structure is strong enough to maintain cell integrity against an osmotic pressure differential of over four atmospheres, but also flexible enough to allow the cell to move, grow and divide. The construction of the peptidoglycan begins in the cytoplasm with an activated sugar molecule, UDP-N-acetylglucosamine. After two reactions (catalyzed by MurA and MurB) that result in the placement of a lactyl group on the 3-OH of the glucosamine moiety, a series of ATP-dependent amino acid ligases (MurC, -D, -E, and -F) catalyze the stepwise synthesis of the pentapeptide sidechain using the newly synthesized lactyl carboxylate as the first acceptor site. After attachment of the sugar pentapeptide to a lipid carrier in the plasma membrane, another glucosamine unit is added to the 4-OH of the muramic acid moiety. The completed monomeric building block is moved across the membrane into the periplasm where the penicillin- binding proteins enzymatically add it into the growing cell wall. Because the pentapeptide sidechain is not synthesized ribosomally it contains more diverse chemical functionality than a typical peptide, both structurally and stereochemically. Two of the enzymes catalyze the addition of D-amino acids (MurD and MurF) and MurE mediates the formation of a peptide bond between the g- carboxylate of D-glutamate and the amino group of L-lysine. Presumably these structures render the exposed peptidoglycan resistant to the action of proteases, but they also imply that the active sites of the enzymes must have unusual structures in order to handle the somewhat uncommon substrates. These unusual active sites are targets to bind novel inhibitors that can have antimicrobial activity. Among these potential enzyme targets is MurD. The first partial purification and characterization of a D-glutamate-adding enzyme was from S. aureus (Ito, E. and J. L. Strominger, 1962, Enzymatic synthesis of the peptide in bacterial uridine nucleotides: Enzymatic addition of L-alanine, D-glutamic acid, and L-lysine. J. Biol. Chem. 237: 2689-2695; Nathenson, S. G., J. L. Strominger, and E. Ito, 1964, Enzymatic synthesis of the peptide in bacterial uridine nucleotides: purification and properties of D-Glutamic acid-adding enzyme, J. Biol. Chem. 239: 1773-177), followed by studies in more detail on the isolated E. coli enzyme (Blanot, D., A. Kretsovali, M. Abo-Ghalia, D. Mengin- Lecreulx, and J. van Heijenoort, 1983. Synthesis of analogues of precusors of bacterial peptidoglycan. p. 311-314. In Peptides. Blaha, K. and P. Malon, eds. pp. 311-314, Walter de Gryter and Co. Berlin, New York.; Jin, H., Emanuele, J. J., Jr., Fairman, R., Robertson, J. G., Hail, M. E., Ho, H.-T., Falk, P. and Villafranca, J. J., 1996. Structural studies of Escherichia coli UDP-N-acetylmuramate: L-alanine ligase. Biochemistry 35: 14423-14431; Ito E. and J. L. Strominger, 1973. Enzymatic synthesis of the peptide in bacterial uridine nucleotides: Comparative biochemistry. J. Biol. Chem. 248: 3131-3136; Michaud, C. D. Blanot, B. Flouret, and J. van Heijenoort, 1987. Partial purification and specificity studies of the D-glutamate-adding and D-alanyl-D- alanine- adding enzymes from Escherichia coli K12. Eur. J. Biochem. 166: 631-637). Recently, a purified recombinant E. coli MurD was reported (Pratviel-Sosa F, D. Mengin-Lecreulx and J. van Heijenoort, 1991. Over-production, purification and properties of the uridine diphosphate N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli. Eur. J. Biochem. 202 (3):1169-1176) and genes encoding MurD have been cloned from several species of bacteria including E. coli (Ikeda, M., M. Wachi, F. Ishino, and M. Matsuhashi, 1990, Nucleotide sequence involving murD and an open reading frame ORF-Y spacing murF and ftsW in Escherichia coli. Nucleic Acids Res. 18:1058; Mengin-Lecreulx, D., C Parquet, L. Desviat, J. Pla, B. Flouret, J. Ayala and J. van Heijenoort, 1989, Organization of the murE-murG region of Escherichia coli: Identification of the murD gene encoding the D- glutamic-acid-adding enzyme. J. Bacteriol. 171: 6126-6134) and B. subtilis (Daniel, R. A., and J. Errington, 1993, DNA sequence of the murE-murD region of Bacillus subtilis 168. J. Gen. Microbiol. 139:361- 370; Henriques, A. O. de Lencaster, H. and P. J. Piggot, 1992, A Bacillus subtilis morphogene cluster that includes spoVE is homologous to the mra region of Escherichia coli. Biochimie. 74: 735-748). Compounds have been designed and synthesized that have inhibitory activity against the E. coli enzyme (Tanner, M.E., S. Vaganay, van Heijenoort, J., and D. Blanot, 1996, Phosphinate Inhibitors of the D-Glutamic Acid-Adding Enzyme of Peptidoglycan Biosynthesis. J. Org. Chem. 61: 1756-1760), although they do not have antibacterial activity. SUMMARY OF THE INVENTION Polynucleotides and polypeptides of Staphylococcus aureus MurD, an enzyme involved in bacterial cell wall biosynthesis are provided. The recombinant MurD enzyme is catalytically active in ATP- dependent D-glutamate addition reactions. The enzyme is used in in vitro assays to screen for antibacterial compounds that target cell wall biosynthesis. The invention includes the purified polynucleotides, purified enzymes encoded by the polynucleotides, and host cells expressing the recombinant enzyme. BRIEF DESCRIPTION OF THE DRAWINGS FIGS. 1A & IB. Nucleotide sequence and the predicted amino acid sequence of S. aureus murD. The amino acid sequence (SEQ ID NO:2) is presented in three-letter code below the nucleotide sequence (nucleotides 13 to 1363 of SEQ ID NO:l). FIGS. 2A & 2B. Alignment of the deduced amino acid sequence of S. aureus MurD with MurD homologs of E. coli (Eco) SEQ ID NO:3, H. influenzae (Hin) SEQ ID NO:4, B. subtilis (Bsu) SEQ ID NO:5 and S. pyogenes (Spy) SEQ ID NO:6. Single letters amino acids are used. Identical residues are indicated by boxes. Gaps are indicated by dashes. FIG. 3. Comparison of the murein consensus sequence with MurD of S. aureus (Sau). The murein consensus sequence (shown in bold) was generated by multiple alignments of murein genes murC, - D, -E, and -F from various bacterial genera (Eveland, S. S., D. L. Pompliano, and M. S. Anderson, 1997, Conditionally lethal Escherichia coli murein mutants contain point defects that map to regions conserved among murein and folyl poly-g-glutamate ligases: Identification of a ligase superfamily. Biochemistry. 36: 6223-6229). FIGS. 4A & 4B. Purification and catalytic activity of S. aureus MurD. The murD gene cloned into pET-15b was expressed in E. coli strain BL21(DE3)plysS and the recombinant protein was affinity purified and eluted in 100 mM imidazole and 0.5 ml fractions were collected and analyzed by SDS-PAGE (FIG. 4A) and assayed for MurD activity (FIG. 4B). Lane 1, Molecular weight markers; Lane2, uninduced cell lysate; lane 3, induced cell lysate; lanes 4-10 are fractions numbers 2-8. The MurD activities of fractions 2-8 are presented by the histogram. DETAILED DESCRIPTION OF THE INVENTION This invention provides polynucleotides and polypeptides of a cell wall biosynthesis gene from Staphytococcus aureus, referred to herein as MurD. The polynucleotides and polypeptides are used to further provide expression vectors, host cells comprising the vectors, probes and primers, antibodies against the MurD protein and polypeptides thereof, assays for the presence or expression of MurD and assays for the identification of modulators and inhibitors of MurD. Bacterial UDP-N-acetylmuramyl-L-alanine:D-glutamate ligase (MurD), a cytoplasmic peptidoglycan biosynthetic enzyme, catalyzes the ATP-dependent addition of D-glutamate to an alanyl residue of the UDP-N-acetylmuramyl-L-alanine precursor, generating the dipeptide. The murD gene was cloned from Staphylococcus aureus. Sequence analysis of the S. aureus murD gene revealed an open reading frame of 449 amino acids. The deduced amino acid sequence of S. aureus MurD is highly homologous to MurD from Escherichia coli, Haemophilus influenzae, Bacillus subtilis and Streptococcus pyogenes. Recombinant MurD protein from S. aureus was over-produced as His- tagged fusion protein in Escherichia coli host cells. The S. aureus MurD enzyme was purified to apparent homogeneity. The recombinant enzyme catalyzed the ATP-dependent addition of D-glutamate to the precursor sugar peptide. As used herein an "antagonist" or inhibitor is a compound or molecule that interacts with and inhibits or prevents a poiypeptide of MurD from catalyzing the ATP-dependent addition of D-glutamate to an alanyl residue of the UDP-N-acetylmuramyl-L-alanine precursor. As used herein a "modulator" is a compound or molecule that interacts with an aspect of cellular biochemistry to effect an increase or decrease in the amount of a poiypeptide of MurD present at the surface of a cell, or in the surrounding serum or media. The change in amount of the MurD poiypeptide can be mediated by the effect of a modulator on the expression of the protein, e.g., the transcription, translation, post-translational processing, translocation or folding of the protein, or by affecting a components) of cellular biochemistry that directly or indirectly participates in the expression of the protein. Alternatively, a modulator can act by accelerating or decelerating the turnover of the protein either by direct interaction with the receptor or by interacting with another component(s) of cellular biochemistry which directly or indirectly effects the change. Nucleic acids encoding murD from Staphylococcus aureus are useful in the expression and production of the S. aureus MurD protein. The nucleic acids are also useful in providing probes for detecting the presence of S. aureus. Polynucleotides A preferred aspect of the present invention is disclosed in FIGS. 1 A & IB and SEQ ID NO:l, an isolated polynucleotide encoding a MurD protein from Staphylococcus aureus, disclosed as follows: GAGTGCATTA AG ATGCTTAATT ATACAGGGTT AGAAAATAAA AATGTATTAG TTGTCGGTTT GGCAAAAAGT GGTTATGAAG CAGCTAAATT ATTAAGTAAA TTAGGTGCGA ATGTAACTGT CAATGATGGA AAAGACTTAT CACAAGATGC TCATGCAAAA GATTTAGAAT CTATGGGCAT TTCTGTTGTA AGTGGAAGTC ATCCATTAAC GTTGCTTGAT AATAATCCAA TAATTGTTAA AAATCCTGGA ATACCTTATA CAGTATCTAT TATTGATGAA GCAGTGAAAC GAGGTTTGAA AATTTTAACA GAAGTTGAGT TAAGTTATCT AATCTCTGAA GCACCAATCA TAGCTGTAAC GGGTACAAAT GGTAAAACGA CAGTTACTTC TCTAATTGGA GATATGTTTA AAAAAAGTCG CTTAACTGGA AGATTATCCG GCAATATTGG TTATGTTGCA TCTAAAGTAG CACAAGAAGT AAAGCCTACA GATTATTTAG TTACAGAGTT GTCGTCATTC CAGTTACTTG GAATCGAAAA GTATAAACCA CACATTGCTA TAATTACTAA CATTTATTCG GCGCATCTAG ATTACCATGA AAATTTAGAA AACTATCAAA ATGCTAAAAA GCAAATATAT AAAAATCAAA CGGAAGAGGA TTATTTGATT TGTAATTATC ATCAAAGACA AGTGATAGAG TCGGAAGAAT TAAAAGCTAA GACATTGTAT TTCTCAACTC AACAAGAAGT TGATGGTATT TATATTAAAG ATGGTTTTAT CGTTTATAAA GGTGTTCGTA TTATTAACAC TGAAGATCTA GTATTGCCTG GTGAACATAA TTTAGAAAAT ATATTAGCAG CTGTGCTTGC TTGTATTTTA GCTGGTGTAC CTATTAAAGC AATTATTGAT AGTTTAACTA CATTTTCAGG AATAGAGCAT AGATTGCAAT ATGTTGGTAC TAATAGAACT AATAAATATT ATAATGATTC CAAAGCAACA AACACGCTAG CAACACAGTT TGCCTTAAAT TCATTTAATC AACCAATCAT TTGGTTATGT GGTGGTTTGG ATCGAGGGAA TGAATTTGAC GAACTCATTC CTTATATGGA AAATGTTCGC GCGATGGTTG TATTCGGACA AACGAAAGCT AAGTTTGCTA AACTAGGTAA TAGTCAAGGG AAATCGGTCA TTGAAGCGAA CAATGTCGAA GACGCTGTTG ATAAAGTACA AGATATTATA GAACCAAATG ATGTTGTATT ATTGTCACCT GCTTGTGCGA GTTGGGATCA ATATAGTACT TTTGAAGAGC GTGGAGAGAA ATTTATTGAA AGATTCCGTG CCCATTTACC ATCTTATTAA AGGGTGTGAG The isolated nucleic acid molecule of the present invention can include a deoxyribonucleic acid molecule (DNA), which can be single (coding or noncoding strand) or double stranded, as well as synthetic DNA, such as a synthesized, single stranded polynucleotide. The isolated nucleic acid molecule of the present invention can also include a ribonucleic acid molecule (RNA). The present invention also relates to recombinant vectors and recombinant hosts, both prokaryotic and eukaryotic, which contain the substantially purified nucleic acid molecules disclosed throughout this specification. As used herein a "polynucleotide" is a nucleic acid of more than one nucleotide. A polynucleotide can be made up of multiple polynucleotide units that are referred to by description of the unit. For example, a polynucleotide can comprise within its bounds a polynucleotide(s) having a coding sequence(s), a polynucleotide(s) that is a regulatory region(s) and/or other polynucleotide units commonly used in the art. An "expression vector" is a polynucleotide having regulatory regions operably linked to a coding region such that, when in a host cell, the vector can direct the expression of the coding sequence. The use of expression vectors is well known in the art. Expression vectors can be used in a variety of host cells and, therefore, the regulatory regions are preferably chosen as appropriate for the particular host cell. A "regulatory region" is a polynucleotide that can promote or enhance the initiation or termination of transcription or translation of a coding sequence. A regulatory region includes a sequence that is recognized by the RNA polymerase, ribosome, or associated transcription or translation initiation or termination factors of a host cell. Regulatory regions that direct the initiation of transcription or translation can direct constitutive or inducible expression of a coding sequence. Polynucleotides of this invention contain full length or partial length sequences of the murD gene sequences disclosed herein. Polynucleotides of this invention can be single or double stranded. If single stranded, the polynucleotides can be a coding, "sense," strand or a complementary, "antisense," strand. Antisense strands can be useful as modulators of the gene by interacting with RNA encoding the MurD protein. Antisense strands are preferably less than full length strands having sequences unique or highly specific for RNA encoding the protein. The polynucleotides can include deoxyribonucleotides, ribonucleotides or mixtures of both. The polynucleotides can be produced by cells, in cell-free biochemical reactions or through chemical synthesis. Non- natural or modified nucleotides, including inosine, methyl-cytosine, deaza- guanosine, etc., can be present. Natural phosphodiester internucleotide linkages can be appropriate. However, polynucleotides can have non-natural linkages between the nucleotides. Non-natural linkages are well known in the art and include, without limitation, methylphosphonates, phosphorothioates, phosphorodithionates, phosphoroamidites and phosphate ester linkages. Dephospho-linkages are also known, as bridges between nucleotides. Examples of these include siloxane, carbonate, carboxymethyl ester, acetamidate, carbamate, and thioether bridges. "Plastic DNA," having, for example, N-vinyl, methacryloxytethyl, methacrylamide or ethyleneimine internucleotide linkages, can be used. "Peptide Nucleic Acid" (PNA) is also useful and resists degradation by nucleases. These linkages can be mixed in a polynucleotide. As used herein, "purified" and "isolated" are utilized interchangeably to stand for the proposition that the polynucleotides, proteins and polypeptides, or respective fragments thereof in question has been removed from its in vivo environment so that it can be manipulated by the skilled artisan, such as but not limited to sequencing, restriction digestion, site- directed mutagenesis, and subcloning into expression vectors for a nucleic acid fragment as well as obtaining the protein or protein fragment in pure quantities so as to afford the opportunity to generate polyclonal antibodies, monoclonal antibodies, amino acid sequencing, and peptide digestion. Therefore, the nucleic acids claimed herein can be present in whole cells or in cell lysates or in a partially purified or substantially purified form. A polynucleotide is considered purified when it is purified away from environmental contaminants. Thus, a polynucleotide isolated from cells is considered to be substantially purified when purified from cellular components by standard methods while a chemically synthesized nucleic acid sequence is considered to be substantially purified when purified from its chemical precursors. Polypeptides The present invention also relates to a substantially purified form of the MurD protein from Staphylococcus aureus, which is shown in FIGS. 1 A & IB and as set forth in SEQ ID NO:2, disclosed as follows: MetLeuAsnTyrThrGlyLeuGluAsnLysAsnVal euValValGlyLeuAlaLysSer Gly yrGluAlaAlaLysLeuLeuSerLysLeuGlyAlaAsnValThrValAsnAspGly LysAspLeuSerGlnAspAlaHisAlaLysAspLeuGluSerMetGlylleSerValVal SerGlySerHisProLeuThrLeuLeuAspAsnAsnProIlelleValLysAsnProGly IleProTyrThrValSerllelleAspGluAlaValLysArgGlyLeuLysIleLeuThr GluValGluLe Ser yrLe IleSerGluAlaProIlelleAlaValThrGlyThr sn GlyLysThrThrValThrSerLeuIleGlyAspMetPheLysLysSerArgLeuThrGly ArgLeuSerGlyAsnlleGlyTyrValAlaSerLysValAlaGlnGluValLysProThr AspTyrLeuValThrGluLeuSerSerPheGlnLeuLeuGlylleGluLys yrLysPro HisIleAlallelleThrAsnlle yrSerAlaHisLeuAspTyrHisGluAsnLeuGlu AsnTyrGlnAsnAlaLysLysGlnlleTyrLysAsnGlnThrGluGluAspTyrLeuIle CysAsnTyrHisGlnArgGlnVallleGluSerGluGluLeuLysAlaLysThrLeuTyr PheSerThrGlnGlnGluValAspGlylleTyrlleLysAspGlyPhelleValTyr ys GlyValArgllelleAsnThrGluAspLeuValLeuProGlyGluHisAsnLeuGluAsn Ile euAlaAlaValLeuAlaCysIleLeuAlaGlyValProIleLysAlallelleAsp SerLeuThrThrPheSerGlylleGluHisArgLeuGlnTyrValGlyThrAsnArgThr AsnLys yrTyrAsnAspSerLysAlaThrAsnThrLeuAlaThrGlnPheAlaLeuAsn SerPheAsnGlnProIlelleTrpLeuCysGlyGlyLeuAspArgGlyAsnGluPheAsp GluLeuIlePro yrMetGluAsnValArgAlaMetValValPheGlyGlnThrLysAla ysPheAlaLys euGlyAsnSerGlnGlyLysSerVallleGluAlaAsnAsnValGlu AspAlaValAspLysValGlnAspIlelleGluProAsnAspValValLeuLeuSerPro AlaCysAlaSerTrpAspGlnTyrSerThrPheGluGluArgGlyGluLysPhelleGlu ArgPheArgAlaHisLeuProSer yr The present invention also relates to biologically active fragments and mutant or polymorphic forms of MurD poiypeptide sequence as set forth as SEQ ID NO: 2, including but not necessarily limited to amino acid substitutions, deletions, additions, amino terminal truncations and carboxy- terminal truncations such that these mutations provide for proteins or protein fragments of diagnostic, therapeutic or prophylactic use and would be useful for screening for modulators, and/or antagonists of MurD function. Using the disclosure of polynucleotide and poiypeptide sequences provided herein to isolate polynucleotides encoding naturally occurring forms of MurD, one of skill in the art can determine whether such naturally occurring forms are mutant or polymorphic forms of MurD by sequence comparison. One can further determine whether the encoded protein, or fragments of any MurD protein, is biologically active by routine testing of the protein of fragment in a in vitro or in vivo assay for the biological activity of the MurD protein. For example, one can express N- terminal or C-terminal truncations, or internal additions or deletions, in host cells and test for their ability to catalyzing the ATP-dependent addition of D- glutamate to an alanyl residue of the UDP-N-acetylmuramyl-L-alanine precursor. It is known that there is a substantial amount of redundancy in the various codons which code for specific amino acids. Therefore, this invention is also directed to those DNA sequences encode RNA comprising alternative codons which code for the eventual translation of the identical amino acid, as shown below: A=Ala=Alanine: codons GCA, GCC, GCG, GCU C=Cys=Cysteine: codons UGC, UGU D=Asp=Aspartic acid: codons GAC, GAU E=Glu=Glutamic acid: codons GAA, GAG F=Phe=Phenylalanine: codons UUC, UUU G=Gly=Glycine: codons GGA, GGC, GGG, GGU H=His =Histidine: codons CAC, CAU I=Ile =Isoleucine: codons AUA, AUC, AUU K=Lys=Lysine: codons AAA, AAG L=Leu=Leucine: codons UUA, UUG, CUA, CUC, CUG, CUU M=Met=Methionine: codon AUG N=Asp=Asparagine: codons AAC, AAU P=Pro=Proline: codons CCA, CCC, CCG, CCU Q=Gln=Glutamine: codons CAA, CAG R=Arg=Arginine: codons AGA, AGG, CGA, CGC, CGG, CGU S=Ser=Serine: codons AGC, AGU, UCA, UCC, UCG, UCU T=Thr=Threonine: codons ACA, ACC, ACG, ACU V=Val=Valine: codons GUA, GUC, GUG, GUU W=Trp=Tryptophan: codon UGG Y=Tyr=Tyrosine: codons UAC, UAU Therefore, the present invention discloses codon redundancy which can result in differing DNA molecules expressing an identical protein. For purposes of this specification, a sequence bearing one or more replaced codons will be defined as a degenerate variation. Also included within the scope of this invention are mutations either in the DNA sequence or the translated protein which do not substantially alter the ultimate physical properties of the expressed protein. For example, substitution of valine for leucine, arginine for lysine, or asparagine for glutamine may not cause a change in functionality of the poiypeptide. However, any given change can be examined for any effect on biological function by simply assaying for the ability to catalyze the ATP- dependent addition of D-glutamate to an alanyl residue of the UDP-N- acetylmuramyl-L-alanine precursor as compared to an unaltered MurD protein. It is known that DNA sequences coding for a peptide can be altered so as to code for a peptide having properties that are different than those of the naturally occurring peptide. Methods of altering the DNA sequences include but are not limited to site directed mutagenesis. Examples of altered properties include but are not limited to changes in the affinity of an enzyme for a substrate or a receptor for a ligand. As used herein, a "biologically active equivalent" or "functional derivative" of a wild-type MurD possesses a biological activity that is substantially similar to the biological activity of a wild type MurD. The term "functional derivative" is intended to include the "fragments," "mutants," "variants," "degenerate variants," "analogs" and "homologues" or to "chemical derivatives" of a wild type MurD protein. The term "fragment" is meant to refer to any poiypeptide subset of wild- type MurD. The term "mutant" is meant to refer to a molecule that may be substantially similar to the wild-type form but possesses distinguishing biological characteristics. Such altered characteristics include but are in no way limited to altered substrate binding, altered substrate affinity and altered sensitivity to chemical compounds affecting biological activity of the MurD or MurD functional derivative. The term "variant" is meant to refer to a molecule substantially similar in structure and function to either the entire wild-type protein or to a fragment thereof. A molecule is "substantially similar" to a wild-type MurD-like protein if both molecules have substantially similar structures or if both molecules possess similar biological activity. Therefore, if the two molecules possess substantially similar activity, they are considered to be variants even if the structure of one of the molecules is not found in the other or even if the two amino acid sequences are not identical. The term "analog" refers to a molecule substantially similar in function to either the full-length MurD protein or to a biologically active fragment thereof. As used herein in reference to a MurD gene or encoded protein, a "polymorphic" MurD is a MurD that is naturally found in the population of Staphlocooci at large. A polymorphic form of MurD can have a different nucleotide sequence from the particular MurD genes and proteins disclosed herein. However, because of silent mutations, a polymorphic MurD gene can encode the same or different amino acid sequence as that disclosed herein. Further, some polymorphic forms MurD will exhibit biological characteristics that distinguish the form from wild-type MurD activity, in which case the polymorphic form is also a mutant. A protein or fragment thereof is considered purified or isolated when it is obtained at least partially free from it's natural environment at a concentration at least about five-fold to ten-fold higher than that found in nature. A protein or fragment thereof is considered substantially pure if it is obtained at a concentration of at least about 100-fold higher than that found in nature. A protein or fragment thereof is considered essentially pure if it is obtained at a concentration of at least about 1000- fold higher than that found in nature. We most prefer proteins that have been purified to homogeneity, that is, at least 10,000 -100,000 fold. Probes and Primers Polynucleotide probes comprising full length or partial sequences of SEQ ID NO: 1 can be used to determine whether a cell or sample contains S. aureus MurD DNA or RNA. The effect of modulators that effect the transcription of the S. aureus murD gene can be studied via the use of these probes. A preferred probe is a single stranded antisense probe having at least the full length of the coding sequence of MurD. It is also prefened to use probes that have less than the full length sequence, and contain sequences highly specific for S. aureus murD DNA or RNA. The identification of a sequence(s) for use as a specific probe is well known in the art and involves choosing a sequence(s) that is unique to the target sequence, or is highly specific thereto. It is prefened that polynucleotides that are probes have at least about 25 nucleotides, more preferably about 30 to 35 nucleotides. The longer probes are believed to be more specific for S. aureus murD genes and RNAs and can be used under more stringent hybridization conditions. Longer probes can be used but can be more difficult to prepare synthetically, or can result in lower yields from a synthesis. Examples of sequences that are useful as probes or primers for S. aureus murD polynucleotides are Primer A (sense) 5'-GAG TGC ATT AAG ATG CTT AAT TAT ACA GGG TTA G-3' and Primer B (antisense) 5'-CTC ACA CCC TTT AAT AAG ATG GTA AAT GGG CAC GG-3'. These primers are the first 34 (A) and the complement of the last 35 (B) nucleotides of SEQ ID NO: 1. However, one skilled in the art will recognize that these are only a few of the useful probe or primer sequences that can be derived from SEQ ID NO:l . Polynucleotides having sequences that are unique or highly specific for S. aureus murD can be used as primers in amplification reaction assays. These assays can be used in tissue typing as described herein. Additionally, amplification reactions employing primers derived from murD sequences can be used to obtain amplified S. aureus murD DNA using the murD DNA of the cells as an initial template. The murD DNA so obtained can be a mutant or polymorphic form of S. aureus murD that differs from SEQ ID NO:l by one or more nucleotides of the MurD open reading frame or sequences flanking the ORF. The differences can be associated with a non-defective naturally occurring form or with a defective form of MurD. Thus, polynucleotides of this invention can be used in identification of various S. aureus murD genes or the detection of an organism having a S. aureus murD gene. Many types of amplification reactions are known in the art and include, without limitation, Polymerase Chain Reaction, Reverse Transcriptase Polymerase Chain Reaction, Strand Displacement Amplification and Self-Sustained Sequence Reaction. Any of these or like reactions can be used with primers derived from SEQ ID NO:l. Expression of MurD A variety of expression vectors can be used to express recombinant MurD in host cells. Expression vectors are defined herein as DNA sequences that are required for the transcription of cloned DNA and the translation of their mRNAs in an appropriate host. Such vectors can be used to express bacteria DNA in a variety of hosts such as bacteria, bluegreen algae, plant cells, insect cells and animal cells. Specifically designed vectors allow the shuttling of DNA between hosts such as bacteria-yeast or bacteria-animal cells. An appropriately constructed expression vector should contain: an origin of replication for autonomous replication in host cells, selectable markers, a limited number of useful restriction enzyme sites, a potential for high copy number, and active promoters. A promoter is defined as a DNA sequence that directs RNA polymerase to bind to DNA and initiate RNA synthesis. A strong promoter is one which causes mRNAs to be initiated at high frequency. Expression vectors can include, but are not limited to, cloning vectors, modified cloning vectors, specifically designed plasmids or viruses. In particular, a variety of bacterial expression vectors can be used to express recombinant MurD in bacterial cells. Commercially available bacterial expression vectors which are suitable for recombinant MurD expression include, but are not limited to pQE (Qiagen), pETlla or pETlδb (Novagen), lambda gtll (Invitrogen), and pKK223-3 (Pharmacia). Alternatively, one can express murD DNA in cell-free transcription-translation systems, or murD RNA in cell-free translation systems. Cell-free synthesis of MurD can be in batch or continuous formats known in the art. One can also synthesize MurD chemically, although this method is not preferred. A variety of host cells can be employed with expression vectors to synthesize MurD protein. These can include E. coli, Bacillus, andSalmonella. Insect and yeast cells can also be appropriate. Following expression of MurD in a host cell, MurD polypeptides can be recovered. Several protein purification procedures. are available and suitable for use. MurD protein and polypeptides can be purified from cell lysates and extracts, or from culture medium, by various combinations of, or individual application of methods including ultrafiltration, acid extraction, alcohol precipitation, salt fractionation, ionic exchange chromatography, phosphocellulose chromatography, lecithin chromatography, affinity (e.g., antibody or His-Ni) chromatography, size exclusion chromatography, hydroxylapatite adsorption chromatography and chromatography based on hydrophobic or hydrophillic interactions. In some instances, protein denaturation and refolding steps can be employed. High performance liquid chromatography (HPLC) and reversed phase HPLC can also be useful. Dialysis can be used to adjust the final buffer composition. The MurD protein itself is useful in assays to identify compounds that modulate the activity of the proteins ~ including compounds that inhibit the activity of the protein. The MurD protein is also useful for the generation of antibodies against the protein, structural studies of the protein, and structure/function relationships of the protein. Modulators and Inhibitors of MurD The present invention is also directed to methods for screening for compounds or molecules which modulate or inhibit the expression of DNA or RNA encoding a MurD protein. Compounds or molecules which modulate or inhibit MurD can be DNA, RNA, peptides, proteins, or non-proteinaceous organic compounds or molecules. Compounds that modulate the expression of DNA or RNA encoding MurD or are inhibitors of the biological function thereof can be detected by a variety of assays. The assay can be a simple "yes/no" assay to determine whether there is a change in expression or function. The assay can be made quantitative by comparing the expression or function of a test sample with the levels of expression or function in a standard sample, that is, a control. Kits containing MurD, antibodies to MurD, or modified MurD can be prepared by known methods for such uses. The DNA molecules, RNA molecules, recombinant protein and antibodies of the present invention can be used to screen and measure levels of MurD. The recombinant proteins, DNA molecules, RNA molecules and antibodies lend themselves to the formulation of kits suitable for the detection and anaysis of MurD. Such a kit would comprise a compartmentalized carrier suitable to hold in close confinement at least one container. The earner would further comprise reagents such as recombinant MurD or anti- MurD antibodies suitable for detecting MurD. The carrier can also contain a means for detection such as labeled antigen or enzyme substrates or the like. Pharmaceutical Compositions Pharmaceutically useful compositions comprising inhibitors of MurD can be formulated according to known methods such as by the admixture of a pharmaceutically acceptable carrier. Examples of such carriers and methods of formulation can be found in Remington's Pharmaceutical Sciences. To form a pharmaceutically acceptable composition suitable for effective administration, such compositions will contain an effective amount of the inhibitor. Therapeutic or diagnostic compositions of the invention are administered to an individual in amounts sufficient to treat or diagnose disorders. The effective amount can vary according to a variety of factors such as the individual's condition, weight, sex and age. Other factors include the mode of administration. The appropriate amount can be determined by a skilled physician The pharmaceutical compositions can be provided to the individual by a variety of routes such as subcutaneous, topical, oral and intramuscular. The term "chemical derivative" describes a molecule that contains additional chemical moieties which are not normally a part of the base molecule. Such moieties can improve the solubility, half-life, absorption, etc. of the base molecule. Alternatively the moieties can attenuate undesirable side effects of the base molecule or decrease the toxicity of the base molecule. Examples of such moieties are described in a variety of texts, such as Remington's Pharmaceutical Sciences. Compounds identified according to the methods disclosed herein can be used alone at appropriate dosages. Alternatively, co- administration or sequential administration of other agents can be desirable. The present invention also provides a means to obtain suitable topical, oral, systemic and parenteral pharmaceutical formulations for use in the methods of treatment of the present invention. The compositions containing compounds or molecules identified according to this invention as the active ingredient can be administered in a wide variety of therapeutic dosage forms in conventional vehicles for administration. For example, the compounds can be administered in such oral dosage forms as tablets, capsules (each including timed release and sustained release formulations), pills, powders, granules, elixirs, tinctures, solutions, suspensions, syrups and emulsions, or by injection. Likewise, they can also be administered in intravenous (both bolus and infusion), intraperitoneal, subcutaneous, topical with or without occlusion, or intramuscular form, all using forms well known to those of ordinary skill in the pharmaceutical arts. Advantageously, compounds of the present invention can be administered in a single daily dose, or the total daily dosage can be administered in divided doses of two, three or four times daily. Furthermore, compounds for the present invention can be administered in intranasal form via topical use of suitable intranasal vehicles, or via transdermal routes, using those forms of transdermal skin patches well known to those of ordinary skill in that art. To be administered in the form of a transdermal delivery system, the dosage administration will, of course, be continuous rather than intermittent throughout the dosage regimen. For combination treatment with more than one active agent, where the active agents are in separate dosage formulations, the active agents can be administered concmrently, or they each can be administered at separately staggered times. The dosage regimen utilizing the compounds of the present invention is selected in accordance with a variety of factors including type, species, age, weight, sex and medical condition of the patient; the severity of the condition to be treated; the route of administration; the renal, hepatic and cardiovascular function of the patient; and the particular compound thereof employed. A physician or veterinarian of ordinary skill can readily determine and prescribe the effective amount of the drug required to prevent, counter or arrest the progress of the condition. Optimal precision in achieving concentrations of drug within the range that yields efficacy without toxicity requires a regimen based on the kinetics of the drug's availability to target sites. This involves a consideration of the distribution, equilibrium, and elimination of a drug. The following examples are presented by the way of illustration and, because various other embodiments will be apparent to those in the art, the following is not to be construed as a limitation on the scope of the invention: EXAMPLE 1 General Materials and Methods All reagents were purchased from Sigma Chemical Co, St. Louis, MO, unless otherwise indicated. UDP-N-acetylmuramyl-L- alanine was synthesized and purified by a method known in the art (Jin, H., Emanuele, J. J., Jr., Fairman, R., Robertson, J. G., Hail, M. E., Ho, H.-T., Falk, P. and Villafranca, J. J, 1996, Structural studies of Escherichia coli UDP-N-acetylmuramate: L-alanine ligase, Biochemistry 35: 14423-14431). DNA manipulations reagents and techniques. Restriction endonucleases and T4 ligase were obtained from Gibco-BRL. Agarose gel electrophoresis and plasmid DNA preparations were performed according to published procedures (Sambrook, J., E. F. Fritsch, and T. Maniatis, 1989, Molecular cloning: a L, Laboratory Manual, 2nd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory). Recombinant plasmids containing S. aureus murD were propagated in E. coli DH5a (Gibco-BRL, Rockville, MD) prior to protein expression in E. coli BL21(DE3)/plysS (Novagen, Madison, WI). SDS-PAGE was performed with precast gels (Novagen). DNA sequences were determined using an automated ABI Prism DNA sequencer (Perkin-Elmer ABI, Foster City, CA). EXAMPLE 2 Cloning' of Staphylococcus aureus murD Screening of a Staphylococcus aureus genomic library. In overview, the murD gene from E. coli and B. subtilis is known to reside in a cluster of cell division and peptidoglycan biosynthetic genes. The S. aureus cell division gene ftsZ was used as probe since its DNA sequence is known, and its location is proximal to the murD gene in E. coli and B. subtilis. An analogous region of cell division and peptidoglycan biosynthetic genes was identified in the genome of S. aureus by Southern hybridization using the S. aureus ftsZ gene. Once this region was cloned, the murD gene was located by chromosome walking and sequence analysis. First, the ftsZ gene was cloned from S. aureus strain R27 by PCR using primers based on the sequence deposited under GenBank accession number U06462. Using the random priming method, the ftsZ gene was radiolabelled to high specific activity and used as a probe to screen S. aureus a phagemid libraries. Screening of a cosmid library prepared from strain R27 failed to detect fcsZ-hybridizing clones— perhaps due to toxicity associated with overexpression of the cloned genes. A commercially available lambda phage packaged library of S. aureus genomic DNA in the lambda Zap II vector was obtained (Stratagene, La Jolla, CA). E. coli XLlBlue MRF' cells were grown to a density of Aβoo = 0-5, mixed with appropriate dilutions of the lambda phage in 10 nιM MgS04, and incubated for 20 minutes at 37°°C. The cells were then plated onto NZY plates, and incubated overnight at 37°°C. Some 35,000 plaques were screened by filter lift assay using radiolabelled ftsZ as a probe. Filters were denatured in 0.5 N NaOH containing 1.5 M NaCl, neutralized in 0.5 M Tris, pH 7.5, containing 1.5 M NaCl, and rinsed in 5X SSC. DNA was crosslinked to the filters by UV light using a Stratalinker (Stratagene). Filters were hybridized in 5X SSC, 10% dextran sulfate, 50 mM phosphate buffer (0.685 M NaH 2 P0 and 0.315 M Na 2 HP0 ), containing 0.1% SDS, IX Denhardt's solution, and 100 mg/ml salmon sperm DNA in the presence of 1 X 10 cpm/ml of radiolabelled ftsZ probe. The hybridization probe was prepared from ftsZ DNA using the random priming method (Gibco- BRL). Hybridizations were performed overnight at 42°°C in a Micro-4 Hybridization oven (Hybaid, Middlesex. UK) Washes were performed twice at room temperature in 2X SSC containing 0.1% SDS, twice at 42°°C in 2X SSC containing 0.1% SDS, and twice at 42°°C in 0.2X SSC containing 0.1% SDS. Finally, filters were exposed overnight at -80°°C to X-Omat AR film (Kodak, Rochester, NY). Library DNA inserts were amplified by PCR using Taq Plus Long (Stratagene) with T3 and T7 as primers (Gibco-BRL). PCR products were digested with Sau3AI and cloned into pUC18 for sequencing. Thirteen plaques (of about 35000 screened) hybridized to the ftsZ probe. From the 13 positive plaques, two overlapping clones (designated 2A and 2B) containing ftsZ and encompassing 12 kb of contiguous sequence were further analyzed. Clones 2A and 2B were partially digested with Sau3AI and the resultant DNA fragments of average size 1-2 kb were randomly cloned into pUClδ and sequenced. The sequences of several clones in this sub-library overlapped to reveal a contigous cDNA with an open reading frame (ORF) of 449 amino acids with strong homology to the murD genes of B. subtilis (Daniel, R. A., and J. Errington, 1993, DNA sequence of the murE-murD region of Bacillus subtilis 168. J. Gen. Microbiol. 139:361-370; Henriques, A. O. de - 20 - Lencaster, H. and P. J. Piggot. 1992, A Bacillus subtilis morphogene cluster that includes spoVE is homologous to the mra region of Escherichia coli. Biochimie. 74: 735-748) and E. coli (Ikeda, M., M. Wachi, F. Ishino, and M. Matsuhashi, 1990, Nucleotide sequence involving murD and an open reading frame ORF-Y spacing murF and ftsW in Escherichia coli. Nucleic Acids Res. 18:1058; Mengin-Lecreulx, D., C Parquet, L. Desviat, J. Pla, B. Flouret, J. Ayala and J. van Heijenoort. 1989, Organization of the murE-murG region of Escherichia coli: Identification of the murD gene encoding the D-glutamic-acid- adding enzyme. J. Bacteriol. 171: 6126-6134). From the overlapping sequence information, the contiguous murD sequence was amplified as described in Example 4. EXAMPLE 3 Sequence analvsis of Staohlcoccus aureus murD The nucleotide sequence of murD, determined in both orientations, from S. aureus strain R27 and the deduced amino acid sequence is depicted in FIGS. 1A &1B. Sequence comparison using the BLAST (1) algorithm against the GenBank data base showed that, to varying degrees, the cloned region is homologous (% similar, % identical) to murD genes from E.coli (54%, 32%), H. influenzae (55%, 32%), B. subtilis (65%, 47%) and S. pyogenes (66%, 47%). In addition to the several regions of homology that are conserved among MurD proteins from both Gram-positive and Gram- negative bacteria (FIGS. 2A & 2B), there are at least two regions that are particularly conserved among MurD proteins of Gram-negative bacteria. The first region is amino acid residues ValLysAsnProGlylleProTyr (codons 76-83 of S. aureus murD , SEQ ID NO: 2) and the second region is amino acid residues GlyGlyLeuAspArgGlyAsnGluPheAsp (codons 351-360 of S. aureus murD , SEQ ID NO: 2). Multiple sequence alignments of MurC (Ikeda, M., M. Wachi, H. K. Jung, F. Ishino, and M. Matsuhashi, 1990, Nucleotide sequence involving murG and murC in the mra gene cluster of Escherichia coli. Nucleic Acids Res. 18:4014), MurD, MurE (Tao, J.S, and E. E., Ishiguro, 1989, Nucleotide sequence of the murE gene of Escherichia coli. Can. J. Microbiol. 35:1051-1054), and MurF (Parquet, C, D. Mengin-Lecreulx, B. Flouret, D. Mengin-Lecreulx, and J. van Heijenoort, 1989, Nucleotide sequence of the murF gene encoding the UDP-MurNAc-pentapeptide synthetase of Escherichia coli., Nucleic Acids Res. 17:5379) proteins from several bacterial genera revealed four regions of homology with certain residues conserved amongst Mur ligases of both Gram-positive and Gram-negative bacteria (Eveland, S. S., D. L. Pompliano, and M. S. Anderson, 1997, Conditionally lethal Escherichia coli murein mutants contain point defects that map to regions conserved among murein and folyl poly-g-glutamate ligases: Identification of a ligase superfamily. Biochemistry, 36: 6223-6229, Ikeda, M., M. Wachi, H. K. Jung, F. Ishino, and M. Matsuhashi, 1990, Homology among MurC, MurD, MurE and MurF proteins in Escherichia coli and that between E. coli murG and a possible murG protein in Bacillus subtilis. J. Gen. Appl. Microbiol. 36: 179-187). The homologous regions may correlate with the catalytic functions of these enzymes (Eveland, et al., 1997). Most notable is the putative ATP binding region I that was found in MurF (Parquet, C, D. Mengin-Lecreulx, B. Flouret, D. Mengin-Lecreulx, and J. van Heijenoort, 1989, Nucleotide sequence of the murF gene encoding the UDP-MurNAc-pentapeptide synthetase of Escherichia coli., Nucleic Acids Res. 17:5379) and is also conserved in S. aureus MurD protein (codons 117 to 124, FIGS. 1 and 2). While region I is an ATP-binding domain (Ikeda, et al., 1990), the function of the other homologous regions is unknown. Of these three other regions, only two of them appear to be present in S. aureus (FIG. 3). Region III, which contains two contiguous Asp residues, is not conserved in S. aureus MurD, although it is present in MurD of B. subtilis. Within regions I, II, and IV, the specific residues conserved in the known murein ligases are also present in S. aureus MurD (FIG. 3). EXAMPLE 4 Overexpression. purification and enzymatic activity of Staphylococcus aureus MurD murD was cloned from S. aureus strain R27 by using Taq Plus Long (Stratagene) in polymerase chain reactions (PCR). The primers used were as follows: 5'-GAG TGC ATT AAG GAA TTC CAT ATG CTT AAT TAT ACA GGG TTA G-3' (nucleotides 1 to 34 of SEQ ID NO:l) and 5'-CTC ACA CCC TGG ATC CTT AAT AAG ATG GTA AAT GGG CAC GG-3' (the complement of the last 35 nucleotides of SEQ ID NO:l). A PCR product of the expected size of murD coding region was purified using a Promega PCR-Prep column, digested with Ndel and BamHI, and cloned between the Ndel and BamHI sites of the expression vector pET-15b (Novagen) to create plasmid pSauMurD. The plasmid pSauMurD has been deposited with the American Type Culture Collection on October 31, 1997 under the terms of the Budapest Treaty for the Deposit of Microorganisms and has been designated as ATCC 98576. The deposited material is provided as a convenience and is not an admission that the deposited material is required to describe or practice the invention. The sequence of the polynucleotide of the deposit, and the encoded amino acid sequence, are incorporated herein by reference and are controlling in the event of a conflict with any description of the sequences provided in this specification or the associated drawings. A license may be required to make, use, sell or offer to sell the polynucleotide of the deposit or a protein of the amino acid sequence encoded by the polynucleotide. No such license is granted herein. The pET-15b vector incorporates the 6xHistidine-tag into the protein construct to allow rapid purification of MurD by affinity chromatography. The pET (Plasmids for Expression by T7 RNA polymerase) plasmids are derived from pBR322 and designed for protein over-production in E. coli. The vector pET-15b contains the ampicillin resistance gene, ColEl origin of replication in addition to T7 phage promoter and terminator. The T7 promoter is recognized by the phage T7 RNA polymerase but not by the E. coli RNA polymerase. A host E coli strain such as BL21(DE3)pLysS is engineered to contain integrated copies of T7 RNA polymerase under the control of lacUVδ that is inducible by IPTG. Production of a recombinant proteins such as S.aureus MurD in the E. coli strain BL21(DE3)pLysS occurs after expression of T7RNA polymerase is induced. The pSauMurD plasmid was introduced into the host strain BL21 DE3/pLysS (Novagen) for expression of His-tagged murD. Colonies were grown at 37°C in 100 ml of LB broth containing 100 mg/ml ampicillin and 32 μg/ml chloramphenicol. When cultures reached a cell density of AβQQ=0.5, cells were pelleted and then resuspended in M9ZB medium (Novagen) containing 1 mM IPTG. Cells were induced for 3 h at 30°C, pelleted at 3000#, and frozen at -80°C. Cultures containing either the recombinant plasmid pSauMurD or the control plasmid vector, pET-15b were grown at 30°C and induced with IPTG. Cells transformed with pSauMurD contained an inducible protein of approximately 52 kDa, conesponding to the expected size of S. aureus MurD protein as shown by SDS-PAGE (FIG. 4A, lane 3). There were no detectable protein bands after induction of cells transformed with the control plasmid vector, pET- 15b. Purification of recombinant MurD enzvme The cell pellet from 100 ml of induced culture prepared as described above was resuspended in 10 ml BT buffer (50 mM bis-tris- propane, pH 8.0, containing 100 mM potassium chloride and 1% glycerol) at 4°C. Cell lysate, prepared by several cycles of freezing and thawing, was pushed through a 20 gauge needle to shear the genomic DNA. After centrifugation, the supernatant was mixed with 15 ml of freshly prepared Talon resin and incubated for 30 min at room temp. The resin was washed twice by centrifugation with 25 ml of BT buffer at room temperature. Finally, the resin loaded into a column and washed with 20 ml of BT, pH 7.0, containing 5 mM imidazole. Protein was eluted with 20 ml of BT buffer pH 8.0, containing 100 mM imidazole. Fractions (0.5 ml) were collected and assayed for MurD activity. Active fractions were pooled and dialyzed in 100 mM MOPS, pH 7.5, using a Slide-A-Lyzer (Pierce, Rockford, IL). Assay for activity of MurD enzyme. The ATP-dependent MurD activity was assayed by monitoring the formation of product ADP using the pyruvate kinase and lactate dehydrogenase coupled enzyme assay. The reaction was monitored spectrophotometrically. Typically, the assay contained 100 mM BIS-TRIS-propane, pH 8.0, 200 μM NADH, 1 mM ATP, 20 mM PEP, 5 mM MgCl2, 1 mM DTT, 125 μM UDP-N-acetyl-muramyl-L-alanine, 1 mM D-glutamate, 33 units/ml of pyruvate kinase and 1660 units/ml of lactate dehydrogenase in a final volume of 200 or 400 μL The mixture was incubated at 25°C for 5 min and the reaction initiated by the addition of 1-10 μg of MurD. ADP formation was monitored by the decrease in absorbance at 340 nm as a function of time using a Molecular Devices SpectramaxPlus microtiterplate spectrophotomer (for 200 μl assays) or a Hewlett-Packard HP8452A spectrophotometer equipped with a circulating water bath (for 400 μl assays). Rates were calculated from the linear portions of the progress curves using the extinction coefficient for NADH, e = 6220 cm ~ l M"l. One unit of MurD activity is equal to 1 μmol of ADP formed per min at 25°C. FIG. 4B, shows that MurD activity co-eluted with a -52 kDa protein. For the fusion protein, the peak fraction had a specific activity of 5 unit/mg at 25 °C. After thrombin cleavage and further purification, the non-fusion MurD has a specific activity of 2.0 U/mg at 25°C. . Assays have been conducted using 120 and 350 μM UDP-N- acetyl-muramyl-L-alanine. However, it has been observed that at the higher level of 350 μM UDP-N-acetyl-muramyl-L-alanine, substrate inhibition of the E. coli MurD occurs. For example, the specific activity of the E. coli enzyme can drop into the area of 4.5 units/mg. It is unclear whether the S. aureus enzyme is similarly inhibited. EXAMPLE 5 Screening for inhibitors of MurD One assay for the measurement of the activity of MurD is provided in Example 5. That assay, and other assays for MurD activity can be adapted for screening assays to detect inhibitors of MurD. For inhibition studies, inhibitors in DMSO are added at the desired concentration to the assay mixture. In a separate, control reaction, only DMSO is added to the assay mixture. The reactions are initiated by the addition of enzyme (MurD). Rates were calculated as described above. Relative activities were calculated from the equation 1: relative activity = rate with inhibitor/rate without inhibitor. (1) Inhibition constant (IC50) values were determined from a range of inhibitor concentrations and calculated from the equation 2 using Sigma Plot (Jandel Scientific). relative activity= 1/(1 + [TJ/IC50) (2) We prefer inhibitors of MurD that result in relative activities of the MurD enzyme of at least less than 75%, more preferably, 25-50% or 10-25%. We most prefer inhibitors resulting in relative activities of less than 20%, particularly less than 10% of the activity or Mur D in the absence of the inhibitor. We also prefer inhibitors that effectively lower the relative activity of MurD when present at very low levels. EXAMPLE 6 Pharmaceutical compositions An appropriate amount of an inhibitor of MurD is formulated in a pharmaceutically acceptable carrier, in an appropriate dosage form. EXAMPLE 7 Therapy using inhibitors of MurD A patient presenting with an indication of infection with a microorganism susceptible to inhibitors of MurD, e.g. , gram positive organisms, including S. aureus, can be treated by administration of inhibitors of MurD. Physicians skilled in the art are familiar with administering therapeutically effective amounts of inhibitors of microbial enzymes. Such skilled persons can readily determine an appropriate dosing scheme to achieve a desired therapeutic effect. REFERENCES Altschul, S. F., W. Gish, W. Miller, E. Myers, and D. J. Lipman, 1990, Basic local alignment search tool. J. Mol. Biol. 215:403- 410. Blanot, D., A. Kretsovali, M. Abo-Ghalia, D. Mengin- Lecreulx, and J. van Heijenoort, 1983, Synthesis of analogues of precusors of bacterial peptidoglycan. p. 311-314. In peptides. Blaha, K. and P. Malon, eds. PP311-314. Walter de Gryter and Co. Berlin, New York. Daniel, R. A., and J. Errington, 1993, DNA sequence of the murE-murD region of Bacillus subtilis 168, J. Gen. Microbiol. 139:361- 370. Eveland, S. S., D. L. Pompliano, and M. S. Anderson, 1997, Conditionally lethal Escherichia coli murein mutants contain point defects that map to regions conserved among murein and folyl poly-g- glutamate ligases: Identification of a ligase superfamily. Biochemistry, 36: 6223-6229. Flouret, B., D. Mengin-Lecreulx, and J. van Heijenoort, 1981, Reverse-phase high-pressure liquid chromatography of Uridine Diphosphate N-Acetylmuramyl peptide precursors of bacterial cell wall peptidoglycan, Anal. Biochem. 114:59-63. Henriques, A. O. de Lencaster, H. and P. J. Piggot, 1992, A Bacillus subtilis morphogene cluster that includes spoVE is homologous to the mra region of Escherichia coli. Biochimie. 74: 735-748. Ikeda, M., M. Wachi, F. Ishino, and M. Matsuhashi, 1990, Nucleotide sequence involving murD and an open reading frame ORF-Y spacing murF and ftsW in Escherichia coli. Nucleic Acids Res. 18:1058. Ikeda, M., M. Wachi, H. K. Jung, F. Ishino, and M. Matsuhashi, 1990, Nucleotide sequence involving murG and murC in the mra gene cluster of Escherichia coli. Nucleic Acids Res. 18:4014. Ikeda, M., M. Wachi, H. K. Jung, F. Ishino, and M. Matsuhashi, 1990, Homology among MurC, MurD, MurE and MurF proteins in Escherichia coli and that between E. coli murG and a possible murG protein in Bacillus subtilis. J. Gen. Appl. Microbiol. 36: 179-187. Ito, E. and J. L. Strominger, 1962, Enzymatic synthesis of the peptide in bacterial uridine nucleotides: Enzymatic addition of L- alanine, D-glutamic acid, and L-lysine. J. Biol. Chem. 237: 2689-2695. Ito E. and J. L. Strominger, 1973, Enzymatic synthesis of the peptide in bacterial uridine nucleotides: Comparative biochemistry, J. Biol. Chem. 248: 3131-3136. Jin, H., Emanuele, J. J., Jr., Fairman, R., Robertson, J. G., Hail, M. E„ Ho, H.-T., Falk, P. and Villafranca, J. J., 1996, Structural studies of Escherichia coli UDP-N-acetylmuramate: L- alanine ligase, Biochemistry 35: 14423-14431. Lugtenberg, E. J. J., 1972, Studies on Escherichia coli enzymes involved in the synthesis of Uridine Diphosphate-N-Acetyl- Muramyl-pentapeptide. J. Bacteriol. 110:26-34. Mengin-Lecreulx, D., B. Flouret, and J. van Heijenoort, 1982, Cytoplasmic steps of peptidoglycan synthesis in Escherichia coli. J. Bacteriol. 151: 1109-1117. Mengin-Lecreulx, D., C Michaud, C. Richaud, D. Blanot and J. van Heijenoort, 1988, Incorporation of LL-diaminopimelic acid into peptidoglycan of Escherichia coli mutants lacking diaminopimelate epimerase encoded by dapF, J. Bacteriol. 170:2031-2039. Mengin-Lecreulx, D., C Parquet, L. Desviat, J. Pla, B. Flouret, J. Ayala and and J. van Heijenoort, 1989, Organization of the murE-murG region of Escherichia coli: Identification of the murD gene encoding the D-glutamic-acid-adding enzyme, J. Bacteriol. 171: 6126- 6134. Mengin-Lecreulx, D. and J. van Heijenoort, 1990, Nucleotide sequence of the murD gene encoding the UDP-MurNAc-L- Ala-D-Glu synthetase of Escherichia coli. Nucleic Acids Research 18:183. Michaud, C. D. Blanot, B. Flouret, and J. van Heijenoort, 1987, Partial purification and specificity studies of the D-glutamate- adding and D-alanyl-D-alanine-adding enzymes from Escherichia coli K12. Eur. J. Biochem. 166: 631-637. Michaud, C. , C, Parquet, B. Flouret, D. Blanot, and J. van Heijenoort, 1990, Revised interpretation of the sequence containing the murE gene encoding the UDP-N-acetyl-muramyl-tripeptide synthetase of Escherichia coli. Biochem. J. 269:277-280. Nathenson, S. G., J. L. Strominger, and E. Ito, 1964, Enzymatic synthesis of the peptide in bacterial uridine nucleotides: purification and properties of D-Glutamic acid-adding enzyme, J. Biol. Chem. 239: 1773-1776. Parquet, C, D. Mengin-Lecreulx, B. Flouret, D. Mengin- Lecreulx, and J. van Heijenoort, 1989, Nucleotide sequence of the murF gene encoding the UDP-MurNAc-pentapeptide synthetase of Escherichia coli., Nucleic Acids Res. 17:5379. Pratviel-Sosa F, D. Mengin-Lecreulx and J. van Heijenoort, 1991, Over-production, purification and properties of the uridine diphosphate N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli. Eur. J. Biochem. 202 (3):1169-1176. Roe, B. A., S. Clifton, M. McShan and J. Ferretti. The Streptococcal genome sequencing project, University of Oklahoma, Oklahoma, USA. Rogers, H. J„ H. R. Perkins, and J. B. Ward, 1980, Biosynthesis of peptidoglycan. p. 239-297. In Microbial cell walls and membranes. Chapman & Hall Ltd. London. Sambrook, J., E. F. Fritch, and T. Maniatis, 1989, Molecular cloning: a L, Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory. Schleifer, K. H. and O. Kandler, 1972, Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol. Review. 36:407-477. Tanner, M.E., S. Vaganay, van Heijenoort, J., and D. Blanot, 1996, Phosphinate Inhibitors of the D-Glutamic Acid-Adding Enzyme of Peptidoglycan Biosynthesis. J. Org. Chem. 61:1756-1760. Tao, J.S, and E. E., Ishiguro, 1989, Nucleotide sequence of the murE gene of Escherichia coli. Can. J. Microbiol. 35:1051-1054.

Claims: WHAT IS CLAIMED: 1. An isolated polynucleotide selected from the group consisting of: (a) a polynucleotide encoding a poiypeptide having an amino acid sequence of SEQ ID NO: 2. (b) a polynucleotide which is complementary to the polynucleotide of (a), (c) a polynucleotide representing a naturally occ ring mutant or polymorphic form of (a), and (d) a polynucleotide comprising at least 25 nucleotides of the polynucleotide of (a), (b) or (c), said 25 nucleotides being highly specific for murD gene of Staphylococcus aureus. 2. The polynucleotide of claim 1 wherein the polynucleotide comprises nucleotides selected from the group consisting of natural, non- natural and modified nucleotides. 3. The polynucleotide of claim 1 wherein the internucleotide linkages are selected from the group consisting of natural and non-natural linkages. 4. The polynucleotide of claim 1 comprising the nucleotide sequence of SEQ ID NO: 1. 5. A polynucleotide that is an expression vector comprising a polynucleotide of claim 1. 6. A host cell comprising the expression vector of claim 5. 7. A process for expressing a MurD protein of Staphylococcus aureus in a recombinant host cell, comprising: (a) transfecting a suitable host cell with an expression vector of claim 5; and, (b) culturing the host cell of step (a) in conditions under which allow expression of said the MurD protein from said expression vector. 8. A substantially purified poiypeptide having an amino acid sequence selected from the group consisting of (a) a poiypeptide having an amino acid sequence of SEQ ID NO:2, (b) a poiypeptide representing a naturally occurring mutant or polymorphic form of (a). 9. A method of determining whether candidate compounds or molecules are inhibitors of a MurD poiypeptide of claim 8 comprising: (a) providing a cell according to claim 6, (b) contacting said cell with the candidate under conditions sufficient to permit the interaction of the candidate with the protein of the candidate, and (c) determining whether the candidate is an inhibitor by ascertaining the relative activity of the murd poiypeptide in the presence of the candidate.

Inventors: EL-SHERBEINI MOHAMMED, GEISSLER WAYNE M, WONG KENNY KIN CHUNG, EL-SHERBEINI, MOHAMMED, GEISSLER, WAYNE, M., WONG, KENNY, KIN, CHUNG
Applicants: EL SHERBEINI MOHAMMED, GEISSLER WAYNE M, MERCK & CO INC, WONG KENNY KIN CHUNG, EL-SHERBEINI, MOHAMMED, GEISSLER, WAYNE, M., MERCK & CO., INC., WONG, KENNY, KIN, CHUNG
Application year: 1998
Main classification: C12P21
IPC codes: C12N1, C12N9, C12N15, C12P21