PDBsum entry 2dln

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Ligase(peptidoglycan synthesis) PDB id
Protein chain
306 a.a. *
_MG ×2
Waters ×292
* Residue conservation analysis
PDB id:
Name: Ligase(peptidoglycan synthesis)
Title: Vancomycin resistance: structure of d-alanine:d-alanine ligase at 2.3 angstroms resolution
Structure: D-alanine--d-alanine ligase. Chain: a. Ec:
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: Dimer (from PQS)
2.30Å     R-factor:   0.172    
Authors: J.R.Knox,P.C.Moews,C.Fan
Key ref: C.Fan et al. (1994). Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3 A resolution. Science, 266, 439-443. PubMed id: 7939684 DOI: 10.1126/science.7939684
18-Jul-94     Release date:   01-Nov-95    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P07862  (DDLB_ECOLI) -  D-alanine--D-alanine ligase B
306 a.a.
306 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - D-alanine--D-alanine ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Peptidoglycan Biosynthesis (Part 1)
      Reaction: ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine
+ 2 × D-alanine
Bound ligand (Het Group name = ADP)
corresponds exactly
+ phosphate
+ D-alanyl-D-alanine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     cell wall organization   3 terms 
  Biochemical function     catalytic activity     8 terms  


DOI no: 10.1126/science.7939684 Science 266:439-443 (1994)
PubMed id: 7939684  
Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3 A resolution.
C.Fan, P.C.Moews, C.T.Walsh, J.R.Knox.
The molecular structure of the D-alanine:D-alanine ligase of the ddlB gene of Escherichia coli, co-crystallized with an S,R-methylphosphinate and adenosine triphosphate, was determined by x-ray diffraction to a resolution of 2.3 angstroms. A catalytic mechanism for the ligation of two D-alanine substrates is proposed in which a helix dipole and a hydrogen-bonded triad of tyrosine, serine, and glutamic acid assist binding and deprotonation steps. From sequence comparison, it is proposed that a different triad exists in a recently discovered D-alanine:D-lactate ligase (VanA) present in vancomycin-resistant enterococci. A molecular mechanism for the altered specificity of VanA is suggested.

Literature references that cite this PDB file's key reference

  PubMed id Reference
22020298 A.Szyk, A.M.Deaconescu, G.Piszczek, and A.Roll-Mecak (2011).
Tubulin tyrosine ligase structure reveals adaptation of an ancient fold to bind and modify tubulin.
  Nat Struct Mol Biol, 18, 1250-1258.
PDB codes: 3tig 3tii 3tin
20142038 S.A.Borisova, B.T.Circello, J.K.Zhang, W.A.van der Donk, and W.W.Metcalf (2010).
Biosynthesis of rhizocticins, antifungal phosphonate oligopeptides produced by Bacillus subtilis ATCC6633.
  Chem Biol, 17, 28-37.  
20815142 S.F.Lei, and J.Huan (2010).
Towards site-based protein functional annotations.
  Int J Data Min Bioinform, 4, 452-470.  
19258279 F.Depardieu, M.L.Foucault, J.Bell, A.Dubouix, M.Guibert, J.P.Lavigne, M.Levast, and P.Courvalin (2009).
New combinations of mutations in VanD-Type vancomycin-resistant Enterococcus faecium, Enterococcus faecalis, and Enterococcus avium strains.
  Antimicrob Agents Chemother, 53, 1952-1963.  
19384989 H.Li, W.Fast, and S.J.Benkovic (2009).
Structural and functional modularity of proteins in the de novo purine biosynthetic pathway.
  Protein Sci, 18, 881-892.  
19563773 J.J.McGuire, D.M.Bartley, J.W.Tomsho, W.H.Haile, and J.K.Coward (2009).
Inhibition of human folylpolyglutamate synthetase by diastereomeric phosphinic acid mimics of the tetrahedral intermediate.
  Arch Biochem Biophys, 488, 140-145.  
19431159 J.Zhan, K.Qiao, and Y.Tang (2009).
Investigation of tailoring modifications in pradimicin biosynthesis.
  Chembiochem, 10, 1447-1452.  
19770507 Y.Kitamura, A.Ebihara, Y.Agari, A.Shinkai, K.Hirotsu, and S.Kuramitsu (2009).
Structure of D-alanine-D-alanine ligase from Thermus thermophilus HB8: cumulative conformational change and enzyme-ligand interactions.
  Acta Crystallogr D Biol Crystallogr, 65, 1098-1106.  
18320587 D.Wu, L.Zhang, Y.Kong, J.Du, S.Chen, J.Chen, J.Ding, H.Jiang, and X.Shen (2008).
Enzymatic characterization and crystal structure analysis of the D-alanine-D-alanine ligase from Helicobacter pylori.
  Proteins, 72, 1148-1160.
PDB code: 2pvp
18266853 H.Barreteau, A.Kovac, A.Boniface, M.Sova, S.Gobec, and D.Blanot (2008).
Cytoplasmic steps of peptidoglycan biosynthesis.
  FEMS Microbiol Rev, 32, 168-207.  
18725455 I.Mochalkin, J.R.Miller, A.Evdokimov, S.Lightle, C.Yan, C.K.Stover, and G.L.Waldrop (2008).
Structural evidence for substrate-induced synergism and half-sites reactivity in biotin carboxylase.
  Protein Sci, 17, 1706-1718.
PDB codes: 2c00 2j9g 2vpq 2vqd 2vr1
18271571 S.O.Nilsson Lill, J.Gao, and G.L.Waldrop (2008).
Molecular dynamics simulations of biotin carboxylase.
  J Phys Chem B, 112, 3149-3156.  
18679674 T.Arai, and K.Kino (2008).
A cyanophycin synthetase from Thermosynechococcus elongatus BP-1 catalyzes primer-independent cyanophycin synthesis.
  Appl Microbiol Biotechnol, 81, 69-78.  
18712276 Y.Zhang, M.Morar, and S.E.Ealick (2008).
Structural biology of the purine biosynthetic pathway.
  Cell Mol Life Sci, 65, 3699-3724.  
17124497 C.H.Pai, B.Y.Chiang, T.P.Ko, C.C.Chou, C.M.Chong, F.J.Yen, S.Chen, J.K.Coward, A.H.Wang, and C.H.Lin (2006).
Dual binding sites for translocation catalysis by Escherichia coli glutathionylspermidine synthetase.
  EMBO J, 25, 5970-5982.
PDB codes: 2io7 2io8 2io9 2ioa 2iob
16779845 J.H.Lee, Y.Na, H.E.Song, D.Kim, B.H.Park, S.H.Rho, Y.J.Im, M.K.Kim, G.B.Kang, D.S.Lee, and S.H.Eom (2006).
Crystal structure of the apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: a basis for the substrate-induced conformational changes.
  Proteins, 64, 1078-1082.
PDB code: 2fb9
17090922 M.Sato, K.Kirimura, and K.Kino (2006).
Substrate specificity of thermostable D-alanine-D-alanine ligase from Thermotoga maritima ATCC 43589.
  Biosci Biotechnol Biochem, 70, 2790-2792.  
17015835 S.Liu, J.S.Chang, J.T.Herberg, M.M.Horng, P.K.Tomich, A.H.Lin, and K.R.Marotti (2006).
Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies.
  Proc Natl Acad Sci U S A, 103, 15178-15183.
PDB codes: 2i80 2i87 2i8c
15948948 A.J.McCoy, and A.T.Maurelli (2005).
Characterization of Chlamydia MurC-Ddl, a fusion protein exhibiting D-alanyl-D-alanine ligase activity involved in peptidoglycan synthesis and D-cycloserine sensitivity.
  Mol Microbiol, 57, 41-52.  
16158456 G.E.Besong, J.M.Bostock, W.Stubbings, I.Chopra, D.I.Roper, A.J.Lloyd, C.W.Fishwick, and A.P.Johnson (2005).
A de novo designed inhibitor of D-Ala-D-Ala ligase from E. coli.
  Angew Chem Int Ed Engl, 44, 6403-6406.  
16041744 J.Hiratake (2005).
Enzyme inhibitors as chemical tools to study enzyme catalysis: rational design, synthesis, and applications.
  Chem Rec, 5, 209-228.  
16233841 M.Sato, K.Kirimura, and K.Kino (2005).
D-Amino acid dipeptide production utilizing D-alanine-D-alanine ligases with novel substrate specificity.
  J Biosci Bioeng, 99, 623-628.  
16037208 R.A.George, R.V.Spriggs, G.J.Bartlett, A.Gutteridge, M.W.MacArthur, C.T.Porter, B.Al-Lazikani, J.M.Thornton, and M.B.Swindells (2005).
Effective function annotation through catalytic residue conservation.
  Proc Natl Acad Sci U S A, 102, 12299-12304.  
15388450 F.Depardieu, M.Kolbert, H.Pruul, J.Bell, and P.Courvalin (2004).
VanD-type vancomycin-resistant Enterococcus faecium and Enterococcus faecalis.
  Antimicrob Agents Chemother, 48, 3892-3904.  
15477603 T.Hibi, H.Nii, T.Nakatsu, A.Kimura, H.Kato, J.Hiratake, and J.Oda (2004).
Crystal structure of gamma-glutamylcysteine synthetase: insights into the mechanism of catalysis by a key enzyme for glutathione homeostasis.
  Proc Natl Acad Sci U S A, 101, 15052-15057.
PDB codes: 1v4g 1va6
12492849 A.El Zoeiby, F.Sanschagrin, and R.C.Levesque (2003).
Structure and function of the Mur enzymes: development of novel inhibitors.
  Mol Microbiol, 47, 1.  
12499162 F.Depardieu, P.E.Reynolds, and P.Courvalin (2003).
VanD-type vancomycin-resistant Enterococcus faecium 10/96A.
  Antimicrob Agents Chemother, 47, 7.  
11807177 J.Pootoolal, J.Neu, and G.D.Wright (2002).
Glycopeptide antibiotic resistance.
  Annu Rev Pharmacol Toxicol, 42, 381-408.  
11751117 O.H.Ambúr, P.E.Reynolds, and C.A.Arias (2002).
D-Ala:D-Ala ligase gene flanking the vanC cluster: evidence for presence of three ligase genes in vancomycin-resistant Enterococcus gallinarum BM4174.
  Antimicrob Agents Chemother, 46, 95.  
12005432 S.Ramón-Maiques, A.Marina, F.Gil-Ortiz, I.Fita, and V.Rubio (2002).
Structure of acetylglutamate kinase, a key enzyme for arginine biosynthesis and a prototype for the amino acid kinase enzyme family, during catalysis.
  Structure, 10, 329-342.
PDB codes: 1gs5 1gsj
11249823 D.C.Hooper (2001).
Mechanisms of action of antimicrobials: focus on fluoroquinolones.
  Clin Infect Dis, 32, S9.  
11705966 G.D.Pullinger, R.Sowdhamini, and A.J.Lax (2001).
Localization of functional domains of the mitogenic toxin of Pasteurella multocida.
  Infect Immun, 69, 7839-7850.  
11455601 K.A.Denessiouk, V.V.Rantanen, and M.S.Johnson (2001).
Adenine recognition: a motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins.
  Proteins, 44, 282-291.  
11274474 Y.Gholizadeh, M.Prevost, F.Van Bambeke, B.Casadewall, P.M.Tulkens, and P.Courvalin (2001).
Sequencing of the ddl gene and modeling of the mutated D-alanine:D-alanine ligase in glycopeptide-dependent strains of Enterococcus faecium.
  Protein Sci, 10, 836-844.  
11073937 A.E.Belanger, J.C.Porter, and G.F.Hatfull (2000).
Genetic analysis of peptidoglycan biosynthesis in mycobacteria: characterization of a ddlA mutant of Mycobacterium smegmatis.
  J Bacteriol, 182, 6854-6856.  
10801495 A.P.Kuzin, T.Sun, J.Jorczak-Baillass, V.L.Healy, C.T.Walsh, and J.R.Knox (2000).
Enzymes of vancomycin resistance: the structure of D-alanine-D-lactate ligase of naturally resistant Leuconostoc mesenteroides.
  Structure, 8, 463-470.
PDB code: 1ehi
10951215 H.Berg, K.Ziegler, K.Piotukh, K.Baier, W.Lockau, and R.Volkmer-Engert (2000).
Biosynthesis of the cyanobacterial reserve polymer multi-L-arginyl-poly-L-aspartic acid (cyanophycin): mechanism of the cyanophycin synthetase reaction studied with synthetic primers.
  Eur J Biochem, 267, 5561-5570.  
10913290 J.B.Thoden, S.Firestine, A.Nixon, S.J.Benkovic, and H.M.Holden (2000).
Molecular structure of Escherichia coli PurT-encoded glycinamide ribonucleotide transformylase.
  Biochemistry, 39, 8791-8802.
PDB codes: 1eyz 1ez1
10713991 K.A.Denessiouk, and M.S.Johnson (2000).
When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families.
  Proteins, 38, 310-326.  
10747803 K.L.Levert, R.B.Lloyd, and G.L.Waldrop (2000).
Do cysteine 230 and lysine 238 of biotin carboxylase play a role in the activation of biotin?
  Biochemistry, 39, 4122-4128.  
10625475 M.A.Joyce, M.E.Fraser, M.N.James, W.A.Bridger, and W.T.Wolodko (2000).
ADP-binding site of Escherichia coli succinyl-CoA synthetase revealed by x-ray crystallography.
  Biochemistry, 39, 17-25.
PDB codes: 1cqi 1cqj
  10892798 S.Ha, D.Walker, Y.Shi, and S.Walker (2000).
The 1.9 A crystal structure of Escherichia coli MurG, a membrane-associated glycosyltransferase involved in peptidoglycan biosynthesis.
  Protein Sci, 9, 1045-1052.
PDB code: 1f0k
10801476 V.L.Healy, I.A.Lessard, D.I.Roper, J.R.Knox, and C.T.Walsh (2000).
Vancomycin resistance in enterococci: reprogramming of the D-ala-D-Ala ligases in bacterial peptidoglycan biosynthesis.
  Chem Biol, 7, R109-R119.  
10903933 V.L.Healy, L.S.Mullins, X.Li, S.E.Hall, F.M.Raushel, and C.T.Walsh (2000).
D-Ala-D-X ligases: evaluation of D-alanyl phosphate intermediate by MIX, PIX and rapid quench studies.
  Chem Biol, 7, 505-514.  
10508786 C.Li, T.J.Kappock, J.Stubbe, T.M.Weaver, and S.E.Ealick (1999).
X-ray crystal structure of aminoimidazole ribonucleotide synthetase (PurM), from the Escherichia coli purine biosynthetic pathway at 2.5 A resolution.
  Structure, 7, 1155-1166.
PDB code: 1cli
9869563 F.Van Bambeke, M.Chauvel, P.E.Reynolds, H.S.Fraimow, and P.Courvalin (1999).
Vancomycin-dependent Enterococcus faecalis clinical isolates and revertant mutants.
  Antimicrob Agents Chemother, 43, 41-47.  
10369661 G.Polekhina, P.G.Board, R.R.Gali, J.Rossjohn, and M.W.Parker (1999).
Molecular basis of glutathione synthetase deficiency and a rare gene permutation event.
  EMBO J, 18, 3204-3213.
PDB code: 2hgs
10074467 I.A.Lessard, and C.T.Walsh (1999).
Mutational analysis of active-site residues of the enterococcal D-ala-D-Ala dipeptidase VanX and comparison with Escherichia coli D-ala-D-Ala ligase and D-ala-D-Ala carboxypeptidase VanY.
  Chem Biol, 6, 177-187.  
10089390 J.B.Thoden, F.M.Raushel, M.M.Benning, I.Rayment, and H.M.Holden (1999).
The structure of carbamoyl phosphate synthetase determined to 2.1 A resolution.
  Acta Crystallogr D Biol Crystallogr, 55, 8.
PDB code: 1jdb
10029528 J.B.Thoden, G.Wesenberg, F.M.Raushel, and H.M.Holden (1999).
Carbamoyl phosphate synthetase: closure of the B-domain as a result of nucleotide binding.
  Biochemistry, 38, 2347-2357.
PDB code: 1bxr
10353839 M.A.Joyce, M.E.Fraser, E.R.Brownie, M.N.James, W.A.Bridger, and W.T.Wolodko (1999).
Probing the nucleotide-binding site of Escherichia coli succinyl-CoA synthetase.
  Biochemistry, 38, 7273-7283.  
10417422 T.Huyton, and D.I.Roper (1999).
Crystallization and preliminary X-ray characterization of VanA from Enterococcus faecium BM4147: towards the molecular basis of bacterial resistance to the glycopeptide antibiotic vancomycin.
  Acta Crystallogr D Biol Crystallogr, 55, 1481-1483.  
10089364 T.M.Weaver, W.Wang, and S.E.Ealick (1999).
Purification, crystallization and preliminary X-ray diffraction data from selenomethionine glycinamide ribonucleotide synthetase.
  Acta Crystallogr D Biol Crystallogr, 55, 518-521.  
10666581 Y.Yan, S.Munshi, Y.Li, K.A.Pryor, F.Marsilio, and B.Leiting (1999).
Crystallization and preliminary X-ray analysis of the Escherichia coli UDP-MurNAc-tripeptide D-alanyl-D-alanine-adding enzyme (MurF).
  Acta Crystallogr D Biol Crystallogr, 55, 2033-2034.  
  9791137 C.G.Marshall, and G.D.Wright (1998).
DdlN from vancomycin-producing Amycolatopsis orientalis C329.2 is a VanA homologue with D-alanyl-D-lactate ligase activity.
  J Bacteriol, 180, 5792-5795.  
9818189 F.M.Raushel, J.B.Thoden, G.D.Reinhart, and H.M.Holden (1998).
Carbamoyl phosphate synthetase: a crooked path from substrates to products.
  Curr Opin Chem Biol, 2, 624-632.  
9665735 F.M.Raushel, L.S.Mullins, and G.E.Gibson (1998).
A stringent test for the nucleotide switch mechanism of carbamoyl phosphate synthetase.
  Biochemistry, 37, 10272-10278.  
9914247 H.M.Holden, J.B.Thoden, and F.M.Raushel (1998).
Carbamoyl phosphate synthetase: a tunnel runs through it.
  Curr Opin Struct Biol, 8, 679-685.  
  10082373 K.A.Denessiouk, J.V.Lehtonen, and M.S.Johnson (1998).
Enzyme-mononucleotide interactions: three different folds share common structural elements for ATP recognition.
  Protein Sci, 7, 1768-1771.  
  9605318 K.A.Denessiouk, J.V.Lehtonen, T.Korpela, and M.S.Johnson (1998).
Two "unrelated" families of ATP-dependent enzymes share extensive structural similarities about their cofactor binding sites.
  Protein Sci, 7, 1136-1146.  
9873406 L.D.Gegnas, S.T.Waddell, R.M.Chabin, S.Reddy, and K.K.Wong (1998).
Inhibitors of the bacterial cell wall biosynthesis enzyme MurD.
  Bioorg Med Chem Lett, 8, 1643-1648.  
9463376 L.Esser, C.R.Wang, M.Hosaka, C.S.Smagula, T.C.Südhof, and J.Deisenhofer (1998).
Synapsin I is structurally similar to ATP-utilizing enzymes.
  EMBO J, 17, 977-984.
PDB codes: 1auv 1aux
10094630 M.Arthur, F.Depardieu, L.Cabanié, P.Reynolds, and P.Courvalin (1998).
Requirement of the VanY and VanX D,D-peptidases for glycopeptide resistance in enterococci.
  Mol Microbiol, 30, 819-830.  
9753432 M.McGuire, K.Huang, G.Kapadia, O.Herzberg, and D.Dunaway-Mariano (1998).
Location of the phosphate binding site within Clostridium symbiosum pyruvate phosphate dikinase.
  Biochemistry, 37, 13463-13474.
PDB codes: 1buk 2dik
9538689 O.Dideberg, and J.Bertrand (1998).
Tubulin tyrosine ligase: a shared fold with the glutathione synthetase ADP-forming family.
  Trends Biochem Sci, 23, 57-58.  
9545431 V.L.Healy, I.S.Park, and C.T.Walsh (1998).
Active-site mutants of the VanC2 D-alanyl-D-serine ligase, characteristic of one vancomycin-resistant bacterial phenotype, revert towards wild-type D-alanyl-D-alanine ligases.
  Chem Biol, 5, 197-207.  
9551557 V.M.Levdikov, V.V.Barynin, A.I.Grebenko, W.R.Melik-Adamyan, V.S.Lamzin, and K.S.Wilson (1998).
The structure of SAICAR synthase: an enzyme in the de novo pathway of purine nucleotide biosynthesis.
  Structure, 6, 363-376.
PDB code: 1a48
9843369 W.Wang, T.J.Kappock, J.Stubbe, and S.E.Ealick (1998).
X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli.
  Biochemistry, 37, 15647-15662.
PDB code: 1gso
9054558 C.Fan, I.S.Park, C.T.Walsh, and J.R.Knox (1997).
D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant.
  Biochemistry, 36, 2531-2538.
PDB codes: 1iov 1iow
9177243 C.G.Marshall, G.Broadhead, B.K.Leskiw, and G.D.Wright (1997).
D-Ala-D-Ala ligases from glycopeptide antibiotic-producing organisms are highly homologous to the enterococcal vancomycin-resistance ligases VanA and VanB.
  Proc Natl Acad Sci U S A, 94, 6480-6483.  
9294159 I.S.Park, C.H.Lin, and C.T.Walsh (1997).
Bacterial resistance to vancomycin: overproduction, purification, and characterization of VanC2 from Enterococcus casseliflavus as a D-Ala-D-Ser ligase.
  Proc Natl Acad Sci U S A, 94, 10040-10044.  
9218784 J.A.Bertrand, G.Auger, E.Fanchon, L.Martin, D.Blanot, J.van Heijenoort, and O.Dideberg (1997).
Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli.
  EMBO J, 16, 3416-3425.
PDB codes: 1e0d 1uag
9174345 J.B.Thoden, H.M.Holden, G.Wesenberg, F.M.Raushel, and I.Rayment (1997).
Structure of carbamoyl phosphate synthetase: a journey of 96 A from substrate to product.
  Biochemistry, 36, 6305-6316.  
9063881 J.P.Shaw, G.A.Petsko, and D.Ringe (1997).
Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9-A resolution.
  Biochemistry, 36, 1329-1342.
PDB code: 1sft
9356452 M.Kothe, B.Eroglu, H.Mazza, H.Samudera, and S.Powers-Lee (1997).
Novel mechanism for carbamoyl-phosphate synthetase: a nucleotide switch for functionally equivalent domains.
  Proc Natl Acad Sci U S A, 94, 12348-12353.  
  9416615 M.Y.Galperin, and E.V.Koonin (1997).
A diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity.
  Protein Sci, 6, 2639-2643.  
8989312 N.Kobayashi, and N.Go (1997).
ATP binding proteins with different folds share a common ATP-binding structural motif.
  Nat Struct Biol, 4, 6-7.  
8804825 A.G.Murzin (1996).
Structural classification of proteins: new superfamilies.
  Curr Opin Struct Biol, 6, 386-394.  
8605620 A.M.Thunnissen, and B.W.Dijkstra (1996).
Cure for a crisis?
  Nat Struct Biol, 3, 218-221.  
8807826 B.A.Ellsworth, N.J.Tom, and P.A.Bartlett (1996).
Synthesis and evaluation of inhibitors of bacterial D-alanine:D-alanine ligases.
  Chem Biol, 3, 37-44.  
8807824 C.T.Walsh, S.L.Fisher, I.S.Park, M.Prahalad, and Z.Wu (1996).
Bacterial resistance to vancomycin: five genes and one missing hydrogen bond tell the story.
  Chem Biol, 3, 21-28.  
8916923 F.Javid-Majd, M.A.Stapleton, M.F.Harmon, B.A.Hanks, L.S.Mullins, and F.M.Raushel (1996).
Comparison of the functional differences for the homologous residues within the carboxy phosphate and carbamate domains of carbamoyl phosphate synthetase.
  Biochemistry, 35, 14362-14369.  
8756703 I.S.Park, C.H.Lin, and C.T.Walsh (1996).
Gain of D-alanyl-D-lactate or D-lactyl-D-alanine synthetase activities in three active-site mutants of the Escherichia coli D-alanyl-D-alanine ligase B.
  Biochemistry, 35, 10464-10471.  
  9158755 J.M.Ghuysen, P.Charlier, J.Coyette, C.Duez, E.Fonzé, C.Fraipont, C.Goffin, B.Joris, and M.Nguyen-Distèche (1996).
Penicillin and beyond: evolution, protein fold, multimodular polypeptides, and multiprotein complexes.
  Microb Drug Resist, 2, 163-175.  
8916922 M.A.Stapleton, F.Javid-Majd, M.F.Harmon, B.A.Hanks, J.L.Grahmann, L.S.Mullins, and F.M.Raushel (1996).
Role of conserved residues within the carboxy phosphate domain of carbamoyl phosphate synthetase.
  Biochemistry, 35, 14352-14361.  
8679615 M.McGuire, L.J.Carroll, L.Yankie, S.H.Thrall, D.Dunaway-Mariano, O.Herzberg, B.Jayaram, and B.H.Haley (1996).
Determination of the nucleotide binding site within Clostridium symbiosum pyruvate phosphate dikinase by photoaffinity labeling, site-directed mutagenesis, and structural analysis.
  Biochemistry, 35, 8544-8552.  
8610096 O.Herzberg, C.C.Chen, G.Kapadia, M.McGuire, L.J.Carroll, S.J.Noh, and D.Dunaway-Mariano (1996).
Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites.
  Proc Natl Acad Sci U S A, 93, 2652-2657.
PDB code: 1dik
8564538 P.J.Artymiuk, A.R.Poirrette, D.W.Rice, and P.Willett (1996).
Biotin carboxylase comes into the fold.
  Nat Struct Biol, 3, 128-132.  
8662022 S.Evers, B.Casadewall, M.Charles, S.Dutka-Malen, M.Galimand, and P.Courvalin (1996).
Evolution of structure and substrate specificity in D-alanine:D-alanine ligases and related enzymes.
  J Mol Evol, 42, 706-712.  
8810901 T.Hara, H.Kato, Y.Katsube, and J.Oda (1996).
A pseudo-michaelis quaternary complex in the reverse reaction of a ligase: structure of Escherichia coli B glutathione synthetase complexed with ADP, glutathione, and sulfate at 2.0 A resolution.
  Biochemistry, 35, 11967-11974.
PDB code: 1gsa
8994972 T.Skarzynski, A.Mistry, A.Wonacott, S.E.Hutchinson, V.A.Kelly, and K.Duncan (1996).
Structure of UDP-N-acetylglucosamine enolpyruvyl transferase, an enzyme essential for the synthesis of bacterial peptidoglycan, complexed with substrate UDP-N-acetylglucosamine and the drug fosfomycin.
  Structure, 4, 1465-1474.
PDB code: 1uae
7862655 C.Fan, P.C.Moews, Y.Shi, C.T.Walsh, and J.R.Knox (1995).
A common fold for peptide synthetases cleaving ATP to ADP: glutathione synthetase and D-alanine:d-alanine ligase of Escherichia coli.
  Proc Natl Acad Sci U S A, 92, 1172-1176.  
8591031 D.Alexeev, R.L.Baxter, O.Smekal, and L.Sawyer (1995).
Substrate binding and carboxylation by dethiobiotin synthetase--a kinetic and X-ray study.
  Structure, 3, 1207-1215.  
8527834 R.C.Jackson (1995).
Update on computer-aided drug design.
  Curr Opin Biotechnol, 6, 646-651.  
8524812 Z.Wu, and C.T.Walsh (1995).
Phosphinate analogs of D-, D-dipeptides: slow-binding inhibition and proteolysis protection of VanX, a D-, D-dipeptidase required for vancomycin resistance in Enterococcus faecium.
  Proc Natl Acad Sci U S A, 92, 11603-11607.  
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