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PDBsum entry 2dln
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Ligase(peptidoglycan synthesis) PDB id
2dln

 

 

 

 

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Contents
Protein chain
306 a.a. *
Ligands
ADP
PHY
Metals
_MG ×2
Waters ×292
* Residue conservation analysis
PDB id:
2dln
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: 6.3.2.4
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
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
Date:
18-Jul-94     Release date:   01-Nov-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07862  (DDLB_ECOLI) -  D-alanine--D-alanine ligase B from Escherichia coli (strain K12)
Seq:
Struc: 		306 a.a.
306 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.3.2.4  - D-alanine--D-alanine ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Peptidoglycan Biosynthesis (Part 1)
      Reaction: 2 D-alanine + ATP = D-alanyl-D-alanine + ADP + phosphate + H+
2 × D-alanine
 + ATP
 =
D-alanyl-D-alanine
Bound ligand (Het Group name = ADP)
corresponds exactly 		+ ADP
 + phosphate
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
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.
 
  ABSTRACT  
 
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.
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PDB codes: 3tig 3tii 3tin
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New combinations of mutations in VanD-Type vancomycin-resistant Enterococcus faecium, Enterococcus faecalis, and Enterococcus avium strains.
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19770507 Y.Kitamura, A.Ebihara, Y.Agari, A.Shinkai, K.Hirotsu, and S.Kuramitsu (2009).
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Enzymatic characterization and crystal structure analysis of the D-alanine-D-alanine ligase from Helicobacter pylori.
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PDB code: 2pvp
18266853 H.Barreteau, A.Kovac, A.Boniface, M.Sova, S.Gobec, and D.Blanot (2008).
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Structural evidence for substrate-induced synergism and half-sites reactivity in biotin carboxylase.
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PDB codes: 2c00 2j9g 2vpq 2vqd 2vr1
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Molecular dynamics simulations of biotin carboxylase.
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Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies.
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Effective function annotation through catalytic residue conservation.
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VanD-type vancomycin-resistant Enterococcus faecium and Enterococcus faecalis.
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VanD-type vancomycin-resistant Enterococcus faecium 10/96A.
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Glycopeptide antibiotic resistance.
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D-Ala:D-Ala ligase gene flanking the vanC cluster: evidence for presence of three ligase genes in vancomycin-resistant Enterococcus gallinarum BM4174.
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Sequencing of the ddl gene and modeling of the mutated D-alanine:D-alanine ligase in glycopeptide-dependent strains of Enterococcus faecium.
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  Structure, 8, 463-470.
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  Eur J Biochem, 267, 5561-5570.  
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Molecular structure of Escherichia coli PurT-encoded glycinamide ribonucleotide transformylase.
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PDB codes: 1eyz 1ez1
10713991 K.A.Denessiouk, and M.S.Johnson (2000).
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  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.  
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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.
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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).
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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.
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PDB code: 1cli
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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.
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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.
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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 code: 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.  
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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.  
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A diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity.
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ATP binding proteins with different folds share a common ATP-binding structural motif.
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Structural classification of proteins: new superfamilies.
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Cure for a crisis?
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Synthesis and evaluation of inhibitors of bacterial D-alanine:D-alanine ligases.
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Bacterial resistance to vancomycin: five genes and one missing hydrogen bond tell the story.
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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.
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Role of conserved residues within the carboxy phosphate domain of carbamoyl phosphate synthetase.
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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.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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