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PDBsum entry 2dln

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Ligase(peptidoglycan synthesis) PDB id
2dln
Jmol
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
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: ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine
ATP
+ 2 × D-alanine
=
ADP
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  

 

 
    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

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PDB codes: 3tig 3tii 3tin
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PDB code: 2pvp
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PDB codes: 2c00 2j9g 2vpq 2vqd 2vr1
18271571 S.O.Nilsson Lill, J.Gao, and G.L.Waldrop (2008).
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PDB codes: 2io7 2io8 2io9 2ioa 2iob
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PDB code: 2fb9
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Substrate specificity of thermostable D-alanine-D-alanine ligase from Thermotoga maritima ATCC 43589.
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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.
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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.
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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).
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D-Amino acid dipeptide production utilizing D-alanine-D-alanine ligases with novel substrate specificity.
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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.
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15388450 F.Depardieu, M.Kolbert, H.Pruul, J.Bell, and P.Courvalin (2004).
VanD-type vancomycin-resistant Enterococcus faecium and Enterococcus faecalis.
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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.
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PDB codes: 1v4g 1va6
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Structure and function of the Mur enzymes: development of novel inhibitors.
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VanD-type vancomycin-resistant Enterococcus faecium 10/96A.
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Glycopeptide antibiotic resistance.
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Structure of acetylglutamate kinase, a key enzyme for arginine biosynthesis and a prototype for the amino acid kinase enzyme family, during catalysis.
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PDB codes: 1gs5 1gsj
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Enzymes of vancomycin resistance: the structure of D-alanine-D-lactate ligase of naturally resistant Leuconostoc mesenteroides.
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PDB code: 1ehi
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Biosynthesis of the cyanobacterial reserve polymer multi-L-arginyl-poly-L-aspartic acid (cyanophycin): mechanism of the cyanophycin synthetase reaction studied with synthetic primers.
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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.
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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.
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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.
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PDB codes: 1cqi 1cqj
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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.
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D-Ala-D-X ligases: evaluation of D-alanyl phosphate intermediate by MIX, PIX and rapid quench studies.
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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.
  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.
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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.
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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.
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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.
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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.
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Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9-A resolution.
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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.
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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.
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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.
  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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