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PDBsum entry 1r44

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protein metals Protein-protein interface(s) links
Hydrolase PDB id
1r44
Jmol
Contents
Protein chains
(+ 0 more) 202 a.a. *
Metals
_ZN ×6
Waters ×12
* Residue conservation analysis
PDB id:
1r44
Name: Hydrolase
Title: Crystal structure of vanx
Structure: D-alanyl-d-alanine dipeptidase. Chain: a, b, c, d, e, f. Synonym: d-ala-d-ala dipeptidase, vancomycin b-type resistance protein vanx. Engineered: yes
Source: Enterococcus faecium. Organism_taxid: 1352. Gene: vanx. Expressed in: escherichia coli str. K12 substr. W3110. Expression_system_taxid: 316407.
Resolution:
2.25Å     R-factor:   0.254     R-free:   0.301
Authors: S.D.Pratt,L.Katz,J.M.Severin,T.Holzman,C.H.Park
Key ref:
D.E.Bussiere et al. (1998). The structure of VanX reveals a novel amino-dipeptidase involved in mediating transposon-based vancomycin resistance. Mol Cell, 2, 75-84. PubMed id: 9702193 DOI: 10.1016/S1097-2765(00)80115-X
Date:
03-Oct-03     Release date:   15-Jun-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q06241  (VANX_ENTFC) -  D-alanyl-D-alanine dipeptidase
Seq:
Struc:
202 a.a.
202 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.13.22  - D-Ala-D-Ala dipeptidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-Ala-D-Ala + H2O = 2 D-Ala
D-Ala-D-Ala
+ H(2)O
= 2 × D-Ala
      Cofactor: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cell wall   1 term 
  Biological process     cell wall organization   3 terms 
  Biochemical function     hydrolase activity     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/S1097-2765(00)80115-X Mol Cell 2:75-84 (1998)
PubMed id: 9702193  
 
 
The structure of VanX reveals a novel amino-dipeptidase involved in mediating transposon-based vancomycin resistance.
D.E.Bussiere, S.D.Pratt, L.Katz, J.M.Severin, T.Holzman, C.H.Park.
 
  ABSTRACT  
 
VanX is a zinc-dependent D-alanyl-D-alanine dipeptidase that is a critical component in a system that mediates transposon-based vancomycin resistance in enterococci. It is also a key drug target in circumventing clinical vancomycin resistance. The structure of VanX from E. faecium has been solved by X-ray crystallography and reveals a Zn(2+)-dipeptidase with a unique overall fold and a well-defined active site confined within a cavity of limited size. The crystal structures of VanX, the VanX:D-alanyl-D-alanine complex, the VanX:D-alanine complex, and VanX in complex with phosphonate and phosphinate transition-state analog inhibitors, are also presented at high resolution. Structural homology searches of known structures revealed that the fold of VanX is similar to those of two proteins: the N-terminal fragment of murine Sonic hedgehog and the Zn(2+)-dependent N-acyl-D-alanyl-D-alanine carboxypeptidase of S. albus G.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Mechanism and Inhibitors of VanX(A) The proposed mechanism of VanX. (i) An incoming dipeptide displaces a zinc-bound water molecule toward Glu-181; (ii) the water molecule is activated by the influence of the catalytic zinc and Glu-181 and attacks the polarized carbonyl to form a tetrahedral intermediate; (iii) the tetrahedral intermediate forms a bidentate complex with the zinc and is stablized further by interactions with Arg-71; Glu-181 subsequently donates the proton to the scissile nitrogen, completing the reaction; (iv) D-alanine is released.(B) The phosphinate transition-state analog. This compound has a reported K[i] of 0.3 μM ([43]).(C) The phosphonate transition-state analog. This compound has a reported K[i] of 0.3 mM ([43]).
Figure 6.
Figure 6. Structural Homologies of the VanX Protein(A) Structural alignments of the VanX protein (red) with the N-terminal fragment of murine Sonic hedgehog (green), and D-ala-D-ala carboxypeptidase (gold). The active site position of all of the enzymes is labelled. All structural alignments were done using the program SARF ([2]).(B) Structural homology within the VanX (red), N-terminal murine Sonic hedgehog (green), and D-ala-D-ala carboxypeptidase of S. albus G (gold) active sites. Homologous side chains and main chains are shown and are labeled in equivalent colors to their respective molecules.
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (1998, 2, 75-84) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20404117 C.M.Hill, K.M.Krause, S.R.Lewis, J.Blais, B.M.Benton, M.Mammen, P.P.Humphrey, A.Kinana, and J.W.Janc (2010).
Specificity of induction of the vanA and vanB operons in vancomycin-resistant enterococci by telavancin.
  Antimicrob Agents Chemother, 54, 2814-2818.  
20536384 H.R.Maun, D.Kirchhofer, and R.A.Lazarus (2010).
Pseudo-active sites of protease domains: HGF/Met and Sonic hedgehog signaling in cancer.
  Biol Chem, 391, 881-892.  
20704569 R.Ganesan, C.Eigenbrot, and D.Kirchhofer (2010).
Structural and mechanistic insight into how antibodies inhibit serine proteases.
  Biochem J, 430, 179-189.  
19361422 D.N.Cohen, Y.Y.Sham, G.D.Haugstad, Y.Xiang, M.G.Rossmann, D.L.Anderson, and D.L.Popham (2009).
Shared catalysis in virus entry and bacterial cell wall depolymerization.
  J Mol Biol, 387, 607-618.  
19561609 I.Bosanac, H.R.Maun, S.J.Scales, X.Wen, A.Lingel, J.F.Bazan, F.J.de Sauvage, S.G.Hymowitz, and R.A.Lazarus (2009).
The structure of SHH in complex with HHIP reveals a recognition role for the Shh pseudo active site in signaling.
  Nat Struct Mol Biol, 16, 691-697.
PDB codes: 3ho3 3ho4 3ho5
18560152 I.P.Korndörfer, A.Kanitz, J.Danzer, M.Zimmer, M.J.Loessner, and A.Skerra (2008).
Structural analysis of the L-alanoyl-D-glutamate endopeptidase domain of Listeria bacteriophage endolysin Ply500 reveals a new member of the LAS peptidase family.
  Acta Crystallogr D Biol Crystallogr, 64, 644-650.
PDB code: 2vo9
18498110 S.Ragumani, D.Kumaran, S.K.Burley, and S.Swaminathan (2008).
Crystal structure of a putative lysostaphin peptidase from Vibrio cholerae.
  Proteins, 72, 1096-1103.
PDB code: 2gu1
18266855 W.Vollmer, B.Joris, P.Charlier, and S.Foster (2008).
Bacterial peptidoglycan (murein) hydrolases.
  FEMS Microbiol Rev, 32, 259-286.  
17400741 M.Deghorain, P.Goffin, L.Fontaine, J.L.Mainardi, R.Daniel, J.Errington, B.Hallet, and P.Hols (2007).
Selectivity for D-lactate incorporation into the peptidoglycan precursors of Lactobacillus plantarum: role of Aad, a VanX-like D-alanyl-D-alanine dipeptidase.
  J Bacteriol, 189, 4332-4337.  
17888003 M.Firczuk, and M.Bochtler (2007).
Folds and activities of peptidoglycan amidases.
  FEMS Microbiol Rev, 31, 676-691.  
17017774 M.L.Matthews, G.Periyannan, C.Hajdin, T.K.Sidgel, B.Bennett, and M.W.Crowder (2006).
Probing the reaction mechanism of the D-ala-D-ala dipeptidase, VanX, by using stopped-flow kinetic and rapid-freeze quench EPR studies on the Co(II)-substituted enzyme.
  J Am Chem Soc, 128, 13050-13051.  
15657055 R.M.Breece, A.Costello, B.Bennett, T.K.Sigdel, M.L.Matthews, D.L.Tierney, and M.W.Crowder (2005).
A five-coordinate metal center in Co(II)-substituted VanX.
  J Biol Chem, 280, 11074-11081.  
15044722 M.Bochtler, S.G.Odintsov, M.Marcyjaniak, and I.Sabala (2004).
Similar active sites in lysostaphins and D-Ala-D-Ala metallopeptidases.
  Protein Sci, 13, 854-861.  
15292190 M.Marcyjaniak, S.G.Odintsov, I.Sabala, and M.Bochtler (2004).
Peptidoglycan amidase MepA is a LAS metallopeptidase.
  J Biol Chem, 279, 43982-43989.
PDB codes: 1tzp 1u10
12620121 V.Anantharaman, and L.Aravind (2003).
Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes.
  Genome Biol, 4, R11.  
12047383 A.H.Podmore, and P.E.Reynolds (2002).
Purification and characterization of VanXY(C), a D,D-dipeptidase/D,D-carboxypeptidase in vancomycin-resistant Enterococcus gallinarum BM4174.
  Eur J Biochem, 269, 2740-2746.  
12111749 C.T.Supuran, A.Scozzafava, and B.W.Clare (2002).
Bacterial protease inhibitors.
  Med Res Rev, 22, 329-372.  
11807177 J.Pootoolal, J.Neu, and G.D.Wright (2002).
Glycopeptide antibiotic resistance.
  Annu Rev Pharmacol Toxicol, 42, 381-408.  
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.  
  10094694 F.Hilbert, F.García-del Portillo, and E.A.Groisman (1999).
A periplasmic D-alanyl-D-alanine dipeptidase in the gram-negative bacterium Salmonella enterica.
  J Bacteriol, 181, 2158-2165.  
10500118 I.A.Lessard, and C.T.Walsh (1999).
VanX, a bacterial D-alanyl-D-alanine dipeptidase: resistance, immunity, or survival function?
  Proc Natl Acad Sci U S A, 96, 11028-11032.  
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.  
10500113 N.Fuse, T.Maiti, B.Wang, J.A.Porter, T.M.Hall, D.J.Leahy, and P.A.Beachy (1999).
Sonic hedgehog protein signals not as a hydrolytic enzyme but as an apparent ligand for patched.
  Proc Natl Acad Sci U S A, 96, 10992-10999.  
10564477 P.E.Reynolds, C.A.Arias, and P.Courvalin (1999).
Gene vanXYC encodes D,D -dipeptidase (VanX) and D,D-carboxypeptidase (VanY) activities in vancomycin-resistant Enterococcus gallinarum BM4174.
  Mol Microbiol, 34, 341-349.  
9751644 I.A.Lessard, S.D.Pratt, D.G.McCafferty, D.E.Bussiere, C.Hutchins, B.L.Wanner, L.Katz, and C.T.Walsh (1998).
Homologs of the vancomycin resistance D-Ala-D-Ala dipeptidase VanX in Streptomyces toyocaensis, Escherichia coli and Synechocystis: attributes of catalytic efficiency, stereoselectivity and regulation with implications for function.
  Chem Biol, 5, 489-504.  
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.