1R44

Crystal Structure of VanX

• PDB DOI:  https://doi.org/10.2210/pdb1R44/pdb

• Classification: HYDROLASE
• Organism(s): Enterococcus faecium
• Expression System: Escherichia coli str. K-12 substr. W3110
• Mutation(s): No 


• Deposited: 2003-10-03 Released: 2004-06-15 
• Deposition Author(s): Pratt, S.D., Katz, L., Severin, J.M., Holzman, T., Park, C.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.301 
• R-Value Work: 0.254 
• R-Value Observed: 0.258 

Literature

The Structure of VanX Reveals a Novel Amino-Dipeptidase Involved in Mediating Transposon-Based Vancomycin Resistance

Bussiere, D.E., Pratt, S.D., Katz, L., Severin, J.M., Holzman, T., Park, C.H.

(1998) Mol Cell 2: 75-84

• PubMed: 9702193 
• DOI: https://doi.org/10.1016/s1097-2765(00)80115-x
• Primary Citation of Related Structures:  
  1R44


• PubMed 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.

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Organizational Affiliation: 

Laboratory of Protein Crystallography, Abbott Laboratories, Illinois 60064, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 assigned by authors.

Macromolecule Content

• Total Structure Weight: 140.84 kDa 
• Atom Count: 9,924 
• Modelled Residue Count: 1,212 
• Deposited Residue Count: 1,212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanyl-D-alanine dipeptidase	A, B, C, D, E, F	202	Enterococcus faecium	Mutation(s): 0  Gene Names: vanX EC: 3.4.13 (PDB Primary Data), 3.4.13.22 (UniProt)
UniProt
Find proteins for Q06241 (Enterococcus faecium) Explore Q06241  Go to UniProtKB:  Q06241

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.301 
• R-Value Work: 0.254 
• R-Value Observed: 0.258 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.597	α = 90
b = 44.694	β = 103.76
c = 169.428	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
MLPHARE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-15 
Deposition Author(s): Pratt, S.D., Katz, L., Severin, J.M., Holzman, T., Park, C.H.

Revision History  

• Version 1.0: 2004-06-15
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description