1R44

Crystal Structure of VanX

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 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


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

  • 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 ...

    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.

    Organizational Affiliation: 

    Laboratory of Protein Crystallography, Abbott Laboratories, Illinois 60064, USA. bussierd@tvsfrank.pprd.abbott.com



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-alanyl-D-alanine dipeptidase
A, B, C, D, E, F
A, B, C, D, E, F
202Enterococcus faeciumMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06241
Protein Feature View
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  • Reference Sequence
Small Molecules
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 = 82.597α = 90
b = 44.694β = 103.76
c = 169.428γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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