4BEU

Structure of Vibrio cholerae broad spectrum racemase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for the Broad Specificity of a New Family of Amino-Acid Racemases.

Espaillat, A.Carrasco-Lopez, C.Bernardo-Garcia, N.Pietrosemoli, N.Otero, L.H.Alvarez, L.De Pedro, M.A.Pazos, F.Davis, B.M.Waldor, M.K.Hermoso, J.A.Cava, F.

(2014) Acta Crystallogr.,Sect.D 70: 79

  • DOI: 10.1107/S1399004713024838
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Broad-spectrum amino-acid racemases (Bsrs) enable bacteria to generate noncanonical D-amino acids, the roles of which in microbial physiology, including the modulation of cell-wall structure and the dissolution of biofilms, are just beginning to be a ...

    Broad-spectrum amino-acid racemases (Bsrs) enable bacteria to generate noncanonical D-amino acids, the roles of which in microbial physiology, including the modulation of cell-wall structure and the dissolution of biofilms, are just beginning to be appreciated. Here, extensive crystallographic, mutational, biochemical and bioinformatic studies were used to define the molecular features of the racemase BsrV that enable this enzyme to accommodate more diverse substrates than the related PLP-dependent alanine racemases. Conserved residues were identified that distinguish BsrV and a newly defined family of broad-spectrum racemases from alanine racemases, and these residues were found to be key mediators of the multispecificity of BrsV. Finally, the structural analysis of an additional Bsr that was identified in the bioinformatic analysis confirmed that the distinguishing features of BrsV are conserved among Bsr family members.


    Organizational Affiliation

    Department of Crystallography and Structural Biology, Instituto de Química-Física `Rocasolano'-CSIC, 28006 Madrid, Spain.,Division of Infectious Diseases, Brigham and Women's Hospital and Department of Microbiology and Immunobiology, Harvard Medical School and HHMI, Boston, MA 02115, USA.,Centro de Biología Molecular `Severo Ochoa', Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain.,Centro Nacional de Biotecnología-CSIC, 28049 Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALANINE RACEMASE
A
392Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)Mutation(s): 0 
Gene Names: bsrV
EC: 5.1.1.10
Find proteins for Q9KSE5 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  Q9KSE5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.163 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 96.621α = 90.00
b = 51.093β = 101.15
c = 76.731γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-01-22
    Type: Database references
  • Version 1.2: 2014-07-09
    Type: Database references