Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42923.74 
• Atom Count: 3074 
• Residue Count: 392 
• Unique protein chains: 1

4BEU

Structure of Vibrio cholerae broad spectrum racemase

• DOI: 10.2210/pdb4BEU/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2013-03-12 Released: 2014-01-15 
• Deposition Author(s): Carrasco-Lopez, C., Hermoso, J.A.

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Experimental Data Snapshot

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

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

• PubMed: 24419381 
• DOI: 10.1107/S1399004713024838
• Primary Citation of Related Structures:  
  4BHY, 4BF5, 4BEQ


• 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 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.

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Organizational Affiliation: 

Centro de Biología Molecular `Severo Ochoa', Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ALANINE RACEMASE	A	392	Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)	Mutation(s): 0  Gene Names: alr2 EC: 5.1.1.1
Find proteins for Q9KSE5 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Go to UniProtKB:  Q9KSE5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
PLP	A	PYRIDOXAL-5'-PHOSPHATE VITAMIN B6 Phosphate C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

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 = 96.621	α = 90.00
b = 51.093	β = 101.15
c = 76.731	γ = 90.00

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
PHENIX	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-03-12 
• Released Date: 2014-01-15 
• Deposition Author(s): Carrasco-Lopez, C., Hermoso, J.A.

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