Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 42.92 kDa 
• Atom Count: 3592 
• Modelled Residue Count: 392 
• Deposited Residue Count: 392 
• Unique protein chains: 1

4BEU

Structure of Vibrio cholerae broad spectrum racemase

• PDB DOI: 10.2210/pdb4BEU/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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 
• R-Value Observed: 0.164 

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 D Biol Crystallogr 70: 79

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


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALANINE RACEMASE	A	392	Vibrio cholerae	Mutation(s): 0  EC: 5.1.1.1 (PDB Primary Data), 5.1.1.10 (UniProt)
UniProt
Find proteins for Q9KSE5 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KSE5  Go to UniProtKB:  Q9KSE5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.173 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.621	α = 90
b = 51.093	β = 101.15
c = 76.731	γ = 90

Software Package:

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

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
  Changes: Database references
• Version 1.2: 2014-07-09
  Changes: Database references
• Version 2.0: 2020-01-15
  Changes: Atomic model, Derived calculations, Other