4BHY

Structure of alanine racemase from Aeromonas hydrophila


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.260 

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 D Biol Crystallogr 70: 79

  • 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 ...

    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

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALANINE RACEMASEA, B, C, D378Aeromonas hydrophila subsp. hydrophilaMutation(s): 0 
EC: 5.1.1.1
UniProt
Find proteins for A0KH11 (Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / BCRC 13018 / CCUG 14551 / JCM 1027 / KCTC 2358 / NCIMB 9240 / NCTC 8049))
Explore A0KH11 
Go to UniProtKB:  A0KH11
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0KH11
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, B, C, D L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.260 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.804α = 90
b = 134.738β = 90
c = 192.147γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
BALBESphasing
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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