4BHY | pdb_00004bhy

Structure of alanine racemase from Aeromonas hydrophila

• PDB DOI: https://doi.org/10.2210/pdb4BHY/pdb

• Classification: ISOMERASE
• Organism(s): Aeromonas hydrophila subsp. hydrophila
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-04-09 Released: 2014-01-15 
• Deposition Author(s): Otero, L.H., Carrasco-Lopez, C., Bernardo-Garcia, N., Hermoso, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 
  0.292 (Depositor), 0.349 (DCC) 
• R-Value Work: 
  0.256 (Depositor), 0.302 (DCC) 
• R-Value Observed: 
  0.260 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1107/S1399004713024838
• Primary Citation 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.
Department of Crystallography and Structural Biology, Instituto de Química-Física `Rocasolano'-CSIC, 28006 Madrid, Spain.
Centro Nacional de Biotecnología-CSIC, 28049 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.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 166.02 kDa 
• Atom Count: 10,083 
• Modeled Residue Count: 1,298 
• Deposited Residue Count: 1,512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALANINE RACEMASE	A, B, C, D	378	Aeromonas hydrophila subsp. hydrophila	Mutation(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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B, C, D	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free:  0.292 (Depositor), 0.349 (DCC) 
• R-Value Work:  0.256 (Depositor), 0.302 (DCC) 
• R-Value Observed: 0.260 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.804	α = 90
b = 134.738	β = 90
c = 192.147	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
BALBES	phasing
PHASER	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): Otero, L.H., Carrasco-Lopez, C., Bernardo-Garcia, N., 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 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description