6Q70

Crystal structure of the alanine racemase Bsu17640 from Bacillus subtilis in the presence of HEPES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Cold-induced aldimine bond cleavage by Tris in Bacillus subtilis alanine racemase.

Bernardo-Garcia, N.Sanchez-Murcia, P.A.Espaillat, A.Martinez-Caballero, S.Cava, F.Hermoso, J.A.Gago, F.

(2019) Org Biomol Chem 17: 4350-4358

  • DOI: https://doi.org/10.1039/c9ob00223e
  • Primary Citation of Related Structures:  
    5IRP, 6Q70, 6Q71, 6Q72

  • PubMed Abstract: 

    Pyridoxal 5'-phosphate (PLP) is a versatile cofactor involved in a large variety of enzymatic processes. Most of PLP-catalysed reactions, such as those of alanine racemases (AlaRs), present a common resting state in which the PLP is covalently bound to an active-site lysine to form an internal aldimine. The crystal structure of BsAlaR grown in the presence of Tris lacks this covalent linkage and the PLP cofactor appears deformylated. However, loss of activity in a Tris buffer only occurred after the solution was frozen prior to carrying out the enzymatic assay. This evidence strongly suggests that Tris can access the active site at subzero temperatures and behave as an alternate racemase substrate leading to mechanism-based enzyme inactivation, a hypothesis that is supported by additional X-ray structures and theoretical results from QM/MM calculations. Taken together, our findings highlight a possibly underappreciated role for a common buffer component widely used in biochemical and biophysical experiments.


  • Organizational Affiliation

    Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, 28006 Madrid, Spain. xjuan@iqfr.csic.es.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alanine racemase 2
A, B
394Bacillus subtilisMutation(s): 0 
Gene Names: alr2yncDBSU17640
EC: 5.1.1.1
UniProt
Find proteins for P94494 (Bacillus subtilis (strain 168))
Explore P94494 
Go to UniProtKB:  P94494
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP94494
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.655α = 90
b = 73.655β = 90
c = 331.612γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description