6Q71 image
Deposition Date 2018-12-12
Release Date 2019-04-24
Last Version Date 2024-01-24
Entry Detail
PDB ID:
6Q71
Keywords:
Title:
Crystal structure of the alanine racemase Bsu17640 from Bacillus subtilis in the presence of Bis-Tris propane
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.92 Å
R-Value Free:
0.23
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 43 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Alanine racemase 2
Chain IDs:A, B
Chain Length:394
Number of Molecules:2
Biological Source:Bacillus subtilis
Primary Citation
Cold-induced aldimine bond cleavage by Tris in Bacillus subtilis alanine racemase.
Org.Biomol.Chem. 17 4350 4358 (2019)
PMID: 30977502 DOI: 10.1039/c9ob00223e

Abstact

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.

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