6Q72

Crystal structure of the alanine racemase from Bacillus subtilis in the presence of only PEG 4000 and Magnesium chloride in the crystallization condition

Summary for 6Q72

• Entry DOI: 10.2210/pdb6q72/pdb
• Related: 5IRP
• Descriptor: Alanine racemase 2, PYRIDOXAL-5'-PHOSPHATE, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: racemase, alanine racemase, isomerase
• Biological source: Bacillus subtilis
• Total number of polymer chains: 4
• Total formula weight: 175965.74

Authors

Bernardo-Garcia, N.,Gago, F.,Hermoso, J.A. (deposition date: 2018-12-12, release date: 2019-04-24, Last modification date: 2024-01-24)

Primary citation

Bernardo-Garcia, N.,Sanchez-Murcia, P.A.,Espaillat, A.,Martinez-Caballero, S.,Cava, F.,Hermoso, J.A.,Gago, F.
Cold-induced aldimine bond cleavage by Tris in Bacillus subtilis alanine racemase.
Org.Biomol.Chem., 17:4350-4358, 2019

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.

PubMed: 30977502
DOI: 10.1039/c9ob00223e

Experimental method

X-RAY DIFFRACTION (3 Å)