Acta Crystallographica Section D

Biological Crystallography

Volume 70, Part 2 (February 2014)

research papers

Acta Cryst. (2014). D70, 596-606    [ doi:10.1107/S1399004713031283 ]

PLP undergoes conformational changes during the course of an enzymatic reaction

H.-P.-T. Ngo, N. M. F. S. A. Cerqueira, J.-K. Kim, M.-K. Hong, P. A. Fernandes, M. J. Ramos and L.-W. Kang

Abstract: Numerous enzymes, such as the pyridoxal 5'-phosphate (PLP)-dependent enzymes, require cofactors for their activities. Using X-ray crystallography, structural snapshots of the L-­serine dehydratase catalytic reaction of a bacterial PLP-dependent enzyme were determined. In the structures, the dihedral angle between the pyridine ring and the Schiff-base linkage of PLP varied from 18° to 52°. It is proposed that the organic cofactor PLP directly catalyzes reactions by active conformational changes, and the novel catalytic mechanism involving the PLP cofactor was confirmed by high-level quantum-mechanical calculations. The conformational change was essential for nucleophilic attack of the substrate on PLP, for concerted proton transfer from the substrate to the protein and for directing carbanion formation of the substrate. Over the whole catalytic cycle, the organic cofactor catalyzes a series of reactions, like the enzyme. The conformational change of the PLP cofactor in catalysis serves as a starting point for identifying the previously unknown catalytic roles of organic cofactors.

PDB references: 4ixz, 4iy7 and 4iyo

Keywords: pyridoxal 5'-phosphate; XometC; PLP-dependent enzymes; cofactor conformational change; cofactor-based catalysis; Xanthomonas oryzae pv. oryzae.

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