4IXZ

Native structure of cystathionine gamma lyase (XometC) from xanthomonas oryzae pv. oryzae at pH 9.0

Replaces:  3NMY

Summary for 4IXZ

• Entry DOI: 10.2210/pdb4ixz/pdb
• Related: 4IXS 4IY7 4IYO
• Descriptor: Cystathionine gamma-lyase-like protein, BICARBONATE ION, BETA-MERCAPTOETHANOL, ... (5 entities in total)
• Functional Keywords: plp dependent enzyme, lyase, xocgl, native, cys-met metabolism plp dependent enzyme, cystathionine gamma lyase, plp binding
• Biological source: Xanthomonas oryzae pv. oryzae
• Total number of polymer chains: 4
• Total formula weight: 171842.29

Authors

Ngo, H.P.T.,Kim, J.K.,Kang, L.W. (deposition date: 2013-01-28, release date: 2014-01-29, Last modification date: 2023-12-06)

Primary citation

Ngo, H.P.,Cerqueira, N.M.,Kim, J.K.,Hong, M.K.,Fernandes, P.A.,Ramos, M.J.,Kang, L.W.
PLP undergoes conformational changes during the course of an enzymatic reaction.
Acta Crystallogr.,Sect.D, 70:596-606, 2014

PubMed 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.

PubMed: 24531493
DOI: 10.1107/S1399004713031283

Experimental method

X-RAY DIFFRACTION (2.07 Å)