4IY7
crystal structure of cystathionine gamma lyase (XometC) from Xanthomonas oryzae pv. oryzae in complex with E-site serine, A-site external aldimine structure with serine and A-site external aldimine structure with aminoacrylate intermediates
Summary for 4IY7
| Entry DOI | 10.2210/pdb4iy7/pdb |
| Related | 4IXS 4IXZ 4IYO |
| Descriptor | Cystathionine gamma-lyase-like protein, SERINE, GLYCEROL, ... (8 entities in total) |
| Functional Keywords | xocgl, serine external schiff base, aminoacrylate external schiff base, plp dependent enzyme, lyase, 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 | 172737.92 |
| Authors | Ngo, H.P.T.,Kim, J.K.,Kang, L.W. (deposition date: 2013-01-28, release date: 2014-01-29, Last modification date: 2023-11-15) |
| 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 Cited by 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: 24531493DOI: 10.1107/S1399004713031283 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.7 Å) |
Structure validation
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