4IXZ: Native Structure Of Cystathionine Gamma Lyase (xometc) From Xanthomonas Oryzae Pv. Oryzae At Ph 9.0

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 degrees to 52 degrees . 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 ID: 4IXZDownload
MMDB ID: 117005
PDB Deposition Date: 2013/1/28
Updated in MMDB: 2017/05
Experimental Method:
x-ray diffraction
Resolution: 2.07  Å
Source Organism:
Similar Structures:
Biological Unit for 4IXZ: tetrameric; determined by author and by software (PISA)
Molecular Components in 4IXZ
Label Count Molecule
Proteins (4 molecules)
Cystathionine Gamma-lyase-like Protein
Molecule annotation
Chemicals (5 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB