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Catalytic Site Atlas

CSA LITERATURE entry for 1h2r

E.C. namecytochrome-c3 hydrogenase
SpeciesDesulfovibrio vulgaris (strain DP4)
E.C. Number (IntEnz) 1.12.2.1
CSA Homologues of 1h2rThere are 23 Homologs
CSA Entries With UniProtID P21852
CSA Entries With EC Number 1.12.2.1
PDBe Entry 1h2r
PDBSum Entry 1h2r
MACiE Entry 1h2r

Literature Report

IntroductionHydrogenases are enzymes that catalyse the reversible heterolytic dissociation of molecular hydrogen H2 a H+ + H-. The largest class of hydrogenases contains a NiFe center that is believed to be the catalytic site for hydrogen activation.The active site comprises a heterobimetallic clusterof Ni and Fe atoms. The bridging ligand X is proposed to be sulphur species due to the release of H2S during the course of the reaction.
MechansimNo catalytic amino acid residues have been identified so far according to our definition. The 4 cysteine residues only serve to coordinate to the catalytic metal cofactors, however one could act as a general base, but there is no experimental evidence as yet to identify one.
Dihydrogen coordinates to the Ni(II) centre, and a single electron is transferred from Ni(II) to the electron acceptor through the iron-sulfur clusters. A general base, deprotonates the hydrogen molecules, which forms a hydride ion that bridges the two metal centres. The general base loses its proton to bulk solvent in which another residue acts as a proton relay. A general base accepts the bridging hydride, with the electron pair being donated to the Ni(III) centre. The general base loses its proton to bulk solvent in which another residue acts as a proton relay. A single electron is transferred from the Ni(III) centre to the electron acceptor via the iron-sulfur clusters.

Catalytic Sites for 1h2r

Literature References

Notes:
Stein M
Relativistic DFT calculations of the paramagnetic intermediates of [NiFe] hydrogenase. Implications for the enzymatic mechanism.
J Am Chem Soc 2001 123 5839-5840
PubMed: 11403633
Higuchi Y
Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution.
Structure 1999 7 549-556
PubMed: 10378274
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