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Catalytic Site Atlas

CSA LITERATURE entry for 1hfe

E.C. nameferredoxin hydrogenase
SpeciesDesulfovibrio vulgaris (strain DP4)
E.C. Number (IntEnz) 1.12.7.2
CSA Homologues of 1hfe1c4a,1c4c,1e08,1feh,1gx7,3c8y,
CSA Entries With UniProtID P07598
CSA Entries With EC Number 1.12.7.2
PDBe Entry 1hfe
PDBSum Entry 1hfe
MACiE Entry M0127

Literature Report

IntroductionThe Fe only hydrogenase from Desulphovibrio desulphuricans is able to catalyse the heterolytic fission of molecular hydrogen to release protons and electrons. It is part of a family of Fe only hydrogenases which all have two iron centres at the active site, in contrast to the better known Ni-Fe hydrogenases with which they share no sequence or structural homology. The mechanism by which the hydrogenases work is of great interest to biologists and engineers alike as it offers the possibility of using hydrogen as a fuel more effectively.
MechansimThe catalytically active redox state for the binuclear iron centre is, for the formation of hydrogen, Fe(I) Fe(I). This becomes protonated by Lys 237 with the proximal Fe (I) centre accepting a proton. The proximal centre then passes two electrons to the proton to form a hydride ion which stays bonded to the iron, and the distal iron centre assists with this by passing an electron to the proximal centre, forming a Fe (II) Fe (II)H- centre. The bidentate iron ligand DTN is then able to accept a further proton from Cys 178 which allows the hydride ion to act as a base and form molecular hydrogen. This stays bound to the proximal iron centre until an electron is passed from the protein to the centre, at which point H2 is released, generating an Fe (I) Fe (II) centre, which must be further reduced by accepting an electron from the surrounding protein to reform the catalytically active structure. The electrons are presumed to come from the nearby iron sulphur centre, which in turn connects with reducing agents in the cell.

Catalytic Sites for 1hfe

Annotated By Reference To The Literature - Site 3 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysL237237macie:sideChainActs as general acid-base to protonate the proximal iron centre in the first stage of the reaction.
CysL178178macie:sideChainActs as general acid-base for transfer of the second proton to the iron ligand DTN.

Annotated By Reference To The Literature - Site 4 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysM237237macie:sideChainActs as general acid-base to protonate the proximal iron centre in the first stage of the reaction.
CysM178178macie:sideChainActs as general acid-base for transfer of the second proton to the iron ligand DTN.

Literature References

Notes:
Z.-P. Liu
Mechanism of H2 Metabolism on Fe-Only Hydrogenases
J. Chem. Phys. 2002 117 8177-8180
PubMed: Liu2002
Peters JW
X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution.
Science 1998 282 1853-1858
PubMed: 9836629
Nicolet Y
Fe-only hydrogenases: structure, function and evolution.
J Inorg Biochem 2002 91 1-8
PubMed: 12121756
Nicolet Y
Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center.
Structure 1999 7 13-23
PubMed: 10368269
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