Get   for     ? 
 Site search     ? 
Catalytic Site Atlas Version 2.2.12
Find Annotated Site: PDB code:
Swiss-Prot code:
EC number:
Help
CSA entry for 1hfe
Original Entry
Title:
Hydrogenase
Compound:
Fe-only hydrogenase (larger subunit)
Mutant:
No
UniProt/Swiss-Prot:
P07598-PHFL_DESVH
P07603-PHFS_DESVH
EC Class:
1.12.7.2
Other CSA Entries:
Overview of all sites for 1hfe
Homologues of 1hfe
Entries for UniProt/Swiss-Prot: P07598
Entries for UniProt/Swiss-Prot: P07603
Entries for EC: 1.12.7.2
Other Databases:
PDB entry: 1hfe
PDBsum entry: 1hfe
UniProt/Swiss-Prot: P07598
UniProt/Swiss-Prot: P07603
IntEnz entry: 1.12.7.2
Literature Report:
Introduction:
The 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.
Mechanism:
The 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.
Sites:

Click to Display Catalytic Site (Get help with this section)
Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
CYSL 178 178Sidechain
Acid/baseCofactor
Acts as general acid-base for transfer of the second proton to the iron ligand DTN.
Evidence from paper Evidence concerns Evidence type
PubMed ID 9836629 Related protein: UniProt P29166 Residue is positioned appropriately (ligand position hypothetical)
PubMed ID 12121756 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
LYSL 237 237Sidechain
Acid/baseCofactor
Acts as general acid-base to protonate the proximal iron centre in the first stage of the reaction.
Evidence from paper Evidence concerns Evidence type
Evidence from paper listed as having "No PubMed ID available." below. Current protein Residue is positioned appropriately (ligand position hypothetical)
Evidence from paper listed as having "No PubMed ID available." below. Current protein Computer modelling

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
PDTL 425 0
Acid/baseSubstrate
Is protonated by Cys 178 to allow the formation of molecular hydrogen by attack from the hydride ion bound at the proximal Fe centre.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12121756 Current protein Residue is positioned appropriately (ligand position hypothetical)
Evidence from paper listed as having "No PubMed ID available." below. Current protein Computer modelling

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
FE2L 427 0
Electron donor/acceptorCofactor
Acts to supply electrons to the proximal Fe centre (FE2 426) thus allowing it to bind to the hydride ion and to molecular hydrogen. Thus is oxidised and reduced in the reaction cycle.
Evidence from paper Evidence concerns Evidence type
Evidence from paper listed as having "No PubMed ID available." below. Current protein Computer modelling
PubMed ID 10368269 Current protein Ligand is essential for catalysis
References:
1
Mechanism of H2 metabolism on Fe-only hydrogenases
Zhi-Pan Liu and P.Hu
J Chemical Physics 117, (18) 8177-8180, (2002)
No PubMed ID available
2
X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution.
J. W. Peters and W. N. Lanzilotta and B. J. Lemon and L. C. Seefeldt
Science 282, (5395) 1853-8, (1998).
9836629
3
Fe-only hydrogenases: structure, function and evolution.
Y. Nicolet and C. Cavazza and J. C. Fontecilla-Camps
J Inorg Biochem 91, (1) 1-8, (2002).
12121756
4
Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center.
Y. Nicolet and C. Piras and P. Legrand and C. E. Hatchikian and J. C. Fontecilla-Camps
Structure Fold Des 7, (1) 13-23, (1999).
10368269
Which EBI biological databases are available and how do I access them? EBI Site Map