Ferredoxin hydrogenase

 

The iron-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 iron-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.

 

Reference Protein and Structure

Sequences
P07598 UniProt (1.12.7.2)
P07603 UniProt (1.12.7.2) IPR013352 (Sequence Homologues) (PDB Homologues)
Biological species
Desulfovibrio vulgaris str. Hildenborough (Bacteria) Uniprot
PDB
1hfe - 1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS (1.6 Å) PDBe PDBsum 1hfe
Catalytic CATH Domains
3.40.50.1780 CATHdb 3.40.950.10 CATHdb (see all for 1hfe)
Cofactors
Tetra-mu3-sulfido-tetrairon (3), Iron(2+) (2), Water (4), Iminodimethanethiolate (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:1.12.7.2)

hydron
CHEBI:15378ChEBI
+
di-mu-sulfido-diiron(1+)
CHEBI:33738ChEBI
→
dihydrogen
CHEBI:18276ChEBI
+
di-mu-sulfido-diiron(2+)
CHEBI:33737ChEBI
Alternative enzyme names: H(2) oxidizing hydrogenase, H(2) producing hydrogenase, Bidirectional hydrogenase, Hydrogen-lyase, Hydrogenase (ferredoxin), Hydrogenase I, Hydrogenase II, Hydrogenlyase, Uptake hydrogenase, Hydrogenase,

Enzyme Mechanism

Introduction

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.

Catalytic Residues Roles

UniProt PDB* (1hfe)
Glu156, Glu159, Cys178, Ser198, Lys237, Glu240, Glu245 Glu156L(B), Glu159L(B), Cys178L(B), Ser198L(B), Lys237L(B), Glu240L(B), Glu245L(B) Form one of the proton relay chains that links the active site with bulk solvent. proton relay, proton acceptor, proton donor
Cys382 Cys382L(B) Cys382 is a bridging ligand between one of the iron-sulfur clusters and the diiron centre. metal ligand
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

proton transfer, electron transfer, coordination, heterolysis, substitution (not covered by the Ingold mechanisms), bimolecular nucleophilic substitution, native state of cofactor regenerated, native state of enzyme regenerated

References

  1. Zhou T et al. (2004), Inorg Chem, 43, 923-930. Enzymatic Mechanism of Fe-Only Hydrogenase:  Density Functional Study on H−H Making/Breaking at the Diiron Cluster with Concerted Proton and Electron Transfers. DOI:10.1021/ic0342301. PMID:14753812.
  2. Kubas A et al. (2017), Nat Chem, 9, 88-95. Mechanism of O2 diffusion and reduction in FeFe hydrogenases. DOI:10.1038/nchem.2592. PMID:27995927.
  3. Sode O et al. (2014), J Chem Phys, 141, 22D527-. Electron transfer activation of a second water channel for proton transport in [FeFe]-hydrogenase. DOI:10.1063/1.4902236. PMID:25494798.
  4. Myers WK et al. (2014), J Am Chem Soc, 136, 12237-12240. The cyanide ligands of [FeFe] hydrogenase: pulse EPR studies of (13)C and (15)N-labeled H-cluster. DOI:10.1021/ja507046w. PMID:25133957.
  5. Huynh MT et al. (2014), Inorg Chem, 53, 10301-10311. Computational investigation of [FeFe]-hydrogenase models: characterization of singly and doubly protonated intermediates and mechanistic insights. DOI:10.1021/ic5013523. PMID:25207842.
  6. Winkler M et al. (2013), Biochim Biophys Acta, 1827, 974-985. Molecular basis of [FeFe]-hydrogenase function: an insight into the complex interplay between protein and catalytic cofactor. DOI:10.1016/j.bbabio.2013.03.004. PMID:23507618.
  7. Wang N et al. (2013), Dalton Trans, 42, 12059-12071. Reactions of [FeFe]-hydrogenase models involving the formation of hydrides related to proton reduction and hydrogen oxidation. DOI:10.1039/c3dt51371h. PMID:23846321.
  8. Miyake T et al. (2013), J Biol Inorg Chem, 18, 693-700. Does the environment around the H-cluster allow coordination of the pendant amine to the catalytic iron center in [FeFe] hydrogenases? Answers from theory. DOI:10.1007/s00775-013-1014-4. PMID:23793236.
  9. Morra S et al. (2012), PLoS One, 7, e48400-. Site saturation mutagenesis demonstrates a central role for cysteine 298 as proton donor to the catalytic site in CaHydA [FeFe]-hydrogenase. DOI:10.1371/journal.pone.0048400. PMID:23133586.
  10. Knörzer P et al. (2012), J Biol Chem, 287, 1489-1499. Importance of the protein framework for catalytic activity of [FeFe]-hydrogenases. DOI:10.1074/jbc.M111.305797. PMID:22110126.
  11. Hong G et al. (2011), Biochim Biophys Acta, 1807, 510-517. On understanding proton transfer to the biocatalytic [Fe-Fe](H) sub-cluster in [Fe-Fe]H(2)ases: QM/MM MD simulations. DOI:10.1016/j.bbabio.2011.01.011. PMID:21296047.
  12. Cornish AJ et al. (2011), J Biol Chem, 286, 38341-38347. Mechanism of proton transfer in [FeFe]-hydrogenase from Clostridium pasteurianum. DOI:10.1074/jbc.M111.254664. PMID:21900241.
  13. Mulder DW et al. (2011), Structure, 19, 1038-1052. Insights into [FeFe]-hydrogenase structure, mechanism, and maturation. DOI:10.1016/j.str.2011.06.008. PMID:21827941.
  14. Motiu S et al. (2010), Int J Quantum Chem, 110, 2705-2718. [Fe-Fe]-hydrogenase Reactivated by Residue Mutations as Bridging Carbonyl Rearranges: A QM/MM Study. DOI:10.1002/qua.22381. PMID:26045628.
  15. Silakov A et al. (2009), Phys Chem Chem Phys, 11, 6592-6599. (14)N HYSCORE investigation of the H-cluster of [FeFe] hydrogenase: evidence for a nitrogen in the dithiol bridge. DOI:10.1039/b905841a. PMID:19639134.
  16. Dogaru D et al. (2009), Int J Quantum Chem, 110, 1784-1792. Residue Mutations in [Fe-Fe]-hydrogenase Impedes O(2) Binding: A QM/MM Investigation. DOI:10.1002/qua.22331. PMID:20485511.
  17. Lee JW et al. (2009), Dalton Trans, 8532-8537. Effect of Lewis acid on the structure of a diiron dithiolate complex based on the active site of [FeFe]-hydrogenase assessed by density functional theory. DOI:10.1039/b905786b. PMID:19809728.
  18. Dogaru D et al. (2009), Int J Quantum Chem, 109, 876-889. Inactivation of [Fe-Fe]-Hydrogenase by O(2). Thermodynamics and Frontier Molecular Orbitals Analyses. DOI:10.1002/qua.21875. PMID:20160838.
  19. Liu Z et al. (2002), J Chem Phys, 117, 8177-8180. Mechanism of H2 metabolism on Fe-only hydrogenases. DOI:10.1063/1.1519252.
  20. Liu ZP et al. (2002), J Am Chem Soc, 124, 5175-5182. A Density Functional Theory Study on the Active Center of Fe-Only Hydrogenase:  Characterization and Electronic Structure of the Redox States. DOI:10.1021/ja0118690. PMID:11982382.
  21. Nicolet Y et al. (2002), J Inorg Biochem, 91, 1-8. Fe-only hydrogenases: structure, function and evolution. DOI:10.1016/s0162-0134(02)00392-6. PMID:12121756.
  22. Nicolet Y et al. (1999), Structure, 7, 13-23. Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center. DOI:10.1016/s0969-2126(99)80005-7. PMID:10368269.
  23. Peters JW et al. (1998), Science, 282, 1853-1858. X-ray Crystal Structure of the Fe-Only Hydrogenase (CpI) from Clostridium pasteurianum to 1.8 Angstrom Resolution. DOI:10.1126/science.282.5395.1853. PMID:9836629.

Step 1. Each of the Fe(I) centres donates a single electron to one of the Lys237 protons, forming a 2-electron-3-centre bond bridging the two Fe(II) centres. The loss of the proton from Lys237 initiates a proton relay chain that involves Glu240, three water molecules and Glu245 before terminating in the bulk solvent.

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Catalytic Residues Roles

Residue Roles
Lys237L(B) proton donor
Cys382L(B) metal ligand
Glu245L(B) proton donor
Lys237L(B) proton acceptor
Glu240L(B) proton acceptor
Glu245L(B) proton acceptor
Glu240L(B) proton donor
Lys237L(B) proton relay
Glu240L(B) proton relay
Glu245L(B) proton relay

Chemical Components

proton transfer, electron transfer, coordination, heterolysis

Step 2. One of the iron-bound thiolates deprotonates Cys178, which initiates a proton relay chain that involves water,Glu156, Ser198 and Glu159 before terminating in bulk solvent.

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Catalytic Residues Roles

Residue Roles
Cys382L(B) metal ligand
Glu159L(B) proton acceptor
Cys178L(B) proton acceptor
Glu156L(B) proton acceptor
Ser198L(B) proton acceptor
Cys178L(B) proton donor
Glu159L(B) proton donor
Ser198L(B) proton donor
Glu156L(B) proton donor, proton relay
Glu159L(B) proton relay
Cys178L(B) proton relay
Ser198L(B) proton relay

Chemical Components

proton transfer

Step 3. The bridging hydride deprotonates the thiol, reforming the bound thiolate and a hydrogen molecule bound to one of the Fe(II) centres in a bidentate fashion.

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Catalytic Residues Roles

Residue Roles
Cys382L(B) metal ligand

Chemical Components

proton transfer

Step 4. Ferrocytochrome C2 donates a single electron through three iron-sulfur clusters and to the on the Fe(II) centres. This initiates the coordination of the hydrogen molecule through a single hydrogen atom to both iron centres.

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Catalytic Residues Roles

Residue Roles
Cys382L(B) metal ligand

Chemical Components

substitution (not covered by the Ingold mechanisms), electron transfer

Step 5. One of the carbon monoxide ligands initiates a nucleophilic substitution, resulting in the hydrogen molecule being bound to the Fe(II) centre in a bidentate fashion.

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Catalytic Residues Roles

Residue Roles
Cys382L(B) metal ligand

Chemical Components

ingold: bimolecular nucleophilic substitution

Step 6. Ferrocytochrome C3 donates a second electron through three iron-sulfur clusters to the second Fe(II) centre, initiating the heterolysis of the bond between the hydrogen molecule and Fe(II) centre.

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Catalytic Residues Roles

Residue Roles
Cys382L(B) metal ligand

Chemical Components

electron transfer, native state of cofactor regenerated, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. Each of the Fe(I) centres donates a single electron to one of the Lys237 protons, forming a 2-electron-3-centre bond bridging the two Fe(II) centres. The loss of the proton from Lys237 initiates a proton relay chain that involves Glu240, three water molecules and Glu245 before terminating in the bulk solvent.

Step 2. One of the iron-bound thiolates deprotonates Cys178, which initiates a proton relay chain that involves water,Glu156, Ser198 and Glu159 before terminating in bulk solvent.

Step 3. The bridging hydride deprotonates the thiol, reforming the bound thiolate and a hydrogen molecule bound to one of the Fe(II) centres in a bidentate fashion.

Step 4. Ferrocytochrome C2 donates a single electron through three iron-sulfur clusters and to the on the Fe(II) centres. This initiates the coordination of the hydrogen molecule through a single hydrogen atom to both iron centres.

Step 5. One of the carbon monoxide ligands initiates a nucleophilic substitution, resulting in the hydrogen molecule being bound to the Fe(II) centre in a bidentate fashion.

Step 6. Ferrocytochrome C3 donates a second electron through three iron-sulfur clusters to the second Fe(II) centre, initiating the heterolysis of the bond between the hydrogen molecule and Fe(II) centre.

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid, Peter Sarkies