DB code: M00012

RLCP classification 10.22100.110.10570 : Electron transfer
10.22022.100.10751 : Electron transfer
10.120022.100.10610 : Electron transfer
CATH domain 3.40.50.1780 : Rossmann fold Catalytic domain
3.30.70.20 : Alpha-Beta Plaits
3.40.950.10 : Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 Catalytic domain
4.10.260.20 : G Protein Gi Gamma 2
E.C. 1.12.7.2
CSA 1hfe
M-CSA 1hfe
MACiE M0127

CATH domain Related DB codes (homologues)
3.30.70.20 : Alpha-Beta Plaits M00207 M00042
3.40.50.1780 : Rossmann fold M00042
3.40.950.10 : Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 M00042

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P07598 Periplasmic [Fe] hydrogenase large subunit
EC 1.12.7.2
Fe hydrogenlyase
YP_010987.1 (Protein)
NC_002937.3 (DNA/RNA sequence)
PF02906 (Fe_hyd_lg_C)
PF00037 (Fer4)
[Graphical View]
P07603 Periplasmic [Fe] hydrogenase small subunit
EC 1.12.7.2
Fe hydrogenlyase small chain
YP_010988.1 (Protein)
NC_002937.3 (DNA/RNA sequence)
PF02256 (Fe_hyd_SSU)
[Graphical View]

KEGG enzyme name
ferredoxin hydrogenase
H2 oxidizing hydrogenase
H2 producing hydrogenase [ambiguous]
bidirectional hydrogenase
hydrogen-lyase [ambiguous]
hydrogenase (ferredoxin)
hydrogenase I
hydrogenase II
hydrogenlyase [ambiguous]
uptake hydrogenase [ambiguous]

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P07603 PHFS_DESVH H(2) + 2 oxidized ferredoxin = 2 reduced ferredoxin + 2 H(+). Heterodimer of a large and a small subunit. Periplasm.
P07598 PHFL_DESVH H(2) + 2 oxidized ferredoxin = 2 reduced ferredoxin + 2 H(+). Heterodimer of a large and a small subunit. Periplasm. Binds 3 4Fe-4S clusters per subunit. Binds 2 iron ions per subunit.

KEGG Pathways
Map code Pathways E.C.
MAP00680 Methane metabolism
MAP00630 Glyoxylate and dicarboxylate metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id L00024 L00030 C00282 C00125 C00125 C00126 C00126 C00080
E.C.
Compound [4Fe-4S] [4Fe-4S]--diiron/di(thiomethyl)amine/2CN/2CO(H-cluster) H2 Ferricytochrome c3 Ferricytochrome c6 Ferrocytochrome c3 Ferrocytochrome c6 H+
Type heavy metal,sulfide group heavy metal,sulfide group others amide group,amine group,aromatic ring (with nitrogen atoms),carboxyl group,heavy metal,sulfide group amide group,amine group,aromatic ring (with nitrogen atoms),carboxyl group,heavy metal,sulfide group amide group,amine group,aromatic ring (with nitrogen atoms),carboxyl group,heavy metal,sulfide group amide group,amine group,aromatic ring (with nitrogen atoms),carboxyl group,heavy metal,sulfide group others
ChEBI 33725
18276
15378
PubChem 58838673
783
1038
1hfeL01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:SF4-2xFE2-2xCYN-2xCMO-PDT Unbound Unbound Unbound Unbound
1hfeM01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:SF4-2xFE2-2xCYN-2xCMO-PDT Unbound Unbound Unbound Unbound
1e08A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:SF4-2xFE2-2xCYN-2xCMO-PDT Unbound Unbound Unbound Unbound
1hfeL02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2xSF4 Unbound Unbound Unbound Unbound Unbound
1hfeM02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2xSF4 Unbound Unbound Unbound Unbound Unbound
1e08A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2xSF4 Unbound Unbound Bound:HEM(chain E) Unbound Unbound
1hfeL03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1hfeM03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1e08A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1hfeS Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1hfeT Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1e08D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P07598 & literature [8], [10], [12], [15]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1hfeL01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 237 CYS 234(4Fe-4S cluster-3 [H-cluster]);CYS 382(4Fe-4S cluster-3 & diiron [2Fe] subcluster binding [H-cluster])
1hfeM01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 237 CYS 234(4Fe-4S cluster-3 [H-cluster]);CYS 382(4Fe-4S cluster-3 & diiron [2Fe] subcluster binding [H-cluster])
1e08A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 237 CYS 234(4Fe-4S cluster-3 [H-cluster]);CYS 382(4Fe-4S cluster-3 & diiron [2Fe] subcluster binding [H-cluster])
1hfeL02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 38;CYS 41;ILE 50;CYS 69;GLN 71;CYS 72 CYS 35;CYS 38;CYS 41;CYS 76(4Fe-4S cluster-1);CYS 45;CYS 66;CYS 69;CYS 72(4Fe-4S cluster-2)
1hfeM02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 38;CYS 41;ILE 50;CYS 69;GLN 71;CYS 72 CYS 35;CYS 38;CYS 41;CYS 76(4Fe-4S cluster-1);CYS 45;CYS 66;CYS 69;CYS 72(4Fe-4S cluster-2)
1e08A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 38;CYS 41;ILE 50;CYS 69;GLN 71;CYS 72 CYS 35;CYS 38;CYS 41;CYS 76(4Fe-4S cluster-1);CYS 45;CYS 66;CYS 69;CYS 72(4Fe-4S cluster-2)
1hfeL03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 178;CYS 378 CYS 179;CYS 378(4Fe-4S cluster-3 [H-cluster])
1hfeM03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 178;CYS 378 CYS 179;CYS 378(4Fe-4S cluster-3 [H-cluster])
1e08A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 178;CYS 378 CYS 179;CYS 378(4Fe-4S cluster-3 [H-cluster])
1hfeS Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1hfeT Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1e08D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
Fig.12, Fig.13, Fig.14, p.137-138, p.139-140
[8]
p.16-20
[9]
Fig.1
[10]
p.672-674
[11]
[12]
p.141-142
[13]
[16]
Fig.2, p.154-157
[17]
Scheme 1, p.1428-1429
[18]
p.2-4
[19]
[20]
[23]
Scheme 1, Scheme 2, Scheme 3, p.4778-4781
[26]
Fig.5, p.926-930 6

References
[1]
Resource
Comments
Medline ID
PubMed ID 2830138
Journal FEBS Lett
Year 1988
Volume 228
Pages 85-8
Authors Patil DS, He SH, DerVartanian DV, Le Gall J, Huynh BH, Peck HD Jr
Title The relationship between activity and the axial g = 2.06 EPR signal induced by CO in the periplasmic (Fe) hydrogenase from Desulfovibrio vulgaris.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 2848804
Journal J Biol Chem
Year 1988
Volume 263
Pages 18732-8
Authors Patil DS, Moura JJ, He SH, Teixeira M, Prickril BC, DerVartanian DV, Peck HD Jr, LeGall J, Huynh BH
Title EPR-detectable redox centers of the periplasmic hydrogenase from Desulfovibrio vulgaris.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 2173950
Journal Biochim Biophys Acta
Year 1990
Volume 1020
Pages 115-45
Authors Adams MW
Title The structure and mechanism of iron-hydrogenases.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 1327776
Journal Eur J Biochem
Year 1992
Volume 209
Pages 357-65
Authors Hatchikian EC, Forget N, Fernandez VM, Williams R, Cammack R
Title Further characterization of the [Fe]-hydrogenase from Desulfovibrio desulfuricans ATCC 7757.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 8198565
Journal Biochem Biophys Res Commun
Year 1994
Volume 201
Pages 128-34
Authors Mus-Veteau I, Guerlesquin F
Title Involvement of histidine residues in the catalytic mechanism of hydrogenases.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 9346288
Journal Eur J Biochem
Year 1997
Volume 248
Pages 355-61
Authors van Dam PJ, Reijerse EJ, Hagen WR
Title Identification of a putative histidine base and of a non-protein nitrogen ligand in the active site of Fe-hydrogenases by one-dimensional and two-dimensional electron spin-echo envelope-modulation spectroscopy.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 9849942
Journal Proteins
Year 1998
Volume 33
Pages 590-600
Authors Brugna M, Giudici-Orticoni MT, Spinelli S, Brown K, Tegoni M, Bruschi M
Title Kinetics and interaction studies between cytochrome c3 and Fe-only hydrogenase from Desulfovibrio vulgaris Hildenborough.
Related PDB
Related UniProtKB
[8]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
Medline ID
PubMed ID 10368269
Journal Structure Fold Des
Year 1999
Volume 7
Pages 13-23
Authors Nicolet Y, Piras C, Legrand P, Hatchikian CE, Fontecilla-Camps JC
Title Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center.
Related PDB 1hfe
Related UniProtKB P07598 P07603
[9]
Resource
Comments
Medline ID
PubMed ID 9930693
Journal Nature
Year 1999
Volume 397
Pages 214-5
Authors Cammack R
Title Hydrogenase sophistication.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 10607666
Journal Curr Opin Struct Biol
Year 1999
Volume 9
Pages 670-6
Authors Peters JW
Title Structure and mechanism of iron-only hydrogenases.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 10748163
Journal J Biol Chem
Year 2000
Volume 275
Pages 23204-10
Authors Morelli X, Czjzek M, Hatchikian CE, Bornet O, Fontecilla-Camps JC, Palma NP, Moura JJ, Guerlesquin F
Title Structural model of the Fe-hydrogenase/cytochrome c553 complex combining transverse relaxation-optimized spectroscopy experiments and soft docking calculations.
Related PDB 1e08
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 10694885
Journal Trends Biochem Sci
Year 2000
Volume 25
Pages 138-43
Authors Nicolet Y, Lemon BJ, Fontecilla-Camps JC, Peters JW
Title A novel FeS cluster in Fe-only hydrogenases.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 11457119
Journal J Am Chem Soc
Year 2001
Volume 123
Pages 3828-9
Authors Fan HJ, Hall MB
Title A capable bridging ligand for Fe-only hydrogenase: density functional calculations of a low-energy route for heterolytic cleavage and formation of dihydrogen.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 11457062
Journal J Am Chem Soc
Year 2001
Volume 123
Pages 3268-78
Authors Lyon EJ, Georgakaki IP, Reibenspies JH, Darensbourg MY
Title Coordination sphere flexibility of active-site models for Fe-only hydrogenase: studies in intra- and intermolecular diatomic ligand exchange.
Related PDB
Related UniProtKB
[15]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS), ABSORPTION, EPR, AND FOURIER-TRANSFORM INFRARED SPECTROSCOPY.
Medline ID
PubMed ID 11456758
Journal J Am Chem Soc
Year 2001
Volume 123
Pages 1596-601
Authors Nicolet Y, de Lacey AL, Vernede X, Fernandez VM, Hatchikian EC, Fontecilla-Camps JC
Title Crystallographic and FTIR spectroscopic evidence of changes in Fe coordination upon reduction of the active site of the Fe-only hydrogenase from Desulfovibrio desulfuricans.
Related PDB
Related UniProtKB P07598
[16]
Resource
Comments
Medline ID
PubMed ID 11921392
Journal Chembiochem
Year 2002
Volume 3
Pages 153-60
Authors Frey M
Title Hydrogenases: hydrogen-activating enzymes.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11896710
Journal Inorg Chem
Year 2002
Volume 41
Pages 1421-9
Authors Bruschi M, Fantucci P, De Gioia L
Title DFT investigation of structural, electronic, and catalytic properties of diiron complexes related to the [2Fe](H) subcluster of Fe-only hydrogenases.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 12121756
Journal J Inorg Biochem
Year 2002
Volume 91
Pages 1-8
Authors Nicolet Y, Cavazza C, Fontecilla-Camps JC
Title Fe-only hydrogenases: structure, function and evolution.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID [PubMed
Journal J Chem Phys
Year 2002
Volume 117
Pages 8177-80
Authors Liu ZP, Hu P
Title Mechanism of H2 metabolism on Fe-only hydrogenases.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 11982382
Journal characterization and electronic structure of the redox states
Year
Volume
Pages
Authors Liu ZP, Hu P
Title A density functional theory study on the active center of Fe-only hydrogenase:
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 12727516
Journal Curr Opin Struct Biol
Year 2003
Volume 13
Pages 220-6
Authors Drennan CL, Peters JW
Title Surprising cofactors in metalloenzymes.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 12885397
Journal FEBS Lett
Year 2003
Volume 548
Pages 1-4
Authors ElAntak L, Morelli X, Bornet O, Hatchikian C, Czjzek M, Dolla A, Guerlesquin F
Title The cytochrome c3-[Fe]-hydrogenase electron-transfer complex: structural model by NMR restrained docking.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 12870970
Journal Inorg Chem
Year 2003
Volume 42
Pages 4773-81
Authors Bruschi M, Fantucci P, De Gioia L
Title Density functional theory investigation of the active site of [Fe]-hydrogenases: effects of redox state and ligand characteristics on structural, electronic, and reactivity properties of complexes related to the [2Fe]H subcluster.
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 12642671
Journal Proc Natl Acad Sci U S A
Year 2003
Volume 100
Pages 3683-8
Authors Darensbourg MY, Lyon EJ, Zhao X, Georgakaki IP
Title The organometallic active site of [Fe]hydrogenase: models and entatic states.
Related PDB
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 15062773
Journal Curr Opin Chem Biol
Year 2004
Volume 8
Pages 133-40
Authors Armstrong FA
Title Hydrogenases: active site puzzles and progress.
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[26]
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Comments
Medline ID
PubMed ID 14753812
Journal Inorg Chem
Year 2004
Volume 43
Pages 923-30
Authors Zhou T, Mo Y, Liu A, Zhou Z, Tsai KR
Title Enzymatic mechanism of Fe-only hydrogenase: density functional study on H-H making/breaking at the diiron cluster with concerted proton and electron transfers.
Related PDB
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID 15667253
Journal Biochem Soc Trans
Year 2005
Volume 33
Pages 20-1
Authors Sundararajan M, McNamara JP, Mohr M, Hillier IH, Wang H
Title A semi-empirical molecular orbital scheme to study electron transfer in iron-sulphur proteins.
Related PDB
Related UniProtKB
[28]
Resource
Comments
Medline ID
PubMed ID 15762706
Journal Inorg Chem
Year 2005
Volume 44
Pages 1794-809
Authors Fiedler AT, Brunold TC
Title Combined spectroscopic/computational study of binuclear Fe(I)-Fe(I) complexes: implications for the fully-reduced active-site cluster of Fe-only hydrogenases.
Related PDB
Related UniProtKB
[29]
Resource
Comments
Medline ID
PubMed ID 15703733
Journal Nature
Year 2005
Volume 433
Pages 589-91
Authors Darensbourg MY
Title Synthetic chemistry: making a natural fuel cell.
Related PDB
Related UniProtKB
[30]
Resource
Comments
Medline ID
PubMed ID 15703741
Journal Nature
Year 2005
Volume 433
Pages 610-3
Authors Tard C, Liu X, Ibrahim SK, Bruschi M, De Gioia L, Davies SC, Yang X, Wang LS, Sawers G, Pickett CJ
Title Synthesis of the H-cluster framework of iron-only hydrogenase.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to Fe-only hydrogenases. This enzyme is homologous to [Fe] hydrogenase 1 (or CpI) (M00042 in EzCatDB).
This enzyme binds three cofactors, two 4Fe-4S clusters, and one H cluster. The H cluster is composed of 4Fe-4S cluster, diiron (2Fe) subcluster, bridged via a thiolate of Cys328. The diiron subcluster is liganded by di(thiomethyl)amine and 5 cyanide or carbon monoxide molecules.
Although this enzyme is homologous to CpI (M00042), the direction of electron transfer is opposite to the counpterpart enzyme, CpI (see [12]), and the electron transport protein, which should accept electrons from this enzyme, is either cytochrome c3 or cytochrome c6, instead of ferredoxin (see [8]).
Cytochrome c proteins bind heme groups, which are covalently bound to the protein themselves through cysteine residues and vinyl groups of the heme groups. Cytochrome c3 binds 4 heme groups(cf. PDB;1a2i), whereas cytochrome c6 binds only a single heme group (cf. PDB;1c6r). In the both of the cytochrome c proteins, the cysteine residues covalently bound to heme groups are exposed to the surface of the proteins.
According to the literature [8], [9], [11] and [12], this enzyme catalyzes the following reactions:
(A) Hydrogenation (H2 oxidation to 2 H+ ions) at H cluster:
(B) Electron transfer from the H cluster to the 4Fe-4S cluster-2:
(D1) Indirect transfer from Cys378 bound to H cluster to Cys69 bound to 4Fe-4S cluster-2 (probably through Gln71).
(C) Electron transfer from the 4Fe-4S cluster-2 to the 4Fe-4S cluster-1:
(C1) Indirect transfer from Cys72 bound to 4Fe-4S cluster-2 to Cys41 bound to 4Fe-4S cluster-1 (probably through Ile50).
(D) Electron transfer from the 4Fe-4S cluster-1 to cytochrome c3 (or c6):
(D1) Indirect transfer from Cys38 (of large subunit) bound to 4Fe-4S cluster-1 to the heme group of cytochrome c through cysteine residue covalently bonded to heme group, and vinyl group of the heme (see [11]).

Created Updated
2005-08-10 2009-02-26