DB code: M00042

RLCP classification 10.21022.100.10500 : Electron transfer
10.21022.100.10510 : Electron transfer
10.22022.100.10700 : Electron transfer
10.22022.100.10750 : Electron transfer
10.22120.100.10610 : Electron transfer
CATH domain 3.10.20.30 : Ubiquitin-like (UB roll) Catalytic domain
1.10.287.430 : Helix Hairpins Catalytic domain
3.30.70.20 : Alpha-Beta Plaits Catalytic domain
3.40.50.1780 : Rossmann fold Catalytic domain
3.40.950.10 : Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 Catalytic domain
E.C. 1.12.7.2
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.10.20.30 : Ubiquitin-like (UB roll) M00039 M00049
3.30.70.20 : Alpha-Beta Plaits M00207 M00012
3.40.50.1780 : Rossmann fold M00012
3.40.950.10 : Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 M00012

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P29166 Iron hydrogenase 1
EC 1.12.7.2
[Fe] hydrogenase
Fe-only hydrogenase
CpI
PF02906 (Fe_hyd_lg_C)
PF02256 (Fe_hyd_SSU)
PF13237 (Fer4_10)
[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
P29166 PHF1_CLOPA H(2) + 2 oxidized ferredoxin = 2 reduced ferredoxin + 2 H(+). Monomer. Binds 1 2Fe-2S cluster per subunit. Binds 4 4Fe-4S clusters per subunit. Binds 2 iron ions per subunit. Besides cysteine ligand the diiron subcluster contains non-protein ligands including 2 sulfur atoms, 1 water and 5 cyanide or carbon monoxide ligands.

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

Compound table
Cofactors Substrates Products Intermediates
KEGG-id L00023 L00024 L00029 C00138 C00080 C00282 C00139
E.C.
Compound [2Fe-2S] [4Fe-4S] [4Fe-4S]--diiron/2S/5CO(H-cluster) Reduced ferredoxin H+ H2 Oxidized ferredoxin
Type heavy metal,sulfide group heavy metal,sulfide group heavy metal,sulfide group heavy metal,peptide/protein,sulfide group others others heavy metal,peptide/protein,sulfide group
ChEBI 33739
 33739
 		33725
 33725
 		15378
 15378
 		18276
 18276
PubChem 1038
 1038
 		58838673
 783
 58838673
 783
1c4aA01 Bound:FES Unbound Unbound Unbound Unbound
1c4cA01 Bound:FES Unbound Unbound Unbound Unbound
1fehA01 Bound:FES Unbound Unbound Unbound Unbound
1c4aA02 Unbound Bound:SF4 Unbound Unbound Unbound
1c4cA02 Unbound Bound:SF4 Unbound Unbound Unbound
1fehA02 Unbound Bound:SF4 Unbound Unbound Unbound
1c4aA03 Unbound Bound:2xSF4 Unbound Unbound Unbound
1c4cA03 Unbound Bound:2xSF4 Unbound Unbound Unbound
1fehA03 Unbound Bound:2xSF4 Unbound Unbound Unbound
1c4aA04 Unbound Unbound Unbound Unbound Unbound
1c4cA04 Unbound Unbound Unbound Unbound Unbound
1fehA04 Unbound Unbound Unbound Unbound Unbound
1c4aA05 Unbound Unbound Bound:SF4-HC1 Unbound Unbound
1c4cA05 Unbound Unbound Bound:SF4-HC0 Unbound Unbound
1fehA05 Unbound Unbound Bound:SF4-HC1 Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P29166 & literature [17], [19]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1c4aA01 CYS 34 CYS 34;CYS 46;CYS 49;CYS 62(2Fe-2S cluster)
1c4cA01 CYS 34 CYS 34;CYS 46;CYS 49;CYS 62(2Fe-2S cluster)
1fehA01 CYS 34 CYS 34;CYS 46;CYS 49;CYS 62(2Fe-2S cluster)
1c4aA02 HIS 94;CYS 98 HIS 94;CYS 98;CYS 101;CYS 107(4Fe-4S cluster-1)
1c4cA02 HIS 94;CYS 98 HIS 94;CYS 98;CYS 101;CYS 107(4Fe-4S cluster-1)
1fehA02 HIS 94;CYS 98 HIS 94;CYS 98;CYS 101;CYS 107(4Fe-4S cluster-1)
1c4aA03 CYS 147;CYS 150;CYS 153;MET 166;CYS 193;GLN 195;CYS 196;VAL 202 CYS 147;CYS 150;CYS 153;CYS 200(4Fe-4S cluster-2);CYS 157;CYS 190;CYS 193;CYS 196(4Fe-4S cluster-3)
1c4cA03 CYS 147;CYS 150;CYS 153;MET 166;CYS 193;GLN 195;CYS 196;VAL 202 CYS 147;CYS 150;CYS 153;CYS 200(4Fe-4S cluster-2);CYS 157;CYS 190;CYS 193;CYS 196(4Fe-4S cluster-3)
1fehA03 CYS 147;CYS 150;CYS 153;MET 166;CYS 193;GLN 195;CYS 196;VAL 202 CYS 147;CYS 150;CYS 153;CYS 200(4Fe-4S cluster-2);CYS 157;CYS 190;CYS 193;CYS 196(4Fe-4S cluster-3)
1c4aA04 LYS 358 CYS 355(4Fe-4S cluster-4 [H-cluster])
1c4cA04 LYS 358 CYS 355(4Fe-4S cluster-4 [H-cluster])
1fehA04 LYS 358 CYS 355(4Fe-4S cluster-4 [H-cluster])
1c4aA05 CYS 299;CYS 499 CYS 300;CYS 499(4Fe-4S cluster-4 [H-cluster]);CYS 503(4Fe-4S cluster-4 & diiron [2Fe] subcluster [H-cluster])
1c4cA05 CYS 299;CYS 499 CYS 300;CYS 499(4Fe-4S cluster-4 [H-cluster]);CYS 503(4Fe-4S cluster-4 & diiron [2Fe] subcluster [H-cluster])
1fehA05 CYS 299;CYS 499 CYS 300;CYS 499(4Fe-4S cluster-4 [H-cluster]);CYS 503(4Fe-4S cluster-4 & diiron [2Fe] subcluster [H-cluster])

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[10]
Fig.1
[16]
[17]
p.1856-1857
[27]
Scheme 1, p.1428
[30]
Scheme 3, p.4780
[33]
Fig.5, p.926-930 6

References
[1]
Resource
Comments
Medline ID
PubMed ID 6331453
Journal Biochem Biophys Res Commun
Year 1984
Volume 122
Pages 9-16
Authors Chen JS, Blanchard DK
Title Purification and properties of the H2-oxidizing (uptake) hydrogenase of the N2-fixing anaerobe Clostridium pasteurianum W5.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 6327705
Journal J Biol Chem
Year 1984
Volume 259
Pages 7045-55
Authors Adams MW, Mortenson LE
Title The physical and catalytic properties of hydrogenase II of Clostridium pasteurianum. A comparison with hydrogenase I.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 6094552
Journal J Biol Chem
Year 1984
Volume 259
Pages 14328-31
Authors Wang G, Benecky MJ, Huynh BH, Cline JF, Adams MW, Mortenson LE, Hoffman BM, Munck E
Title Mossbauer and electron nuclear double resonance study of oxidized bidirectional hydrogenase from Clostridium pasteurianum W5.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 3015247
Journal Biochimie
Year 1986
Volume 68
Pages 35-42
Authors Adams MW, Johnson MK, Zambrano IC, Mortenson LE
Title On the novel H2-activating iron-sulfur center of the "Fe-only" hydrogenases.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 3025213
Journal J Biol Chem
Year 1987
Volume 262
Pages 38-41
Authors Rusnak FM, Adams MW, Mortenson LE, Munck E
Title Mossbauer study of Clostridium pasteurianum hydrogenase II. Evidence for a novel three-iron cluster.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 2655584
Journal Biochem J
Year 1989
Volume 259
Pages 597-600
Authors George GN, Prince RC, Stokley KE, Adams MW, Stockley KE
Title X-ray-absorption-spectroscopic evidence for a novel iron cluster in hydrogenase II from Clostridium pasteurianum.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 2464579
Journal J Bacteriol
Year 1989
Volume 171
Pages 430-5
Authors Kovacs KL, Seefeldt LC, Tigyi G, Doyle CM, Mortenson LE, Arp DJ
Title Immunological relationship among hydrogenases.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 2538440
Journal J Biol Chem
Year 1989
Volume 264
Pages 4342-8
Authors Kowal AT, Adams MW, Johnson MK
Title Electron paramagnetic resonance studies of the low temperature photolytic behavior of oxidized hydrogenase I from Clostridium pasteurianum.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 2556390
Journal J Biol Chem
Year 1989
Volume 264
Pages 20974-83
Authors Zambrano IC, Kowal AT, Mortenson LE, Adams MW, Johnson MK
Title Magnetic circular dichroism and electron paramagnetic resonance studies of hydrogenases I and II from Clostridium pasteurianum.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 2544883
Journal Proc Natl Acad Sci U S A
Year 1989
Volume 86
Pages 4932-6
Authors Adams MW, Eccleston E, Howard JB
Title Iron-sulfur clusters of hydrogenase I and hydrogenase II of Clostridium pasteurianum.
Related PDB
Related UniProtKB
[11]
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
[12]
Resource
Comments
Medline ID
PubMed ID 1911757
Journal Biochemistry
Year 1991
Volume 30
Pages 9697-704
Authors Meyer J, Gagnon J
Title Primary structure of hydrogenase I from Clostridium pasteurianum.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 8490025
Journal Biochemistry
Year 1993
Volume 32
Pages 4813-9
Authors Fu W, Drozdzewski PM, Morgan TV, Mortenson LE, Juszczak A, Adams MW, He SH, Peck HD Jr, DerVartanian DV, LeGall J, et al
Title Resonance Raman studies of iron-only hydrogenases.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 9843404
Journal Biochemistry
Year 1998
Volume 37
Pages 15974-80
Authors Atta M, Lafferty ME, Johnson MK, Gaillard J, Meyer J
Title Heterologous biosynthesis and characterization of the [2Fe-2S]-containing N-terminal domain of Clostridium pasteurianum hydrogenase.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 9485416
Journal Biochemistry
Year 1998
Volume 37
Pages 2660-5
Authors De Luca G, Asso M, Belaich JP, Dermoun Z
Title Purification and characterization of the HndA subunit of NADP-reducing hydrogenase from Desulfovibrio fructosovorans overproduced in Escherichia coli.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 9874636
Journal Science
Year 1998
Volume 282
Pages 1842-3
Authors Adams MW, Stiefel EI
Title Biological hydrogen production: not so elementary.
Related PDB
Related UniProtKB
[17]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS)
Medline ID 99055388
PubMed ID 9836629
Journal Science
Year 1998
Volume 282
Pages 1853-8
Authors Peters JW, Lanzilotta WN, Lemon BJ, Seefeldt LC
Title X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution.
Related PDB 1feh
Related UniProtKB P29166
[18]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS)
Medline ID 99459241
PubMed ID 10529166
Journal Biochemistry
Year 1999
Volume 38
Pages 12969-73
Authors Lemon BJ, Peters JW
Title Binding of exogenously added carbon monoxide at the active site of the iron-only hydrogenase (CpI) from Clostridium pasteurianum.
Related PDB 1c4a 1c4c
Related UniProtKB P29166
[19]
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
[20]
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
[21]
Resource
Comments
Medline ID
PubMed ID 10858294
Journal Biochemistry
Year 2000
Volume 39
Pages 7455-60
Authors Bennett B, Lemon BJ, Peters JW
Title Reversible carbon monoxide binding and inhibition at the active site of the Fe-only hydrogenase.
Related PDB
Related UniProtKB
[22]
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
[23]
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
[24]
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
[25]
Resource
Comments
Medline ID
PubMed ID 11827551
Journal Biochemistry
Year 2002
Volume 41
Pages 2036-43
Authors Chen Z, Lemon BJ, Huang S, Swartz DJ, Peters JW, Bagley KA
Title Infrared studies of the CO-inhibited form of the Fe-only hydrogenase from Clostridium pasteurianum I: examination of its light sensitivity at cryogenic temperatures.
Related PDB
Related UniProtKB
[26]
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
[27]
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
[28]
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
[29]
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
[30]
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
[31]
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
[32]
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.
Related PDB
Related UniProtKB
[33]
Resource
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
[34]
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
[35]
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
[36]
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
[37]
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 (or DdH) (M00012 in EzCatDB). iomethyl)amine and 5 cyanide or carbon monoxide molecules. Although this enzyme is homologous to DdH (M00012), the direction of electron transfer is opposite to the counpterpart enzyme, DdH (see M00012).
This enzyme binds five cofactors, a 2FE-2S cluster, three 4Fe-4S clusters, and one H cluster. The H cluster is composed of 4Fe-4S cluster, diiron (2Fe) subcluster, bridged via a thiolate of Cys503. The diiron subcluster is liganded by 2 sulfur atoms, 1 water, and 5 cyanide or carbon monoxide molecules.
According to the literature [16], this enzyme catalyzes the following reactions:
(A) Electron transfer from ferredoxin to the 2Fe-2S cluster:
(A') Electron transfer from ferredoxin to the 4Fe-4S cluster-1:
(B) Electron transfer from the 2Fe-2S cluster to the 4Fe-4S cluster-2:
(B') Electron transfer from the 4Fe-4S cluster-1 to the 4Fe-4S cluster-2:
(C) Electron transfer from the 4Fe-4S cluster-2 to the 4Fe-4S cluster-3:
(D) Electron transfer from the 4Fe-4S cluster-3 to the H cluster:
(E) Hydrogenation (H2 production from 2 H+ ions) at H cluster:
The reactions proceeds as follows (see [17]):
(A') Electron transfer from ferredoxin to the 4Fe-4S cluster-1:
(A'1) Indirect transfer from 2Fe-2S of ferredoxin through Cys98 bound to 4Fe-4S cluster-1.
(B) Electron transfer from the 2Fe-2S cluster to the 4Fe-4S cluster-2:
(B1) Indirect transfer from Cys34 bound to 2Fe-2S to Cys150 bound to 4Fe-4S cluster-2.
(B') Electron transfer from the 4Fe-4S cluster-1 to the 4Fe-4S cluster-2:
(B'1) Indirect transfer from His94 bound to 4Fe-4S cluster-1 to either sulfur of the 4Fe-4S cluster-2 or Cys147 through Val202.
(C) Electron transfer from the 4Fe-4S cluster-2 to the 4Fe-4S cluster-3:
(C1) Indirect transfer from Cys153 bound to 4Fe-4S cluster-2 to Cys196 bound to 4Fe-4S cluster-3 (probably through Met166).
(D) Electron transfer from the 4Fe-4S cluster-3 to the H cluster:
(D1) Indirect transfer from Cys193 bound to 4Fe-4S cluster-3 to Cys499 bound to H cluster.

Created Updated
2005-08-11 2009-02-26