DB code: T00238

CATH domain 1.10.645.10 : Cytochrome-c3 Hydrogenase; chain B Catalytic domain
3.40.50.700 : Rossmann fold Catalytic domain
4.10.480.10 : Cytochrome-c3 Hydrogenase; Chain A, domain 2 Catalytic domain
E.C. 1.12.99.6
CSA 1cc1
M-CSA 1cc1
MACiE

CATH domain Related DB codes (homologues)
1.10.645.10 : Cytochrome-c3 Hydrogenase; chain B T00030
3.40.50.700 : Rossmann fold T00030
4.10.480.10 : Cytochrome-c3 Hydrogenase; Chain A, domain 2 T00030

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P13065 Periplasmic [NiFeSe] hydrogenase large subunit
EC 1.12.99.6
NiFeSe hydrogenlyase large chain
PF00374 (NiFeSe_Hases)
[Graphical View]
P13063 Periplasmic [NiFeSe] hydrogenase small subunit
EC 1.12.99.6
NiFeSe hydrogenlyase small chain
PF01058 (Oxidored_q6)
[Graphical View]

KEGG enzyme name
hydrogenase (acceptor)
H2 producing hydrogenase[ambiguous]
hydrogen-lyase[ambiguous]
hydrogenlyase[ambiguous]
uptake hydrogenase[ambiguous]
hydrogen:(acceptor) oxidoreductase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P13063 PHSS_DESBA H(2) + A = AH(2). Heterodimer of a large and a small subunit. Periplasm. Binds 3 4Fe-4S clusters. Cluster 1 is referred to as proximal, cluster 2 as distal, cluster 3 as medial.
P13065 PHSL_DESBA H(2) + A = AH(2). Heterodimer of a large and a small subunit. Periplasm. Binds 2 irons ions. Iron 1 has 3 cyanide and carbon monoxide ligands. Iron 2 has 3 water ligands. Binds 1 nickel ion per subunit.

KEGG Pathways
Map code Pathways E.C.
MAP00633 Trinitrotoluene degradation

Compound table
Cofactors Substrates Products Intermediates
KEGG-id L00024 L00028 C00023 C00282 C00028 C00030
E.C.
Compound [4Fe-4S] Ni--Fe(CN)2(CO) Iron H2 A AH2
Type heavy metal,sulfide group heavy metal,others heavy metal others others others
ChEBI 33725
18248
82664
18276
PubChem 23925
58838673
783
1cc1L Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_NI-FCO Bound:FE2 Unbound Unbound Unbound
1cc1S01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:SF4 Unbound Unbound Unbound Unbound Unbound
1cc1S02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2xSF4 Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P13063, P13065 & literature [12]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1cc1L Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 23;CSE 492 CYS 73;CYS 495(Fe-1 & Nickel binding);GLU 51;ILE 444;HIS 498(Fe-2 binding);CYS 70;CSE 492(Nickel binding) CSE 492
1cc1S01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CYS 18;CYS 21;CYS 126;CYS 164(4Fe-4S cluster-1)
1cc1S02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 208;CYS 211;CYS 231;CYS 237(4Fe-4S cluster-3);CYS 246;CYS 258;CYS 264;CYS 267(4Fe-4S cluster-2)

References for Catalytic Mechanism
References Sections No. of steps in catalysis

References
[1]
Resource
Comments
Medline ID
PubMed ID 3040402
Journal Eur J Biochem
Year 1987
Volume 167
Pages 47-58
Authors Teixeira M, Fauque G, Moura I, Lespinat PA, Berlier Y, Prickril B, Peck HD Jr, Xavier AV, Le Gall J, Moura JJ
Title Nickel-[iron-sulfur]-selenium-containing hydrogenases from Desulfovibrio baculatus (DSM 1743). Redox centers and catalytic properties.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 2536719
Journal J Biol Chem
Year 1989
Volume 264
Pages 2678-82
Authors He SH, Teixeira M, LeGall J, Patil DS, Moura I, Moura JJ, DerVartanian DV, Huynh BH, Peck HD Jr
Title EPR studies with 77Se-enriched (NiFeSe) hydrogenase of Desulfovibrio baculatus. Evidence for a selenium ligand to the active site nickel.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 2521386
Journal Proc Natl Acad Sci U S A
Year 1989
Volume 86
Pages 147-51
Authors Eidsness MK, Scott RA, Prickril BC, DerVartanian DV, Legall J, Moura I, Moura JJ, Peck HD Jr
Title Evidence for selenocysteine coordination to the active site nickel in the [NiFeSe]hydrogenases from Desulfovibrio baculatus.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 2159882
Journal Eur J Biochem
Year 1990
Volume 189
Pages 381-6
Authors Teixeira M, Moura I, Fauque G, Dervartanian DV, Legall J, Peck HD Jr, Moura JJ, Huynh BH
Title The iron-sulfur centers of the soluble [NiFeSe] hydrogenase, from Desulfovibrio baculatus (DSM 1743). EPR and Mossbauer characterization.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 1558764
Journal FEMS Microbiol Rev
Year 1992
Volume 8
Pages 109-35
Authors Przybyla AE, Robbins J, Menon N, Peck HD Jr
Title Structure-function relationships among the nickel-containing hydrogenases.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 1313795
Journal J Biol Chem
Year 1992
Volume 267
Pages 7378-80
Authors Wang CP, Franco R, Moura JJ, Moura I, Day EP
Title The nickel site in active Desulfovibrio baculatus [NiFeSe] hydrogenase is diamagnetic. Multifield saturation magnetization measurement of the spin state of Ni(II).
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 8318259
Journal FEMS Microbiol Rev
Year 1993
Volume 10
Pages 243-69
Authors Wu LF, Mandrand MA
Title Microbial hydrogenases: primary structure, classification, signatures and phylogeny.
Related PDB
Related UniProtKB
[8]
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
[9]
Resource
Comments
Medline ID
PubMed ID
Journal Biochimica et Biophysica Acta. Bioenergetics
Year 1996
Volume 1275
Pages 227-236
Authors Medina M, Hatchikian EC, Cammack R
Title Studies of light-induced nickel EPR signals in hydrogenase: Comparison of enzymes with and without selenium
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 8605619
Journal Nat Struct Biol
Year 1996
Volume 3
Pages 213-7
Authors Collman JP
Title Coupling H2 to electron transfer.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID
Journal International Journal of Quantum Chemistry
Year 1999
Volume 73
Pages 187-195
Authors L. De Gioia, P. Fantucci, B. Guigliarelli, P. Bertrand
Title Ab initio investigation of the structural and electronic differences between active-site models of [NiFe] and [NiFeSe] hydrogenases
Related PDB
Related UniProtKB
[12]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS)
Medline ID 99306038
PubMed ID 10378275
Journal Structure Fold Des
Year 1999
Volume 7
Pages 557-66
Authors Garcin E, Vernede X, Hatchikian EC, Volbeda A, Frey M, Fontecilla-Camps JC
Title The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center.
Related PDB 1cc1
Related UniProtKB P13063 P13065
[13]
Resource
Comments
Medline ID
PubMed ID 11862554
Journal J Biol Inorg Chem
Year 2002
Volume 7
Pages 177-94
Authors Muller A, Tscherny I, Kappl R, Hatchikian C, Huttermann J, Cammack R
Title Hydrogenases in the "active" state: determination of g-matrix axes and electron spin distribution at the active site by 1H ENDOR spectroscopy.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 15237996
Journal J Am Chem Soc
Year 2004
Volume 126
Pages 8406-12
Authors Lee CM, Chen CH, Ke SC, Lee GH, Liaw WF
Title Mononuclear nickel(III) and nickel(II) thiolate complexes with intramolecular S-H proton interacting with both sulfur and nickel: relevance to the [NiFe]/[NiFeSe] hydrogenases.
Related PDB
Related UniProtKB

Comments
This enzyme catalyzes the following reactions:
(A) Electron transfer from an electron transport protein to [4Fe-4S] cluster-3 located on the surface of small subunit:
(B) Electron transfer from [4Fe-4S] cluster-3 to [4Fe-4S] cluster-2:
(C) Electron transfer from [4Fe-4S] cluster-2 to [4Fe-4S] cluster-1:
(D) Electron transfer from [4Fe-4S] cluster-1 to the Nickel-Iron cluster (reaction center):
(E) Hydrogenation at the Nickel-Iron cluster (reaction center):

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