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
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.
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.

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
 33725
 		18248
 82664
 18248
 82664
 		18276
 18276
PubChem 23925
 23925
 		58838673
 783
 58838673
 783
1cc1L Unbound Bound:_NI-FCO Bound:FE2 Unbound Unbound Unbound
1cc1S01 Bound:SF4 Unbound Unbound Unbound Unbound Unbound
1cc1S02 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 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 CYS 18;CYS 21;CYS 126;CYS 164(4Fe-4S cluster-1)
1cc1S02 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