EzCatDB: T00238

DB codeT00238
CATH domainDomain 11.10.645.10Catalytic domain
Domain 23.40.50.700Catalytic domain
Domain 34.10.480.10Catalytic domain
E.C.1.12.99.6
CSA1cc1

CATH domainRelated DB codes (homologues)
1.10.645.10T00030
3.40.50.700T00030
4.10.480.10T00030

Enzyme Name
Swiss-protKEGG

P13065P13063
Protein namePeriplasmic [NiFeSe] hydrogenase large subunitPeriplasmic [NiFeSe] hydrogenase small subunithydrogenase (acceptor)
H2 producing hydrogenase[ambiguous]
hydrogen-lyase[ambiguous]
hydrogenlyase[ambiguous]
uptake hydrogenase[ambiguous]
hydrogen:(acceptor) oxidoreductase
SynonymsEC 1.12.99.6
NiFeSe hydrogenlyase large chain
EC 1.12.99.6
NiFeSe hydrogenlyase small chain

KEGG pathways
MAP codePathways
MAP00633Trinitrotoluene degradation

Swiss-prot:Accession NumberP13065P13063
Entry namePHSL_DESBAPHSS_DESBA
ActivityH(2) + A = AH(2).H(2) + A = AH(2).
SubunitHeterodimer of a large and a small subunit.Heterodimer of a large and a small subunit.
Subcellular locationPeriplasm.Periplasm.
CofactorBinds 2 irons ions. Iron 1 has 3 cyanide and carbon monoxide ligands. Iron 2 has 3 water ligands.,Binds 1 nickel ion per subunit.Binds 3 4Fe-4S clusters. Cluster 1 is referred to as proximal, cluster 2 as distal, cluster 3 as medial.


CofactorsSubstratesProducts
KEGG-idL00024L00028C00023C00282C00028C00030
Compound[4Fe-4S]Ni--Fe(CN)2(CO)IronH2AAH2
Typeheavy metal,sulfide groupheavy metal,othersheavy metalothersothersothers
1cc1LUnboundBound:_NI-FCOBound:FE2UnboundUnboundUnbound
1cc1S01Bound:SF4UnboundUnboundUnboundUnboundUnbound
1cc1S02Bound:2xSF4UnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P13063, P13065 & literature [12]
pdbCatalytic residuesCofactor-binding residuesModified residues
1cc1LGLU 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
[1]
PubMed ID3040402
JournalEur J Biochem
Year1987
Volume167
Pages47-58
AuthorsTeixeira M, Fauque G, Moura I, Lespinat PA, Berlier Y, Prickril B, Peck HD Jr, Xavier AV, Le Gall J, Moura JJ
TitleNickel-[iron-sulfur]-selenium-containing hydrogenases from Desulfovibrio baculatus (DSM 1743). Redox centers and catalytic properties.
[2]
PubMed ID2536719
JournalJ Biol Chem
Year1989
Volume264
Pages2678-82
AuthorsHe SH, Teixeira M, LeGall J, Patil DS, Moura I, Moura JJ, DerVartanian DV, Huynh BH, Peck HD Jr
TitleEPR studies with 77Se-enriched (NiFeSe) hydrogenase of Desulfovibrio baculatus. Evidence for a selenium ligand to the active site nickel.
[3]
PubMed ID2521386
JournalProc Natl Acad Sci U S A
Year1989
Volume86
Pages147-51
AuthorsEidsness MK, Scott RA, Prickril BC, DerVartanian DV, Legall J, Moura I, Moura JJ, Peck HD Jr
TitleEvidence for selenocysteine coordination to the active site nickel in the [NiFeSe]hydrogenases from Desulfovibrio baculatus.
[4]
PubMed ID2159882
JournalEur J Biochem
Year1990
Volume189
Pages381-6
AuthorsTeixeira M, Moura I, Fauque G, Dervartanian DV, Legall J, Peck HD Jr, Moura JJ, Huynh BH
TitleThe iron-sulfur centers of the soluble [NiFeSe] hydrogenase, from Desulfovibrio baculatus (DSM 1743). EPR and Mossbauer characterization.
[5]
PubMed ID1558764
JournalFEMS Microbiol Rev
Year1992
Volume8
Pages109-35
AuthorsPrzybyla AE, Robbins J, Menon N, Peck HD Jr
TitleStructure-function relationships among the nickel-containing hydrogenases.
[6]
PubMed ID1313795
JournalJ Biol Chem
Year1992
Volume267
Pages7378-80
AuthorsWang CP, Franco R, Moura JJ, Moura I, Day EP
TitleThe nickel site in active Desulfovibrio baculatus [NiFeSe] hydrogenase is diamagnetic. Multifield saturation magnetization measurement of the spin state of Ni(II).
[7]
PubMed ID8318259
JournalFEMS Microbiol Rev
Year1993
Volume10
Pages243-69
AuthorsWu LF, Mandrand MA
TitleMicrobial hydrogenases: primary structure, classification, signatures and phylogeny.
[8]
PubMed ID8198565
JournalBiochem Biophys Res Commun
Year1994
Volume201
Pages128-34
AuthorsMus-Veteau I, Guerlesquin F
TitleInvolvement of histidine residues in the catalytic mechanism of hydrogenases.
[9]
JournalBiochimica et Biophysica Acta. Bioenergetics
Year1996
Volume1275
Pages227-236
AuthorsMedina M, Hatchikian EC, Cammack R
TitleStudies of light-induced nickel EPR signals in hydrogenase: Comparison of enzymes with and without selenium
[10]
PubMed ID8605619
JournalNat Struct Biol
Year1996
Volume3
Pages213-7
AuthorsCollman JP
TitleCoupling H2 to electron transfer.
[11]
JournalInternational Journal of Quantum Chemistry
Year1999
Volume73
Pages187-195
AuthorsL. De Gioia, P. Fantucci, B. Guigliarelli, P. Bertrand
TitleAb initio investigation of the structural and electronic differences between active-site models of [NiFe] and [NiFeSe] hydrogenases
[12]
CommentsX-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS)
Medline ID99306038
PubMed ID10378275
JournalStructure Fold Des
Year1999
Volume7
Pages557-66
AuthorsGarcin E, Vernede X, Hatchikian EC, Volbeda A, Frey M, Fontecilla-Camps JC
TitleThe crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center.
Related PDB1cc1
Related Swiss-protP13063,P13065
[13]
PubMed ID11862554
JournalJ Biol Inorg Chem
Year2002
Volume7
Pages177-94
AuthorsMuller A, Tscherny I, Kappl R, Hatchikian C, Huttermann J, Cammack R
TitleHydrogenases in the "active" state: determination of g-matrix axes and electron spin distribution at the active site by 1H ENDOR spectroscopy.
[14]
PubMed ID15237996
JournalJ Am Chem Soc
Year2004
Volume126
Pages8406-12
AuthorsLee CM, Chen CH, Ke SC, Lee GH, Liaw WF
TitleMononuclear nickel(III) and nickel(II) thiolate complexes with intramolecular S-H proton interacting with both sulfur and nickel: relevance to the [NiFe]/[NiFeSe] hydrogenases.

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):

createdupdated
2005-08-112009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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