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InterPro: IPR018194 Nickel-dependent hydrogenase, large subunit, nickel binding site

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981 proteins

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Accession

IPR018194 Ni-dep_hyd_lsu_Ni_BS

Type

Binding_site

Signatures Help

Database	ID	Name	Proteins
PROSITE pattern	PS00507	NI_HGENASE_L_1	832
PROSITE pattern	PS00508	NI_HGENASE_L_2	724
Signatures in BioMart

InterPro Relationships Help

Found in

IPR001501 Nickel-dependent hydrogenase, large subunit
IPR017682 Coenzyme F420 hydrogenase, subunit alpha

GO Term annotation Help

Process

GO:0055114 oxidation reduction

Function

GO:0008901 ferredoxin hydrogenase activity
GO:0016151 nickel ion binding

InterPro annotation

Entry Details in BioMart

Abstract

Hydrogenases are enzymes that catalyze the reversible activation of hydrogen and which occur widely in prokaryotes as well as in some eukaryotes. There are various types of hydrogenases, but all of them seem to contain at least one iron-sulphur cluster. They can be broadly divided into two groups: hydrogenases containing nickel and, in some cases, also selenium (the [NiFe] and [NiFeSe] hydrogenases) and those lacking nickel (the [Fe] hydrogenases).

The [NiFe] and [NiFeSe] hydrogenases are heterodimer that consist of a small subunit that contains a signal peptide and a large subunit. All the known large subunits seem to be evolutionary related [1]; they contain two Cys-x-x-Cys motifs; one at their N-terminal end; the other at their C-terminal end. These four cysteines are involved in the binding of nickel [2]. In the [NiFeSe] hydrogenases the first cysteine of the C-terminal motif is a selenocysteine which has experimentally been shown to be a nickel ligand [3].

Structural links Help

PDB - click here

SCOP: e.18.1.1

CATH: 1.10.645.10

Database links Help

Enzyme: EC:1.12

Taxonomic coverage Help

Overlapping InterPro entries Help

IPR018194

Numbers of overlapping proteins

Average numbers of overlapping amino acids

Example proteins Help

P0C1V6 F420-non-reducing hydrogenase vhu subunit U

P12944 Periplasmic [NiFe] hydrogenase large subunit

More proteins

Example Proteins Key

InterPro entry accession number/name and structure databases		Colour code
IPR018194	Nickel-dependent hydrogenase, large subunit, nickel binding site
IPR001501	Nickel-dependent hydrogenase, large subunit
	PDB Chain
	CATH Domain
	SCOP Domain

Publications Open in usermanual
1.	Menon NK, Robbins J, Peck HD Jr, Chatelus CY, Choi ES, Przybyla AE. Cloning and sequencing of a putative Escherichia coli [NiFe] hydrogenase-1 operon containing six open reading frames. J. Bacteriol. 172 1969-77 1990 [PubMed: 2180913] http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=2180913
3.	Eidsness MK, Scott RA, Prickril BC, DerVartanian DV, Legall J, Moura I, Moura JJ, Peck HD Jr. Evidence for selenocysteine coordination to the active site nickel in the [NiFeSe]hydrogenases from Desulfovibrio baculatus. Proc. Natl. Acad. Sci. U.S.A. 86 147-51 1989 [PubMed: 2521386] http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=2521386

Additional Reading Open in usermanual
	Tran-Betcke A, Warnecke U, Bocker C, Zaborosch C, Friedrich B. Cloning and nucleotide sequences of the genes for the subunits of NAD-reducing hydrogenase of Alcaligenes eutrophus H16. J. Bacteriol. 172 1990 2920-9 [PubMed: 2188945] http://ukpmc.ac.uk/articlerender.cgi?tool=EBI&pubmedid=2188945
	Ogata H, Hirota S, Nakahara A, Komori H, Shibata N, Kato T, Kano K, Higuchi Y. Activation process of [NiFe] hydrogenase elucidated by high-resolution X-ray analyses: conversion of the ready to the unready state. Structure 13 2005 1635-42 [PubMed: 16271886] http://dx.doi.org/10.1016/j.str.2005.07.018
	Volbeda A, Martin L, Cavazza C, Matho M, Faber BW, Roseboom W, Albracht SP, Garcin E, Rousset M, Fontecilla-Camps JC. Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases. J. Biol. Inorg. Chem. 10 2005 239-49 [PubMed: 15803334] http://dx.doi.org/10.1007/s00775-005-0632-x
	Volbeda A, Charon MH, Piras C, Hatchikian EC, Frey M, Fontecilla-Camps JC. Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas. Nature 373 1995 580-7 [PubMed: 7854413] http://dx.doi.org/10.1038/373580a0
	Ogata H, Mizoguchi Y, Mizuno N, Miki K, Adachi S, Yasuoka N, Yagi T, Yamauchi O, Hirota S, Higuchi Y. Structural studies of the carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: suggestion for the initial activation site for dihydrogen. J. Am. Chem. Soc. 124 2002 11628-35 [PubMed: 12296727] http://dx.doi.org/10.1021/ja012645k
	Higuchi Y, Ogata H, Miki K, Yasuoka N, Yagi T. Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution. Structure 7 1999 549-56 [PubMed: 10378274] http://dx.doi.org/10.1016/S0969-2126(99)80071-9
	Matias PM, Soares CM, Saraiva LM, Coelho R, Morais J, Le Gall J, Carrondo MA. [NiFe] hydrogenase from Desulfovibrio desulfuricans ATCC 27774: gene sequencing, three-dimensional structure determination and refinement at 1.8 A and modelling studies of its interaction with the tetrahaem cytochrome c3. J. Biol. Inorg. Chem. 6 2001 63-81 [PubMed: 11191224] http://dx.doi.org/10.1007/s007750000167

InterPro 23.1