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219  structures 2228  species 5  interactions 6416  sequences 14  architectures

Family: NiFeSe_Hases (PF00374)

Summary: Nickel-dependent hydrogenase

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This is the Wikipedia entry entitled "Nickel-dependent hydrogenase". More...

Nickel-dependent hydrogenase Edit Wikipedia article

Nickel-dependent hydrogenase
Identifiers
Symbol NiFeSe_Hases
Pfam PF00374
InterPro IPR001501
PROSITE PDOC00400
SCOP 1frv
SUPERFAMILY 1frv
TCDB 3.D.7

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]

References

  1. ^ Przybyla AE, Robbins J, Menon NK, Chatelus CY, Peck HD, Choi ES (1990). "Cloning and sequencing of a putative Escherichia coli [NiFe] hydrogenase-1 operon containing six open reading frames". J. Bacteriol. 172 (4): 1969–1977. PMC 208693Freely accessible. PMID 2180913. 
  2. ^ Volbeda A, Hatchikian EC, Piras C, Frey M, Fontecilla-Camps JC, Charon MH (1995). "Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas". Nature. 373 (6515): 580–587. doi:10.1038/373580a0. PMID 7854413. 
  3. ^ Moura I, Eidsness MK, Scott RA, Moura JJ, Legall J, Peck Jr HD, Prickril BC, DerVartanian DV (1989). "Evidence for selenocysteine coordination to the active site nickel in the [NiFeSe]hydrogenases from Desulfovibrio baculatus". Proc. Natl. Acad. Sci. U.S.A. 86 (1): 147–151. doi:10.1073/pnas.86.1.147. PMC 286421Freely accessible. PMID 2521386. 

This article incorporates text from the public domain Pfam and InterPro IPR001501


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Nickel-dependent hydrogenase Provide feedback

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External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001501

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 [PUBMED:2180913]; 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 [PUBMED:7854413]. 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 [PUBMED:2521386].

Gene Ontology

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Domain organisation

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Alignments

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  Seed
(178)
Full
(6416)
Representative proteomes UniProt
(17854)
NCBI
(23246)
Meta
(246)
RP15
(1911)
RP35
(4545)
RP55
(6656)
RP75
(9043)
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  Seed
(178)
Full
(6416)
Representative proteomes UniProt
(17854)
NCBI
(23246)
Meta
(246)
RP15
(1911)
RP35
(4545)
RP55
(6656)
RP75
(9043)
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  Seed
(178)
Full
(6416)
Representative proteomes UniProt
(17854)
NCBI
(23246)
Meta
(246)
RP15
(1911)
RP35
(4545)
RP55
(6656)
RP75
(9043)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

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Curation and family details

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Seed source: Prosite
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD
Number in seed: 178
Number in full: 6416
Average length of the domain: 209.60 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 65.40 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.8 25.8
Trusted cut-off 25.8 25.8
Noise cut-off 25.7 25.7
Model length: 505
Family (HMM) version: 19
Download: download the raw HMM for this family

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Interactions

There are 5 interactions for this family. More...

NiFe_hyd_SSU_C Oxidored_q6 Oxidored_q6 NiFe_hyd_SSU_C NiFeSe_Hases

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the NiFeSe_Hases domain has been found. There are 219 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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