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326  structures 1930  species 0  interactions 6134  sequences 10  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
SymbolNiFeSe_Hases
PfamPF00374
InterProIPR001501
PROSITEPDOC00400
SCOP21frv / SCOPe / SUPFAM
TCDB3.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 Jr 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. PMID 2180913.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  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. PMID 7854413.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  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. PMID 2521386.{{cite journal}}: CS1 maint: multiple names: authors list (link)
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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(150)
Full
(6134)
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(35470)
RP15
(998)
RP35
(3293)
RP55
(6474)
RP75
(10616)
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  Seed
(150)
Full
(6134)
Representative proteomes UniProt
(35470)
RP15
(998)
RP35
(3293)
RP55
(6474)
RP75
(10616)
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  Seed
(150)
Full
(6134)
Representative proteomes UniProt
(35470)
RP15
(998)
RP35
(3293)
RP55
(6474)
RP75
(10616)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

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Seed source: Prosite
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD
Number in seed: 150
Number in full: 6134
Average length of the domain: 219.1 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 67.16 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -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: 508
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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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 326 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0H3H1X8 View 3D Structure Click here
E7FHC4 View 3D Structure Click here
E7FI44 View 3D Structure Click here
F1SVE4 View 3D Structure Click here
O25349 View 3D Structure Click here
O33406 View 3D Structure Click here
P0ACD8 View 3D Structure Click here
P0ACD9 View 3D Structure Click here
P0ACE0 View 3D Structure Click here
P0ACE1 View 3D Structure Click here
P0ACE2 View 3D Structure Click here
P12636 View 3D Structure Click here
P16431 View 3D Structure Click here
P19496 View 3D Structure Click here
P21852 View 3D Structure Click here
P22320 View 3D Structure Click here
P31883 View 3D Structure Click here
P31891 View 3D Structure Click here
P48342 View 3D Structure Click here
P77329 View 3D Structure Click here
P84625 View 3D Structure Click here
Q0P8Z0 View 3D Structure Click here
Q10884 View 3D Structure Click here
Q32C60 View 3D Structure Click here
Q32CK9 View 3D Structure Click here
Q32D79 View 3D Structure Click here
Q32HT4 View 3D Structure Click here
Q50783 View 3D Structure Click here
Q57935 View 3D Structure Click here
Q58137 View 3D Structure Click here
Q58433 View 3D Structure Click here
Q58592 View 3D Structure Click here
Q60338 View 3D Structure Click here
Q8U0Z6 View 3D Structure Click here
Q8ZM16 View 3D Structure Click here
Q8ZMJ0 View 3D Structure Click here
Q8ZP27 View 3D Structure Click here
Q8ZPH0 View 3D Structure Click here