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232  structures 1308  species 0  interactions 1993  sequences 7  architectures

Family: NiFe_hyd_SSU_C (PF14720)

Summary: NiFe/NiFeSe hydrogenase small subunit C-terminal

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NiFe/NiFeSe hydrogenase small subunit C-terminal Provide feedback

This domain is found at the C-terminus of hydrogenase small subunits including periplasmic [NiFeSe] hydrogenase small subunit, uptake hydrogenase small subunit and periplasmic [NiFe] hydrogenase small subunit. This C-terminal domain binds two of the three iron-sulfur clusters in this enzyme [1-3].

Literature references

  1. Ogata H, Kellers P, Lubitz W;, J Mol Biol. 2010;402:428-444.: The crystal structure of the [NiFe] hydrogenase from the photosynthetic bacterium Allochromatium vinosum: characterization of the oxidized enzyme (Ni-A state). PUBMED:20673834 EPMC:20673834

  2. Volbeda A, Charon MH, Piras C, Hatchikian EC, Frey M, Fontecilla-Camps JC; , Nature 1995;373:580-587.: Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas. PUBMED:7854413 EPMC:7854413

  3. Garcin E, Vernede X, Hatchikian EC, Volbeda A, Frey M, Fontecilla-Camps JC;, Structure. 1999;7:557-566.: The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center. PUBMED:10378275 EPMC:10378275


This tab holds annotation information from the InterPro database.

InterPro entry IPR027394

This entry represents the C-terminal domain of periplasmic [NiFe] hydrogenase small subunit, hydrogenase-1 small chain and uptake hydrogenase small subunit.

Hydrogenases catalyse the reversible oxidation of molecular hydrogen and play a vital role in anaerobic metabolism. Metal-containing hydrogenases are subdivided into three classes: Fe ('iron only') hydrogenases; Ni-Fe hydrogenases; and Ni-Fe-Se hydrogenases [ PUBMED:3078655 ]. Hydrogen oxidation is coupled to the reduction of electron acceptors (such as oxygen, nitrate, sulphate, carbon dioxide and fumarate), whereas proton reduction (hydrogen evolution) is essential in pyruvate fermentation or in the disposal of excess electrons.

The Ni-Fe hydrogenases, when isolated, are found to catalyse both hydrogen evolution and uptake, with low-potential multihaem cytochromes, such as cytochrome c3, acting as either electron donors or acceptors, depending on their oxidation state. Both periplasmic (soluble) and membrane-bound hydrogenases are known.

The Ni-Fe hydrogenases are heterodimeric proteins consisting of small (S) and large (L) subunits. The small subunit contains three iron-sulphur clusters (two [4Fe-4S] and one [3Fe-4S]); the large subunit contains a nickel ion [ PUBMED:1558764 ]. Small subunits of membrane-bound Ni-Fe hydrogenases contain a C-terminal domain of about 40 residues that is absent in periplasmic forms.

Domain organisation

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(138)
Full
(1993)
Representative proteomes UniProt
(10873)
RP15
(283)
RP35
(1009)
RP55
(2042)
RP75
(3409)
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PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(138)
Full
(1993)
Representative proteomes UniProt
(10873)
RP15
(283)
RP35
(1009)
RP55
(2042)
RP75
(3409)
Alignment:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(138)
Full
(1993)
Representative proteomes UniProt
(10873)
RP15
(283)
RP35
(1009)
RP55
(2042)
RP75
(3409)
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.

Curation View help on the curation process

Seed source: CATH:1wui_S_02
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Eberhardt R
Number in seed: 138
Number in full: 1993
Average length of the domain: 80.90 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 22.81 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.2 27.2
Noise cut-off 26.2 26.2
Model length: 80
Family (HMM) version: 8
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 NiFe_hyd_SSU_C domain has been found. There are 232 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
P69739 View 3D Structure Click here
P69741 View 3D Structure Click here