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76  structures 1465  species 3  interactions 2865  sequences 24  architectures

Family: Prismane (PF03063)

Summary: Prismane/CO dehydrogenase family

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Prismane/CO dehydrogenase family Provide feedback

This family includes both hybrid-cluster proteins and the beta chain of carbon monoxide dehydrogenase. The hybrid-cluster proteins contain two Fe/S centres - a [4Fe-4S] cubane cluster, and a hybrid [4Fe-2S-2O] cluster. The physiological role of this protein is as yet unknown, although a role in nitrate/nitrite respiration has been suggested [1]. The prismane protein from Escherichia coli was shown to contain hydroxylamine reductase activity (NH2OH + 2e + 2 H+ -> NH3 + H2O). This activity is rather low. Hydroxylamine reductase activity was also found in CO-dehydrogenase in which the active site Ni was replaced by Fe [2]. The CO dehydrogenase contains a Ni-3Fe-2S-3O centre.

Literature references

  1. van den Berg WA, Hagen WR, van Dongen WM; , Eur J Biochem 2000;267:666-676.: The hybrid-cluster protein ('prismane protein') from Escherichia coli. Characterization of the hybrid-cluster protein, redox properties of the [2Fe-2S] and [4Fe-2S-2O] clusters and identification of an associated NADH oxidoreductase containing FAD and [2F PUBMED:10651802 EPMC:10651802

  2. Wolfe MT, Heo J, Garavelli JS, Ludden PW; , J Bacteriol 2002;184:5898-5902.: Hydroxylamine reductase activity of the hybrid cluster protein from Escherichia coli. PUBMED:12374823 EPMC:12374823


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004137

This entry represent the hydroxylamine reductases (Hcp, also known as Prismane) and the Ni-containing CO dehydrogenases (CODH) (EC).

Hydroxylamine reductases have been identified in bacteria, archaea and eukaryotic protozoa. They contain two Fe/S centres - a [4Fe-4S] cubane cluster, and a hybrid [4Fe-2S-2O] cluster. The physiological role of this protein is as yet unknown, although a role in nitrate/nitrite respiration has been suggested [PUBMED:10651802]. The Hcp protein from Escherichia coli was shown to contain hydroxylamine reductase activity (NH2OH + 2e + 2 H+ -> NH3 + H2O). This activity is rather low [PUBMED:12374823].

Hydroxylamine reductase activity was also found in CO-dehydrogenase in which the active site Ni was replaced by Fe [PUBMED:12374823]. The CO dehydrogenase contains a Ni-3Fe-2S-3O centre. Ni-containing CO dehydrogenases allows bacterial growth in a CO-dependent manner in the dark. It oxidizes carbon monoxide coupled, via CooF, to the reduction of a hydrogen cation by a hydrogenase (possibly CooH) [PUBMED:12374822, PUBMED:8561463].

Gene Ontology

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Domain organisation

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Alignments

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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
(159)
Full
(2865)
Representative proteomes UniProt
(14137)
NCBI
(19166)
Meta
(69)
RP15
(600)
RP35
(1772)
RP55
(2827)
RP75
(4558)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

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  Seed
(159)
Full
(2865)
Representative proteomes UniProt
(14137)
NCBI
(19166)
Meta
(69)
RP15
(600)
RP35
(1772)
RP55
(2827)
RP75
(4558)
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
(159)
Full
(2865)
Representative proteomes UniProt
(14137)
NCBI
(19166)
Meta
(69)
RP15
(600)
RP35
(1772)
RP55
(2827)
RP75
(4558)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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: Pfam-B_2956 (release 6.4)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Griffiths-Jones SR , Bateman A
Number in seed: 159
Number in full: 2865
Average length of the domain: 463.40 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 93.15 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.7 21.7
Trusted cut-off 22.6 23.2
Noise cut-off 19.2 20.5
Model length: 511
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

There are 3 interactions for this family. More...

CO_dh Prismane Fer4_7

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 Prismane domain has been found. There are 76 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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