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46  structures 2283  species 3  interactions 4576  sequences 45  architectures

Family: Oxidored_molyb (PF00174)

Summary: Oxidoreductase molybdopterin binding domain

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Oxidoreductase molybdopterin binding domain Provide feedback

This domain is found in a variety of oxidoreductases. This domain binds to a molybdopterin cofactor. Xanthine dehydrogenases, that also bind molybdopterin, have essentially no similarity.

Literature references

  1. Kisker C, Schindelin H, Pacheco A, Wehbi WA, Garrett RM, Rajagopalan KV, Enemark JH, Rees DC; , Cell 1997;91:973-983.: Molecular basis of sulfite oxidase deficiency from the structure of sulfite oxidase. PUBMED:9428520 EPMC:9428520


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000572

A number of different eukaryotic oxidoreductases that require and bind a molybdopterin cofactor have been shown [PUBMED:2015248] to share a few regions of sequence similarity. These enzymes include xanthine dehydrogenase (EC), aldehyde oxidase (EC), nitrate reductase (EC), and sulphite oxidase (EC). The multidomain redox enzyme NAD(P)H:nitrate reductase (NR) catalyses the reduction of nitrate to nitrite in a single polypeptide electron transport chain with electron flow from NAD(P)H-FAD-cytochrome b5-molybdopterin-NO(3). Three forms of NR are known, an NADH-specific enzyme found in higher plants and algae (EC); an NAD(P)H-bispecific enzyme found in higher plants, algae and fungi (EC); and an NADPH-specific enzyme found only in fungi (EC) [PUBMED:2204158]. The mitochondrial enzyme sulphite oxidase (sulphite:ferricytochrome c oxidoreductase; EC) catalyses oxidation of sulphite to sulphate, using cytochrome c as the physiological electron acceptor. Sulphite oxidase consists of two structure/function domains, an N-terminal haem domain, similar to cytochrome b5; and a C-terminal molybdopterin domain [PUBMED:9428520].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

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
(150)
Full
(4576)
Representative proteomes NCBI
(3981)
Meta
(1512)
RP15
(442)
RP35
(944)
RP55
(1319)
RP75
(1578)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(150)
Full
(4576)
Representative proteomes NCBI
(3981)
Meta
(1512)
RP15
(442)
RP35
(944)
RP55
(1319)
RP75
(1578)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(150)
Full
(4576)
Representative proteomes NCBI
(3981)
Meta
(1512)
RP15
(442)
RP35
(944)
RP55
(1319)
RP75
(1578)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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.

Note: You can also download the data file for the tree.

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: Prosite
Previous IDs: oxidored_molyb;
Type: Domain
Author: Sonnhammer ELL, Bateman A
Number in seed: 150
Number in full: 4576
Average length of the domain: 159.10 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 44.65 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.3 21.3
Trusted cut-off 21.3 21.3
Noise cut-off 21.2 21.2
Model length: 169
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Interactions

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

Cyt-b5 Oxidored_molyb Mo-co_dimer

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 Oxidored_molyb domain has been found. There are 46 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 seqence.

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