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53  structures 4439  species 11  interactions 13603  sequences 181  architectures

Family: Molybdop_Fe4S4 (PF04879)

Summary: Molybdopterin oxidoreductase Fe4S4 domain

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Molybdopterin oxidoreductase Fe4S4 domain Provide feedback

This domain is found in formate dehydrogenase H for which the structure is known. This first domain (residues 1 to 60) of PDB:1aa6 is an Fe4S4 cluster just below the protein surface [1].

Literature references

  1. Boyington JC, Gladyshev VN, Khangulov SV, Stadtman TC, Sun PD;, Science. 1997;275:1305-1308.: Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster. PUBMED:9036855 EPMC:9036855


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006963

The molybdopterin oxidoreductase 4Fe-4S domain is found in a number of reductase/dehydrogenase families, which include the periplasmic nitrate reductase precursor and the formate dehydrogenase alpha chain [PUBMED:9036855].

The following proteins contain this domain and belong to the molybdenium (Mo) or tungsten (W) containing enzyme family, the Mo/W bis-MGD (molybdopterin-guanine-dinucleotide) oxydoreductases [PUBMED:2015248, PUBMED:3062312, PUBMED:8125918]:

  • Escherichia coli respiratory nitrate reductase (EC).
  • Escherichia coli anaerobic dimethyl sulfoxide reductase (DMSO reductase).
  • Escherichia coli biotin sulfoxide reductases (genes bisC and bisZ).
  • Methanobacterium formicicum formate dehydrogenase (EC).
  • Escherichia coli formate dehydrogenases -H (gene fdhF), -N (gene fdnG) and -O (gene fdoG).
  • Wolinella succinogenes polysulfide reductase chain.
  • Salmonella typhimurium thiosulfate reductase (gene phsA).
  • Escherichia coli trimethylamine-N-oxide reductase (EC) (gene torA) [PUBMED:8022286].
  • Nitrate reductase (EC) from Klebsiella pneumoniae (gene nasA), Alcaligenes eutrophus, Escherichia coli, Rhodobacter sphaeroides, Thiosphaera pantotropha (gene napA), and Synechococcus PCC 7942 (gene narB).

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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Pfam Clan

This family is a member of clan 4Fe-4S (CL0344), which has the following description:

Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.

The clan contains the following 29 members:

ETF_QO Fer4 Fer4_10 Fer4_11 Fer4_12 Fer4_13 Fer4_14 Fer4_15 Fer4_16 Fer4_17 Fer4_18 Fer4_19 Fer4_2 Fer4_20 Fer4_21 Fer4_22 Fer4_23 Fer4_24 Fer4_3 Fer4_4 Fer4_5 Fer4_6 Fer4_7 Fer4_8 Fer4_9 FeS Molybdop_Fe4S4 Nitr_red_alph_N RLI

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, the UniProtKB sequence database, 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
(52)
Full
(13603)
Representative proteomes UniProt
(77512)
NCBI
(137748)
Meta
(1731)
RP15
(1583)
RP35
(6128)
RP55
(13826)
RP75
(25325)
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PP/heatmap 1                

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

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

Format an alignment

  Seed
(52)
Full
(13603)
Representative proteomes UniProt
(77512)
NCBI
(137748)
Meta
(1731)
RP15
(1583)
RP35
(6128)
RP55
(13826)
RP75
(25325)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(52)
Full
(13603)
Representative proteomes UniProt
(77512)
NCBI
(137748)
Meta
(1731)
RP15
(1583)
RP35
(6128)
RP55
(13826)
RP75
(25325)
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.

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: Bateman A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 52
Number in full: 13603
Average length of the domain: 55.20 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 6.95 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.7 22.7
Trusted cut-off 22.7 22.7
Noise cut-off 22.6 22.6
Model length: 55
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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 11 interactions for this family. More...

NapB Molybdop_Fe4S4 Molydop_binding Fer2_4 Molybdopterin Molybdopterin NapB Fer4_9 Fer2 Fer4_11 Fer4

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 Molybdop_Fe4S4 domain has been found. There are 53 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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