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53  structures 14693  species 11  interactions 48741  sequences 172  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

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 25 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_3 Fer4_4 Fer4_5 Fer4_6 Fer4_7 Fer4_8 Fer4_9 FeS Molybdop_Fe4S4 RLI


    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...

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    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.

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    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: Bateman A
    Previous IDs: none
    Type: Domain
    Author: Bateman A
    Number in seed: 56
    Number in full: 48741
    Average length of the domain: 57.20 aa
    Average identity of full alignment: 29 %
    Average coverage of the sequence by the domain: 7.96 %

    HMM information View help on HMM parameters

    HMM build commands:
    build method: hmmbuild -o /dev/null HMM SEED
    search method: hmmsearch -Z 80369284 -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: 12
    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


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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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    There are 11 interactions for this family. More...

    Molybdop_Fe4S4 Fer4 Fer4_9 NapB Fer4_11 Fer2_4 Molydop_binding Molybdopterin NapB Molybdopterin Fer2


    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 seqence.

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