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2  structures 357  species 0  interactions 2235  sequences 113  architectures

Family: DOMON (PF03351)

Summary: DOMON domain

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DOMON domain Provide feedback

The DOMON (named after dopamine beta-monooxygenase N-terminal) domain is 110-125 residues long. It is predicted to form an all beta fold with up to 11 strands and is secreted to the extracellular compartment. The beta-strand folding produces a hydrophobic pocket which appears to bind soluble haem. This is consistent with the predominant architectures where the protein is associated with cytochromes or enzymatic domains whose activity involves redox or electron transfer reactions potentially as a direct participant in the electron transfer process. The DOMON domain superfamily, of which this is just one member, shows (1) multiple hydrophobic residues that contribute to the hydrophobic core of the strands of the beta-sandwich, and small residues found at the boundaries of strands and loops, (2) a strongly conserved charged residue (usually arginine/lysine) at the end of strand 9, which possibly stabilises the loop between 9 and 10, and (3) a polar residue (usually histidine, lysine or arginine), that interacts or coordinates with ligands [1]. The suggested superfamily includes both haem- and sugar-binding members: the haem-binding families being the ethyl-Benzoate dehydrogenase family EB_dh, PF09459 the cellobiose dehydrogenase family CBDH and this family, and the sugar-binding families being the xylanases, CBM_4_9, PF02018. The common feature of the superfamily is the 11-beta-strand structure, although the first and eleventh strands are not well conserved either within families or between families.

Literature references

  1. Iyer LM, Anantharaman V, Aravind L; , Bioinformatics. 2007;23:2660-2664.: The DOMON domains are involved in heme and sugar recognition. PUBMED:17878204 EPMC:17878204


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005018

The DOMON domain is an 110-125 residue long domain which has been identified in the physiologically important enzyme dopamine beta-monooxygenase and in several other secreted and transmembrane proteins from both plants and animals. It has been named after DOpamine beta-MOnooxygenase N-terminal domain. The DOMON domain can be found in one to four copies and in association with other domains, such as the Cu-ascorbate dependent monooxygenase domain, the epidermal growth factor domain, the trypsin inhibitor-like domain (TIL), the SEA domain and the Reelin domain. The architectures of the DOMON domain proteins strongly suggest a function in extracellular adhesion [PUBMED:11551777].

The sequence conservation is predominantly centred around patches of hydrophobic residues. The secondary structure prediction of the DOMON domain points to an all-beta-strand fold with seven or eight core strands supported by a buried core of conserved hydrophobic residues. There is a chraracteristic motif with two small positions (Gly or Ser) corresponding to a conserved turn immediately C-terminal to strand three. It has been proposed that the DOMON domain might form a beta-sandwich structure, with the strands distributed into two beta sheets as is seen in many extracellular adhesion domains such as the immunoglobulin, fibronectin type III, cadherin and PKD domains [PUBMED:11551777].

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 CBD9-like (CL0559), which has the following description:

This superfamily is characterised by having seven beta strands in 2 sheets in the form of a Greek-key, with an additional strand at the N-terminus. The binding region is defined by a hydrophobic pocket created between the folds.

The clan contains the following 5 members:

CBM9_1 CBM9_2 CDH-cyt DOMON Glucodextran_C

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...

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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
(70)
Full
(2235)
Representative proteomes UniProt
(3648)
NCBI
(5027)
Meta
(6)
RP15
(818)
RP35
(1248)
RP55
(1838)
RP75
(2096)
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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
(70)
Full
(2235)
Representative proteomes UniProt
(3648)
NCBI
(5027)
Meta
(6)
RP15
(818)
RP35
(1248)
RP55
(1838)
RP75
(2096)
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
(70)
Full
(2235)
Representative proteomes UniProt
(3648)
NCBI
(5027)
Meta
(6)
RP15
(818)
RP35
(1248)
RP55
(1838)
RP75
(2096)
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: Aravind L
Previous IDs: none
Type: Domain
Author: Aravind L, Coggill P
Number in seed: 70
Number in full: 2235
Average length of the domain: 116.10 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 23.44 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 32.7 32.7
Trusted cut-off 32.8 32.7
Noise cut-off 32.6 32.6
Model length: 125
Family (HMM) version: 16
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 DOMON domain has been found. There are 2 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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