Summary: Phage Tail Collar Domain
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Phage Tail Collar Domain Provide feedback
This region is occasionally found in conjunction with PF03335. Most of the family appear to be phage tail proteins; however some appear to be involved in other processes. For instance Q03314 from Rhizobium leguminosarum may be involved in plant-microbe interactions (). A related protein Q9L3N1 is involved in the pathogenicity of Microcystis aeruginosa. The finding of this family in a structural component of the phage tail fibre baseplate (P10930) suggests that its function is structural rather than enzymatic. Structural studies show this region consists of a helix and a loop () and three beta-strands. This alignment does not catch the third strand as it is separated from the rest of the structure by around 100 residues. This strand is conserved in homologues but the intervening sequence is not. Much of the function of P10930 appears to reside in this intervening region. In the tertiary structure of the phage baseplate this domain forms part of the 'collar'. The domain may bind SO4, however the residues accredited with this vary between the PDB file and the Swiss-Prot entry. The long unconserved region maybe due to domain swapping in and out of a loop or reflective of rapid evolution.
Cubo MT, Economou A, Murphy G, Johnston AW, Downie JA; , J Bacteriol 1992;174:4026-4035.: Molecular characterization and regulation of the rhizosphere-expressed genes rhiABCR that can influence nodulation by Rhizobium leguminosarum biovar viciae. PUBMED:1597418 EPMC:1597418
Thomassen E, Gielen G, Schutz M, Schoehn G, Abrahams JP, Miller S, van Raaij MJ; , J Mol Biol 2003;331:361-373.: The structure of the receptor-binding domain of the bacteriophage T4 short tail fibre reveals a knitted trimeric metal-binding fold. PUBMED:12888344 EPMC:12888344
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR011083
This entry is represented by a domain found in Bacteriophage T4, Gp12. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
This region is occasionally found in conjunction with INTERPRO. Most of the proteins appear to be phage tail proteins; however some appear to be involved in other processes. For instance the RhiB protein (SWISSPROT) from Rhizobium leguminosarum may be involved in plant-microbe interactions [PUBMED:1597418]. A related protein, microcystin related protein (MrpB, SWISSPROT) is involved in the pathogenicity of Microcystis aeruginosa. The finding of this family in a structural component of the phage tail fibre baseplate (SWISSPROT) suggests that its function is structural rather than enzymatic. Structural studies show this region consists of a helix and a loop [PUBMED:12888344] and three beta-strands. This alignment does not catch the third strand as it is separated from the rest of the structure by around 100 residues. This strand is conserved in homologues but the intervening sequence is not. Much of the function of SWISSPROT appears to reside in this intervening region. In the tertiary structure of the phage baseplate this domain forms part of the collar and may bind SO4. The long unconserved region maybe due to domain swapping in and out of a loop or due to rapid evolution.
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Curation and family details
|Seed source:||Yeats C|
|Number in seed:||181|
|Number in full:||1934|
|Average length of the domain:||51.40 aa|
|Average identity of full alignment:||41 %|
|Average coverage of the sequence by the domain:||13.56 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||7|
|Download:||download the raw HMM for this family|
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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 Collar domain has been found. There are 5 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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