Summary: Agenet domain
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Maurer-Stroh S, Dickens NJ, Hughes-Davies L, Kouzarides T, Eisenhaber F, Ponting CP; , Trends Biochem Sci 2003;28:69-74.: The Tudor domain 'Royal Family': Tudor, plant Agenet, Chromo, PWWP and MBT domains. PUBMED:12575993 EPMC:12575993
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR008395This domain is related to the TUDOR domain INTERPRO [PUBMED:12575993]. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [PUBMED:12575993].
|Molecular function||RNA binding (GO:0003723)|
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This clan covers the Tudor domain 'royal family' . This includes chromo, MBT, PWWP and tudor domains. The chromo domain is a comprised of approximately 50 amino acid residues. There are usually one to three Chromo domains found in a single protein. In some chromo domain containing proteins, a second related chromo domain has been found and is referred to as the Chromo-shadow domain. The structure of the Chromo and Chromo-shadow domains reveal an OB-fold, a fold found in a variety of prokaryotic and eukaryotic nucleic acid binding proteins. More specifically,the chromo-domain structure reveals a three beta strands that are packed against an alpha helix. Interestingly, a similar structure is found in the archaeal chromatin proteins (7kDa DNA-binding domain). These are sequence neutral DNA binding proteins. The DNA binding in these archaeal proteins is mediated through the triple stranded beta sheet. These archaeal domains are though to represent an ancestral chromo domain. Homologs of the chromo domain have been found in fission yeast, ciliated protozoa and all animal species, but appear to be absent in eubacteria, budding yeast and plants . The precise function of the chromo domain is unclear, but the chromo domain is thought to act as a targeting module for chromosomal proteins, although the chromosomal contexts and functional contexts being targeted vary. In all cases studies, the chromo domains are found in proteins that are involved in transcription regulation, positive and negative .
The clan contains the following 14 members:53-BP1_Tudor 7kD_DNA_binding Agenet Chromo Chromo_shadow DUF1325 DUF4537 MBT PWWP Rad9_Rad53_bind RBB1NT SMN TUDOR Tudor-knot
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Seed source:||Pfam-B_2551 (release 8.0)|
|Number in seed:||34|
|Number in full:||609|
|Average length of the domain:||67.00 aa|
|Average identity of full alignment:||32 %|
|Average coverage of the sequence by the domain:||12.42 %|
|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 Agenet domain has been found. There are 4 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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