Summary: Chromo (CHRromatin Organisation MOdifier) domain
This is the Wikipedia entry entitled "Chromodomain". More...
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Chromodomain Edit Wikipedia article
Structure of polycomb chromodomain.
A chromodomain (chromatin organization modifier ) is a protein structural domain of about 40-50 amino acid residues commonly found in proteins associated with the remodeling and manipulation of chromatin. The domain is highly conserved among both plants and animals, and is represented in a large number of different proteins in many genomes, such as that of the mouse. Some chromodomain-containing genes have multiple alternative splicing isoforms that omit the chromodomain entirely. In mammals, chromodomain-containing proteins are responsible for aspects of gene regulation related to chromatin remodeling and formation of heterochromatin regions. Chromodomain-containing proteins also bind methylated histones and appear in the RNA-induced transcriptional silencing complex.
- Min J, Zhang Y, Xu RM (August 2003). "Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27". Genes Dev. 17 (15): 1823–8. doi:10.1101/gad.269603. PMC 196225. PMID 12897052.
- S Messmer, A Franke, R Paro (July 1992). "Analysis of the functional role of the Polycomb chromo domain in Drosophila melanogaster". Genes Dev. 6 (7): 1241–1254. doi:10.1101/gad.6.7.1241. PMID 1628830.
- Tajul-Arifin, K, Teasdale, R, Ravasi, T, Humel, DA, Group, RIKEN GER, Members, GSL, Mattick, JS. (2003). "Identification and Analysis of Chromodomain-Containing Proteins Encoded in the Mouse Transcriptome". Genome Res 13 (6B): 1416–1429. doi:10.1101/gr.1015703. PMC 403676. PMID 12819141.
- Jones, DO, Cowell, IG, Singh, PB. (2000). "Mammalian chromodomain proteins: their role in genome organisation and expression". Bioessays 22 (2): 124–37. doi:10.1002/(SICI)1521-1878(200002)22:2<124::AID-BIES4>3.0.CO;2-E. PMID 10655032.
- Nielsen, PR, Nietlispach, D, Mott, HR, Callaghan, J, Bannister, A, Kouzarides, T, Murzin, AG, Murzina, NV, Laue, ED. et al. (2002). "Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9". Nature 416 (6876): 103–7. doi:10.1038/nature722. PMID 11882902.
- Jacobs, SA, Khorasanizadeh, S. (2002). "Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail". Science 295 (5562): 2080–3. doi:10.1126/science.1069473. PMID 11859155.
- Verdel, A, Jia, S, Gerber, S, Sugiyama, T, Gygi, S, Grewal, S, Moazed, D (2004). "RNAi-Mediated Targeting of Heterochromatin by the RITS Complex". Science 303 (5658): 672–6. doi:10.1126/science.1093686. PMC 3244756. PMID 14704433.
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Chromo (CHRromatin Organisation MOdifier) domain Provide feedback
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Internal database links
|Similarity to PfamA using HHSearch:||Chromo_shadow Mtf2_C|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR023780
The CHROMO (CHRromatin Organization MOdifier) domain [PUBMED:1982376, PUBMED:1708124, PUBMED:7667093, PUBMED:7501439] is a conserved region of around 60 amino acids, originally identified in Drosophila modifiers of variegation. These are proteins that alter the structure of chromatin to the condensed morphology of heterochromatin, a cytologically visible condition where gene expression is repressed. In one of these proteins, Polycomb, the chromo domain has been shown to be important for chromatin targeting.
Proteins that contain a chromo domain appear to fall into 3 classes. The first class includes proteins having an N-terminal chromo domain followed by a region termed the chromo shadow domain, with weak but significant sequence similarity to the N-terminal chromo domain,[PUBMED:7667093], eg. Drosophila and human heterochromatin protein Su(var)205 (HP1). The second class includes proteins with a single chromo domain, eg. Drosophila protein Polycomb (Pc); mammalian modifier 3; human Mi-2 autoantigen and several yeast and Caenorhabditis elegans hypothetical proteins. In the third class paired tandem chromo domains are found, eg. in mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1.
Functional dissections of chromo domain proteins suggests a mechanistic role for chromo domains in targeting chromo domain proteins to specific regions of the nucleus. The mechanism of targeting may involve protein-protein and/or protein/nucleic acid interactions. Hence, several line of evidence show that the HP1 chromo domain is a methyl-specific histone binding module, whereas the chromo domain of two protein components of the drosophila dosage compensation complex, MSL3 and MOF, contain chromo domains that bind to RNA in vitro [PUBMED:11574148].
The high resolution structures of HP1-family protein chromo and chromo shadow domain reveal a conserved chromo domain fold motif consisting of three beta strands packed against an alpha helix. The chromo domain fold belongs to the OB (oligonucleotide/oligosaccharide binding)-fold class found in a variety of prokaryotic and eukaryotic nucleic acid binding protein [PUBMED:11574148].
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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
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Curation and family details
|Number in seed:||173|
|Number in full:||5794|
|Average length of the domain:||53.30 aa|
|Average identity of full alignment:||24 %|
|Average coverage of the sequence by the domain:||6.52 %|
|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:||19|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 Chromo domain has been found. There are 83 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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