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83  structures 405  species 1  interaction 5794  sequences 330  architectures

Family: Chromo (PF00385)

Summary: Chromo (CHRromatin Organisation MOdifier) domain

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This is the Wikipedia entry entitled "Chromodomain". More...

Chromodomain Edit Wikipedia article

Chromodomain
PDB 1pfb EBI.jpg
Structure of polycomb chromodomain.[1]
Identifiers
Symbol Chromodomain
Pfam PF00385
InterPro IPR000953
SMART SM00298
PROSITE PS50013
SCOP 1pfb
SUPERFAMILY 1pfb
CDD cd00024

A chromodomain (chromatin organization modifier [2]) 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.[3] In mammals, chromodomain-containing proteins are responsible for aspects of gene regulation related to chromatin remodeling and formation of heterochromatin regions.[4] Chromodomain-containing proteins also bind methylated histones[5][6] and appear in the RNA-induced transcriptional silencing complex.[7]

See also[edit]

References[edit]

  1. ^ 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. 
  2. ^ 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. 
  3. ^ 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. 
  4. ^ 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. 
  5. ^ Nielsen, PR, Nietlispach, D, Mott, HR, Callaghan, J, Bannister, A, Kouzarides, T, Murzin, AG, Murzina, NV 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. 
  6. ^ 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. 
  7. ^ 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. 

External links[edit]

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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Chromo (CHRromatin Organisation MOdifier) domain Provide feedback

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Internal database links

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].

Domain organisation

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Pfam Clan

Alignments

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  Seed
(173)
Full
(5794)
Representative proteomes NCBI
(5547)
Meta
(121)
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(1222)
RP35
(1720)
RP55
(2571)
RP75
(3614)
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Format an alignment

  Seed
(173)
Full
(5794)
Representative proteomes NCBI
(5547)
Meta
(121)
RP15
(1222)
RP35
(1720)
RP55
(2571)
RP75
(3614)
Alignment:
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Sequence:
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  Seed
(173)
Full
(5794)
Representative proteomes NCBI
(5547)
Meta
(121)
RP15
(1222)
RP35
(1720)
RP55
(2571)
RP75
(3614)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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.

Pfam alignments:

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Curation and family details

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Seed source: Prosite
Previous IDs: chromo;
Type: Domain
Author: Finn RD
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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.4 20.4
Trusted cut-off 20.4 20.4
Noise cut-off 20.3 20.3
Model length: 55
Family (HMM) version: 19
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Species distribution

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Interactions

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Chromo

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 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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