CHROMO

Chromatin organization modifier domain

• SMART accession number: SM00298
• Description: -
• Interpro abstract (IPR000953):

  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) ].

There are 41552 CHROMO domains in 32518 proteins in SMART's nrdb database.

Cellular role (predicted cellular role)

Cellular role: chromatin

Literature (relevant references for this domain)

Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

• Singh PB et al.
• A sequence motif found in a Drosophila heterochromatin protein is conserved in animals and plants.
• Nucleic Acids Res. 1991; 19: 789-94

Modifiers of position-effect-variegation in Drosophila encode proteins that are thought to modify chromatin, rendering it heritably changed in its expressibility. In an attempt to identify similar modifier genes in other species we have utilized a known sequence homology, termed chromo box, between a suppressor of position-effect-variegation, Heterochromatin protein 1 (HP1), and a repressor of homeotic genes, Polycomb (Pc). A PCR generated probe encompassing the HP1 chromo box was used to clone full-length murine cDNAs that contain conserved chromo box motifs. Sequence comparisons, in situ hybridization experiments, and RNA Northern blot analysis suggest that the murine and human sequences presented in this report are homologues of the Drosophila HP1 gene. Chromo box sequences can also be detected in other animal species, and in plants, predicting a strongly conserved structural role for the peptide encoded by this sequence. We propose that epigenetic (yet heritable) changes in gene expressibility, characteristic of chromosomal imprinting phenomena, can largely be explained by the action of such modifier genes. The evolutionary conservation of the chromo box motif now enables the isolation and study of putative modifier genes in those animal and plant species where chromosomal imprinting has been described.

• Paro R
• Imprinting a determined state into the chromatin of Drosophila.
• Trends Genet. 1990; 6: 416-21

The Polycomb gene of Drosophila melanogaster is a member of a class of genes involved in the clonal transmission of the repressed state of bomeotic regulatory genes through development. Genetic evidence, and the finding of a molecular similarity between the Polycomb protein and a heterochromatin-associated protein of Drosophila, suggest that this mechanism of repression might be imprinted in the structure of the chromatin, rather than being sustained through the action of diffusible regulatory factors.

Metabolism (metabolic pathways involving proteins which contain this domain)

% proteins involved	KEGG pathway ID	Description
42.86	map00310	Lysine degradation
28.57	map04310	Wnt signaling pathway
28.57	map00230	Purine metabolism

This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with CHROMO domain which could be assigned to a KEGG orthologous group, and not all proteins containing CHROMO domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

Structure (3D structures containing this domain)

3D Structures of CHROMO domains in PDB

PDB code	Title
1ap0	STRUCTURE OF THE CHROMATIN BINDING (CHROMO) DOMAIN FROM MOUSE MODIFIER PROTEIN 1, NMR, 26 STRUCTURES
1dz1	Mouse HP1 (M31) C terminal (shadow chromo) domain
1g6z	SOLUTION STRUCTURE OF THE CLR4 CHROMO DOMAIN
1guw	STRUCTURE OF THE CHROMODOMAIN FROM MOUSE HP1beta IN COMPLEX WITH THE LYSINE 9-METHYL HISTONE H3 N-TERMINAL PEPTIDE, NMR, 25 STRUCTURES
1kna	Chromo domain of HP1 complexed with histone H3 tail containing dimethyllysine 9.
1kne	Chromo domain of HP1 complexed with histone H3 tail containing trimethyllysine 9
1pdq	Polycomb chromodomain complexed with the histone H3 tail containing trimethyllysine 27.
1pfb	Structural Basis for specific binding of polycomb chromodomain to histone H3 methylated at K27
1q3l	Chromodomain Of HP1 Complexed With Histone H3 Tail Containing monomethyllysine 9.
1s4z	HP1 chromo shadow domain in complex with PXVXL motif of CAF-1
1wgs	Solution Structure of the Tudor Domain from Mouse Hypothetical Protein Homologous to Histone Acetyltransferase
1x32	Three Dimensional Solution Structure of the Chromo1 domain of cpSRP43
1x3p	3D solution structure of the Chromo-3 domain of cpSRP43
1x3q	3D Solution Structure of the Chromo-2 Domain of cpSRP43
2b2t	Tandem chromodomains of human CHD1 complexed with Histone H3 Tail containing trimethyllysine 4 and phosphothreonine 3
2b2u	Tandem chromodomains of human CHD1 complexed with Histone H3 Tail containing trimethyllysine 4 and dimethylarginine 2
2b2v	Crystal structure analysis of human CHD1 chromodomains 1 and 2 bound to histone H3 resi 1-15 MeK4
2b2w	Tandem chromodomains of human CHD1 complexed with Histone H3 Tail containing trimethyllysine 4
2b2y	Tandem chromodomains of human CHD1
2bud	The solution structure of the chromo barrel domain from the males- absent on the first (MOF) protein.
2d9u	Solution structure of the Chromo domain of chromobox homolog 2 from human
2dnt	Solution Structure of RSGI RUH-064, a Chromo Domain from Human cDNA
2dnv	Solution Structure of RSGI RUH-055, a Chromo Domain from Mus musculus cDNA
2dy7	Solution structure of the first chromodomain of yeast Chd1
2dy8	Solution structure of the second chromodomain of yeast Chd1
2ee1	Solution structures of the Chromo domain of human chromodomain helicase-DNA-binding protein 4
2efi	Solution structure of the chromo domain of Mortality factor 4-like protein 1 from human
2eko	Solution structure of RUH-073, a Pseudo Chromo Domain from Human cDNA
2epb	Solution structure of chromo domain 2 in Chromodomain-helicase-DNA-binding protein 6
2f5k	Crystal structure of the chromo domain of human MRG15
2fmm	Crystal Structure of EMSY-HP1 complex
2h1e	Tandem chromodomains of budding yeast CHD1
2hug	3D Solution Structure of the Chromo-2 Domain of cpSRP43 complexed with cpSRP54 peptide
2k1b	Solution NMR structure of the chromo domain of the chromobox protein homolog 7
2k28	Solution NMR structure of the chromo domain of the chromobox protein homolog 4
2k3x	Solution structure of EAF3 chromo barrel domain
2k3y	Solution structure of EAF3 chromo barrel domain bound to histone h3 with a dimethyllysine analog H3K36ME2
2kvm	Solution structure of the CBX7 chromodomain in complex with a H3K27me2 peptide
2l11	Solution NMR structure of the Cbx3 in complex with H3K9me3 peptide
2l12	Solution NMR structure of the chromobox protein 7 with H3K9me3
2l1b	Solution NMR structure of the chromobox protein Cbx7 with H3K27me3
2lcc	Solution structure of RBBP1 chromobarrel domain
2lrq	Chemical Shift Assignment and Solution Structure of Fr822A from Drosophila melanogaster. Northeast Structural Genomics Consortium Target Fr822A
2m2l	Solution structure of Entamoeba histolytica HP1 chromodomain
2mj8	Solution structure of CDYL2 chromodomain
2n88	2N88
2rnz	Solution structure of the presumed chromodomain of the yeast histone acetyltransferase, Esa1
2ro0	Solution structure of the knotted tudor domain of the yeast histone acetyltransferase, Esa1
2rsn	Solution structure of the chromodomain of Chp1 in complex with H3K9me3 peptide
2rso	Solution structure of the chromodomain of Swi6
2rvl	2RVL
2rvm	2RVM
2rvn	2RVN
3deo	Structural basis for specific substrate recognition by the chloroplast signal recognition particle protein cpSRP43
3dep	Structural basis for specific substrate recognition by the chloroplast signal recognition particle protein cpSRP43
3dm1	Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide
3e9f	Crystal structure short-form (residue1-113) of Eaf3 chromo domain
3e9g	Crystal structure long-form (residue1-124) of Eaf3 chromo domain
3f2u	Crystal structure of human chromobox homolog 1 (CBX1)
3fdt	Crystal structure of the complex of human chromobox homolog 5 (CBX5) with H3K9(me)3 peptide
3g7l	Chromodomain of Chp1 in complex with Histone H3K9me3 peptide
3gv6	Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
3h91	Crystal structure of the complex of human chromobox homolog 2 (CBX2) and H3K27 peptide
3i3c	Crystal Structural of CBX5 Chromo Shadow Domain
3i8z	Crystal structure of human chromobox homolog 4 (CBX4)
3i90	Crystal structure of human chromobox homolog 6 (CBX6) with H3K27 peptide
3i91	Crystal structure of human chromobox homolog 8 (CBX8) with H3K9 peptide
3kup	Crystal Structure of the CBX3 Chromo Shadow Domain
3lwe	The crystal structure of MPP8
3m9q	Drosophila MSL3 chromodomain
3mts	Chromo Domain of Human Histone-Lysine N-Methyltransferase SUV39H1
3mwy	Crystal structure of the chromodomain-ATPase portion of the yeast Chd1 chromatin remodeler
3oa6	Human MSL3 Chromodomain bound to DNA and H4K20me1 peptide
3ob9	Structure of the human MSL3 chromo-barrel domain at 2.5 Angstrom resolution
3p7j	Drosophila HP1a chromo shadow domain
3q6s	The crystal structure of the heterochromatin protein 1 beta chromoshadow domain complexed with a peptide from Shugoshin 1
3qo2	Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9
3r93	Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3 peptide
3svm	Human MPP8 - human DNMT3AK47me2 peptide
3tzd	Crystal structure of the complex of Human Chromobox Homolog 3 (CBX3)
3ui2	Crystal structure of the cpSRP54 tail bound to cpSRP43
4fsx	crystal structure of Se-substituted Zea mays ZMET2 in complex with SAH
4ft2	crystal structure of Zea mays ZMET2 in complex H3(1-15)K9me2 peptide and SAH
4ft4	crystal structure of Zea mays ZMET2 in complex H3(1-32)K9me2 peptide and SAH
4hae	Crystal structure of the CDYL2-chromodomain
4mn3	Chromodomain antagonists that target the polycomb-group methyllysine reader protein Chromobox homolog 7 (CBX7)
4nw2	Tandem chromodomains of human CHD1 in complex with Influenza virus NS1 C-terminal tail trimethylated at K229
4o42	Tandem chromodomains of human CHD1 in complex with influenza NS1 C-terminal tail dimethylated at K229
4o9i	4O9I
4pl6	4PL6
4pli	4PLI
4pll	4PLL
4qqg	4QQG
4quc	4QUC
4quf	4QUF
4u68	4U68
4x3k	4X3K
4x3s	4X3S
4x3t	4X3T
4x3u	4X3U
5afw	5AFW
5e4w	5E4W
5e4x	5E4X
5ejw	5EJW
5epj	5EPJ
5epk	5EPK
5epl	5EPL
5eq0	5EQ0
5jjz	5JJZ
5t1g	5T1G
5t1i	5T1I

Links (links to other resources describing this domain)

• PROSITE: CHROMO_2
• PFAM: chromo
• INTERPRO: IPR000953