chromodomain of polycomb; CHRomatin Organization Modifier (chromo) domain of the PcG (polycomb-group) chromodomain protein Polycomb (Pc) from Drosophila melanogaster, anthropod, worm, and sea cucumber, and similar proteins. Pc is a component of the Polycomb-group (PcG) multiprotein PRC1 complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. The core subunits of PRC1 are polycomb (Pc), polyhomeotic (Ph), posterior sex combs (Psc), and sex comb extra (Sce, also known as dRing). Polycomb (Pc) plays a role in modulating life span in flies, it negatively regulates longevity.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 17737701  23 DLVYAAEKIIQKRVKKGVVEYRVKWKGWNQRYNTWEPEVNILDRRLIDIYEQTN 76
Cdd:cd18644   1 DLVYAAEKILKKRVRKGKVEYLVKWKGWSNKHNTWEPEENILDRRLIEIFERTN 54

chromodomain of polycomb; CHRomatin Organization Modifier (chromo) domain of the PcG (polycomb-group) chromodomain protein Polycomb (Pc) from Drosophila melanogaster, anthropod, worm, and sea cucumber, and similar proteins. Pc is a component of the Polycomb-group (PcG) multiprotein PRC1 complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. The core subunits of PRC1 are polycomb (Pc), polyhomeotic (Ph), posterior sex combs (Psc), and sex comb extra (Sce, also known as dRing). Polycomb (Pc) plays a role in modulating life span in flies, it negatively regulates longevity.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 17737701  23 DLVYAAEKIIQKRVKKGVVEYRVKWKGWNQRYNTWEPEVNILDRRLIDIYEQTN 76
Cdd:cd18644   1 DLVYAAEKILKKRVRKGKVEYLVKWKGWSNKHNTWEPEENILDRRLIEIFERTN 54

Chromo (CHRromatin organization MOdifier) domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 17737701    26 YAAEKIIQKRV-KKGVVEYRVKWKGWNQRYNTWEPEVNILDR-RLIDIYEQ 74
Cdd:pfam00385   1 YEVERILDHRKdKGGKEEYLVKWKGYPYDENTWEPEENLSKCpELIEEFKD 51

chromodomain of polycomb; CHRomatin Organization Modifier (chromo) domain of the PcG (polycomb-group) chromodomain protein Polycomb (Pc) from Drosophila melanogaster, anthropod, worm, and sea cucumber, and similar proteins. Pc is a component of the Polycomb-group (PcG) multiprotein PRC1 complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. The core subunits of PRC1 are polycomb (Pc), polyhomeotic (Ph), posterior sex combs (Psc), and sex comb extra (Sce, also known as dRing). Polycomb (Pc) plays a role in modulating life span in flies, it negatively regulates longevity.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 17737701  23 DLVYAAEKIIQKRVKKGVVEYRVKWKGWNQRYNTWEPEVNILDRRLIDIYEQTN 76
Cdd:cd18644   1 DLVYAAEKILKKRVRKGKVEYLVKWKGWSNKHNTWEPEENILDRRLIEIFERTN 54

chromodomain of chromobox homolog 6; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 6 (CBX6), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 17737701  25 VYAAEKIIQKRVKKGVVEYRVKWKGWNQRYNTWEPEVNILDRRLIDIYEQTNK 77
Cdd:cd18648   3 VFAAESIIKRRIRKGRIEYLVKWKGWAIKYSTWEPEENILDSRLIAAFEQKER 55

chromodomain of chromobox homolog 8; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 8 (CBX8), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells. CBX proteins may act as an oncogene or tumor suppressor in a cell-type-dependent manner, CBX8 for example promotes proliferation while suppressing metastasis, in colorectal carcinoma progression.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 17737701  25 VYAAEKIIQKRVKKGVVEYRVKWKGWNQRYNTWEPEVNILDRRLIDIYE 73
Cdd:cd18649   4 VFAAEALLKRRIRKGRMEYLVKWKGWSQKYSTWEPEENILDARLLAAFE 52

chromodomain of chromobox homolog 2; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 2 (CBX2), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 17737701  25 VYAAEKIIQKRVKKGVVEYRVKWKGWNQRYNTWEPEVNILDRRLIDIYEQ 74
Cdd:cd18647   3 VFAAECILSKRLRKGKLEYLVKWRGWSSKHNSWEPEENILDPRLLLAFQK 52

chromodomain of chromobox homolog 4; CHRomatin Organization Modifier (chromo) domain of chromobox homolog 4 (CBX4), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells. In addition to a chromodomain with H3K27me3-binding activity, Cbx4 contains two SUMO-interacting motifs responsible for its small ubiquitin-related modifier (SUMO) E3 ligase activity. CBX proteins may act as an oncogene or tumor suppressor in a cell-type-dependent manner, for example CBX8 promotes proliferation while suppressing metastasis, in colorectal carcinoma progression. CBX4 may serve as a tumor suppressor in colorectal carcinoma, and has been shown to be an oncogene in osteosarcoma and breast cancer.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 17737701  25 VYAAEKIIQKRVKKGVVEYRVKWKGWNQRYNTWEPEVNILDRRLIDIYEQTNK 77
Cdd:cd18645   3 VFAVESIEKKRIRKGRVEYLVKWRGWSPKYNTWEPEENILDPRLLIAFQNRER 55

Chromo (CHRromatin organization MOdifier) domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 17737701    26 YAAEKIIQKRV-KKGVVEYRVKWKGWNQRYNTWEPEVNILDR-RLIDIYEQ 74
Cdd:pfam00385   1 YEVERILDHRKdKGGKEEYLVKWKGYPYDENTWEPEENLSKCpELIEEFKD 51

chromodomain of heterochromatin protein 1 homolog alpha; CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog alpha (also known as HP1alpha, Cbx5, and Chromobox 5), and related proteins. HP1alpha has diverse functions in heterochromatin formation, gene regulation, and mitotic progression, and forms complex networks of gene, RNA, and protein interactions. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha, HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3).

                        10        20        30
                ....*....|....*....|....*....|....*...
gi 17737701  26 YAAEKIIQKRVKKGVVEYRVKWKGWNQRYNTWEPEVNI 63
Cdd:cd18651   2 YVVEKVLDRRVVKGQVEYLLKWKGFSEEHNTWEPEKNL 39

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 17737701  22 VDLVYAAEKIIQKRVKKGVVEYRVKWKGWNQRYNTWEPEVNI-LDRRLID 70
Cdd:cd18968   4 VEVILAARVVKDAESRKKGWKYLVKWAGYPDEENTWEPEESFdGCDDLLE 53

chromodomain of M-phase phosphoprotein 8; The chromodomain of M-phase phosphoprotein 8 (MPP8), a component of the RanBPM-containing large protein complex, binds methylated H3K9. This may in turn recruit the H3K9 methyltransferases GLP and ESET, and DNA methyltransferase 3A to the promoter of the E-cadherin gene, mediating the E-cadherin gene silencing and promoting tumor cell motility and invasion. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 17737701  25 VYAAEKIIQKRVKKGVVEYRVKWKGWNQRYNTWEPEVNILD 65
Cdd:cd18633   1 VFEVEKILDMKTEGGKVLYKVRWKGYTSDDDTWEPEVHLED 41

chromodomain of Rhizopus microsporus putative DDE transposases, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Rhizopus microsporus putative DDE transposases, and similar proteins. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 17737701  23 DLVYAAEKIIQKRVKKGVVEYRVKWKGWNQRYNTWEPEVNILDRRLIDIYEQ 74
Cdd:cd18978   1 DESYEVEKIINHRGEKNRRKYLVKWKGYDDTDNSWVTQEDFNDKDMIDEYEN 52

chromodomain of heterochromatin protein 1 homolog gamma; CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog gamma (also known as HP1gamma, Cbx3, and Chromobox 3), and related proteins. HP1gamma is a highly conserved non-histone protein, which is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. In addition to being involved in transcriptional silencing in heterochromatin-like complexes, HP1gamma also binds lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the protein may explain the association of heterochromatin with the inner nuclear membrane. HP1gamma is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 17737701  26 YAAEKIIQKRVKKGVVEYRVKWKGWNQRYNTWEPEVNILDRRLIDIY 72
Cdd:cd18652   2 FVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAF 48

chromodomain of uncharacterized putative retroelement polyprotein proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in uncharacterized putative retrotransposon proteins, and similar proteins. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 17737701  26 YAAEKIIQKRVKKGVVEYRVKWKGWNQRYNTWEPEVNiLDRRLIDIYEQ 74
Cdd:cd18976   1 YIVESLLDRRKVRGQVQYLVKWRGFPRSEATWEPREE-LMRRCAELVAA 48

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.

                        10        20
                ....*....|....*....|....*.
gi 17737701  25 VYAAEKIIQKRVKKGVVEYRVKWKGW 50
Cdd:cd18963   3 VFAAECIIKRRVRKGRIEYLVKWKGW 28

chromodomain of Rhizoctonia solani AG-1 IB retrotransposable element Tf2 155 kDa protein type 1, and similar proteins; This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Rhizoctonia solani AG-1 IB retrotransposable element Tf2 155 kDa protein type 1 (Tf2-1), and similar proteins. It belongs to the Ty3/gypsy family of long terminal repeat (LTR) retrotransposons. The pol gene in TY3/gypsy elements generally encodes domains in the following order: an aspartyl protease, a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 17737701  26 YAAEKIIQKRVKKGVVEYRVKWKGWNQRYNTWEPEVNILD-RRLIDIYEQ 74
Cdd:cd18973   1 YVVEAILDNKRRKGKWLYLVKWKGYGPEHNTWEPRENLEHaQKLLKKYYQ 50

chromodomain of heterochromatin protein 1 proteins, including HP1alpha, HP1beta, and HP1gamma; uncharacterized subgroup; CHRomatin Organization Modifier (chromo) domain of mammalian HP1alpha (Cbx5), HP1beta (Cbx1), HP1gamma (Cbx5), and similar proteins. HP1 has diverse functions in heterochromatin formation and impacts both gene expression and gene silencing. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3).

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 17737701  25 VYAAEKIIQKRV-KKGVVEYRVKWKGWNQRYNTWEPEVNILDRRLIDIYEQ 74
Cdd:cd18960   1 VFVVERILDKRLgRNGGEEFLIKWQGFPESDSSWEPRENLQCDEMLEEFEK 51

chromodomain of Drosophila melanogaster Rhino, and similar proteins; N-terminal CHRomatin Organization Modifier (chromo) domain of Drosophila melanogaster Rhino (also known as heterochromatin protein 1-like), and similar proteins. Rhino is a female-specific protein that affects chromosome structure and egg polarity that is required for germline PIWI-interacting RNA (piRNA) production. In Drosophila the RDC (rhino, deadlock, and cutoff) complex, composed of rhino, the protein deadlock (Del) and the Rai1-like transcription termination cofactor cutoff (Cuff) binds to chromatin of dual-strand piRNA clusters, special genomic regions, which encode piRNA precursors. The RDC complex is anchored to H3K9me3-marked chromatin in part via the H3K9me3-binding activity of Rhino, and is required for transcription of piRNA precursors. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                        10        20        30
                ....*....|....*....|....*....|....*....
gi 17737701  25 VYAAEKIIQKRVKKGVVEYRVKWKGWNQRYNTWEPEVNI 63
Cdd:cd18630   1 EYVVEKILGKRFVNGRPQVLVKWSGFPNENNTWEPLENL 39

chromodomain of chromodomain-containing protein 1, and similar proteins; CHRomatin Organization Modifier (chromo) domain of chromodomain-containing protein 1 (CHp1), and similar proteins. Chp1 is needed for RNA interference-dependent heterochromatin formation in fission yeast. Chp1 is a member of the RNA-induced transcriptional silencing (RITS) complex which maintains the heterochromatin regions. The chromodomain of the Chp1 component binds the histone H3 lysine 9 methylated tail (H3K9me) and the core of the nucleosome. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 17737701  25 VYAAEKIIQKRVKK-GVVEYRVKWKGWNQRYNTWEPEVNI 63
Cdd:cd18636   1 VYEVEDILADRVNKnGINEYYIKWAGYDWYDNTWEPEQNL 40

repeat 2 of paired tandem chromodomains; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 to CHD9, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 17737701  29 EKIIQKRV-KKGVVEYRVKWKGWNQRYNTWEPEVNI--LDRRLIDIYEQ 74
Cdd:cd18659   6 ERIIAHREdDEGVTEYLVKWKGLPYDECTWESEEDIsdIFQEAIDEYKK 54

CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 17737701  26 YAAEKII----QKRVKKGVVEYRVKWKGWNQRYNTWEPEVNILDR-RLIDIYEQ 74
Cdd:cd18964   1 FFVERIIgrrpSARDGPGKFLWLVKWDGYPIEDATWEPPENLGEHaKLIEDFEK 54

chromodomain-like insertion in an ATPase domain of elongation factor eEF3; Eukaryotic elongation factor eEF3 (also known as EF-3, YEF3, and TEF3), a member of the ATP-binding cassette (ABC) family of proteins, is a ribosomal binding ATPase essential for fungal translation machinery. Until recently it was considered fungal-specific and therefore an attractive target for antifungal therapy; however, recent bioinformatics analysis indicates it may be more widely distributed among other unicellular eukaryotes, and translation elongation factor 3 activity has been demonstrated from a non-fungal species, Phytophthora infestans. eEF3 is a soluble factor lacking a transmembrane domain and having two ABC domains arranged in tandem, with a unique chromodomain inserted within the ABC2 domain. Chromodomain mutations in the ABC2 domain of eEF3 have been shown to reduce ATPase activity, but not ribosome binding. Thus, the chromodomain-like insertion is critical to eEF3 function. In addition to its elongation function, eEF3 has been shown to interact with mRNA in a translation independent manner, suggesting an additional, non-elongation function for this factor.

                        10        20        30
                ....*....|....*....|....*....|.
gi 17737701  29 EKIIQKRVKKGVVEYRVKWKGWNQRYNTWEP 59
Cdd:cd18626   5 EKIVGRRKLKKSYEYEVKWKGMSSKDNSWIP 35

RNA binding activity-knot of a chromodomain; This is a novel knotted tudor domain which is required for binding to RNA. The know influences the loop conformation of the helical turn Ht2 - residues 61-6 3- that is located at the side opposite the knot in the tudor domain-chromodomain; stabilization of Ht2 is essential for RNA binding.

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 17737701    30 KIIQKRVKKGVVEYRVKWKGWNQRYNTWEPEVNIL 64
Cdd:pfam11717  20 EILSIRPKKGKYEYYVHYVGFNKRLDEWVPEDRID 54

chromodomain of Caenorhabditis elegans chromodomain protein 4, and similar proteins; CHRomatin Organization Modifier (chromo) domain of Caenorhabditis elegans CEC-4, and similar proteins. CEC-4 is a perinuclear heterochromatin anchor, it mediates the anchoring of H3K9 methylation-bearing chromatin at the nuclear periphery in early to mid-stage embryos. It is necessary for anchoring, but does not affect transcriptional repression. CEC-4 contributes to the efficiency with which muscle differentiation is induced following ectopic expression of the master regulator, HLH-1 (MyoD in mammals). A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain.

                        10        20        30
                ....*....|....*....|....*....|....*...
gi 17737701  26 YAAEKIIQKRVKKGVVEYRVKWKGW-NQRYNT--WEPE 60
Cdd:cd18961   1 YEVEKILSHRIVNGKPLYLVMWVGYpGPVENSemWEED 38

chromodomain 2 of chloroplast signal recognition particle 43 kDa protein, and similar proteins; This subgroup includes the chromodomain 2 of chloroplast SRP43 (cpSRP43), and similar proteins. CpSRP43 is a component of the chloroplast signal recognition particle (SRP) pathway. It forms a stable complex with cpSRP54 (cpSRP complex) which is required for the efficient posttranslational transport of members of the nuclearly encoded light harvesting chlorophyll-a/b-binding proteins (LHCPs) to the thylakoid membrane. Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromodomain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followed by a related chromo shadow domain.

                        10        20        30
                ....*....|....*....|....*....|....*
gi 17737701  29 EKIIQKRVKKGVVEYRVKWKGWNQRynTWEPEVNI 63
Cdd:cd18629   6 NEILESRGKGKDMEYLIEWKDGGDC--EWVKGVHV 38