repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 and CHD2. 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        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110611184 259 NSETIEKVLDSRLGKKGATGASTTVYAIEANGDPSGDFDTEKDEGEIQYLIKWKGWSYIHSTWESEESLQQQKVKGLKKL 338
Cdd:cd18666    1 EFETIERVLDHRIGRKGATGASTTIYAVEADGDPNAGFDPEDEETEIQYLIKWKGWSHIHNTWESEESLKDQNVKGMKKL 80

                 ....*
gi 110611184 339 ENFKK 343
Cdd:cd18666   81 ENYKK 85

N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 110611184 464 RPRFVALKKQPAYLGGENLELRDYQLEGLNWLAHSWCK 501
Cdd:cd18054    1 RPRFVALKKQPSYIGGENLELRDYQLEGLNWLAHSWCK 38

repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 and CHD2. 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        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110611184 259 NSETIEKVLDSRLGKKGATGASTTVYAIEANGDPSGDFDTEKDEGEIQYLIKWKGWSYIHSTWESEESLQQQKVKGLKKL 338
Cdd:cd18666    1 EFETIERVLDHRIGRKGATGASTTIYAVEADGDPNAGFDPEDEETEIQYLIKWKGWSHIHNTWESEESLKDQNVKGMKKL 80

                 ....*
gi 110611184 339 ENFKK 343
Cdd:cd18666   81 ENYKK 85

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; Chromodomain-helicase-DNA-binding protein 2 (CHD2) is a DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3. It is involved in myogenesis via interaction with MYOD1; it binds to myogenic gene regulatory sequences and mediates incorporation of histone H3.3 prior to the onset of myogenic gene expression, promoting their expression. CHD2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 110611184 464 RPRFVALKKQPAYLGGENLELRDYQLEGLNWLAHSWCK 501
Cdd:cd18054    1 RPRFVALKKQPSYIGGENLELRDYQLEGLNWLAHSWCK 38

Chromo (CHRromatin organization MOdifier) domain;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 110611184  379 IVERVIAVKTSKSTLGqtdfpahsrkpapsnepEYLCKWMGLPYSECSWEDEALIgKKFQNCIDSFHSR 447
Cdd:pfam00385   2 EVERILDHRKDKGGKE-----------------EYLVKWKGYPYDENTWEPEENL-SKCPELIEEFKDR 52

Chromatin organization modifier domain;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 110611184   403 RKPAPSNEPEYLCKWMGLPYSECSWEDEALIgKKFQNCIDSFHSRNN 449
Cdd:smart00298  10 HRWKKKGELEYLVKWKGYSYSEDTWEPEENL-LNCSKKLDNYKKKER 55

repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 and CHD2. 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        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110611184 259 NSETIEKVLDSRLGKKGATGASTTVYAIEANGDPSGDFDTEKDEGEIQYLIKWKGWSYIHSTWESEESLQQQKVKGLKKL 338
Cdd:cd18666    1 EFETIERVLDHRIGRKGATGASTTIYAVEADGDPNAGFDPEDEETEIQYLIKWKGWSHIHNTWESEESLKDQNVKGMKKL 80

                 ....*
gi 110611184 339 ENFKK 343
Cdd:cd18666   81 ENYKK 85

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; Chromodomain-helicase-DNA-binding protein 2 (CHD2) is a DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3. It is involved in myogenesis via interaction with MYOD1; it binds to myogenic gene regulatory sequences and mediates incorporation of histone H3.3 prior to the onset of myogenic gene expression, promoting their expression. CHD2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 110611184 464 RPRFVALKKQPAYLGGENLELRDYQLEGLNWLAHSWCK 501
Cdd:cd18054    1 RPRFVALKKQPSYIGGENLELRDYQLEGLNWLAHSWCK 38

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        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 110611184 376 QYQIVERVIAVKTSKSTlgqtdfpahsrkpapsnEPEYLCKWMGLPYSECSWEDEALIGKKFQNCIDSFHS 446
Cdd:cd18659    1 EYTIVERIIAHREDDEG-----------------VTEYLVKWKGLPYDECTWESEEDISDIFQEAIDEYKK 54

repeat 1 of the paired tandem chromodomains of yeast chromodomain helicase DNA-binding protein 1, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as 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        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 110611184 289 NGDPSGDFDTEKDEGEiqYLIKWKGWSYIHSTWESEESLQQqkVKGLKKLENFKK 343
Cdd:cd18665   15 EGLEEGELDDPKENYE--FLIKWTDESHLHNTWETYESLKQ--VRGLKKVDNYIK 65

Chromo (CHRromatin organization MOdifier) domain;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 110611184  379 IVERVIAVKTSKSTLGqtdfpahsrkpapsnepEYLCKWMGLPYSECSWEDEALIgKKFQNCIDSFHSR 447
Cdd:pfam00385   2 EVERILDHRKDKGGKE-----------------EYLVKWKGYPYDENTWEPEENL-SKCPELIEEFKDR 52

Chromo (CHRromatin organization MOdifier) domain;

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 110611184  300 KDEGEIQYLIKWKGWSYIHSTWESEESLQQQKvkglKKLENFKKK 344
Cdd:pfam00385  12 DKGGKEEYLVKWKGYPYDENTWEPEENLSKCP----ELIEEFKDR 52

CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this group are chromodomains or chromo shadow domains; these are SH3-fold-beta-barrel domains of the chromo-like superfamily. Chromodomains lack the first strand of the SH3-fold-beta-barrel, this first strand is altered by insertion in the chromo shadow domains. The 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. Chromodomain-containing proteins include: i) those having an N-terminal chromodomain followed by a related chromo shadow domain, such as Drosophila and human heterochromatin protein Su(var)205 (HP1), and mammalian modifier 1 and 2; ii) those having a single chromodomain, such as Drosophila protein Polycomb (Pc), mammalian modifier 3, human Mi-2 autoantigen, and several yeast and Caenorhabditis elegans proteins of unknown function; iii) those having paired tandem chromodomains, such as mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1; (iv) and elongation factor eEF3, a member of the ATP-binding cassette (ABC) family of proteins, that serves an essential function in the translation cycle of fungi. 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.

                         10        20        30
                 ....*....|....*....|....*....|...
gi 110611184 297 DTEKDEGEIQYLIKWKGWSYIHSTWESEESLQQ 329
Cdd:cd00024    8 DHRVRKGKLEYLVKWKGYPPEENTWEPEENLTN 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
                 ....*....|....*....|....*....|..
gi 110611184 299 EKDEGEIQYLIKWKGWSYIHSTWESEESLQQQ 330
Cdd:cd18659   13 EDDEGVTEYLVKWKGLPYDECTWESEEDISDI 44

repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD3 and CHD4, 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. Human CHD3 (also named Mi-2 alpha) and CHD4 (also named Mi-2 beta) are coexpressed in many cell lines and tissues and may act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). The proteins form distinct CHD3- and CHD4-NuRD complexes that repress, as well as activate gene transcription of overlapping and specific target genes. 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 110611184 412 EYLCKWMGLPYSECSWEDEALIGKKFQNCIDSFH 445
Cdd:cd18662   21 WYLVKWRDLPYDQSTWESEDDDIPDYEKHIQEYW 54

repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins; Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD5, CHD6, CHD7, CHD8, and CHD9. 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. CHD6, CHD7, and CHD8 enzymes have been demonstrated to have different substrate specificities and remodeling activities. 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        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 110611184 258 DNSETIEKVLDSRLGKKGAtgasttvyaieangdpsgdfDTEKDEGEIQ-YLIKWKGWSYIHSTWESEESLQ------QQ 330
Cdd:cd18668    2 EDTMIIEKILASRKKKKEK--------------------EEGAEEIEVEeYLVKYKNFSYLHCEWKTEEELEkgdkriKQ 61

                 ...
gi 110611184 331 KVK 333
Cdd:cd18668   62 KIK 64

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
                 ....*....|....*....|....*....|.
gi 110611184 297 DTEKDEGEIQYLIKWKGWSYIHSTWESEESL 327
Cdd:cd18968   15 DAESRKKGWKYLVKWAGYPDEENTWEPEESF 45

repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD5, CHD6, CHD7, CHD8, and CHD9. 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. CHD6, CHD7, and CHD8 enzymes have been demonstrated to have different substrate specificities and remodeling activities. 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 110611184 298 TEKDEGE--IQYLIKWKGWSYIHSTWESEESLQQQKVKGLKKLE 339
Cdd:cd18663   16 TDPNTGEpvTHYLVKWCSLPYEDSTWELEEDVDPAKIEEFEKLR 59

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
                 ....*....|....*....|....*.
gi 110611184 302 EGEIQYLIKWKGWSYIHSTWESEESL 327
Cdd:cd18649   17 KGRMEYLVKWKGWSQKYSTWEPEENI 42

repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins; Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD3 and CHD4, 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. Human CHD3 (also named Mi-2 alpha) and CHD4 (also named Mi-2 beta) are coexpressed in many cell lines and tissues and may act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). The proteins form distinct CHD3- and CHD4-NuRD complexes that repress, as well as activate gene transcription of overlapping and specific target genes. 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
                 ....*....|....*....|....*
gi 110611184 302 EGEIQYLIKWKGWSYIHSTWESEES 326
Cdd:cd18662   17 DGNTWYLVKWRDLPYDQSTWESEDD 41

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
                 ....*....|....*....|....*.
gi 110611184 302 EGEIQYLIKWKGWSYIHSTWESEESL 327
Cdd:cd18651   14 KGQVEYLLKWKGFSEEHNTWEPEKNL 39

DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; Chromodomain-helicase-DNA-binding protein 6-9 (CHD6, CHD7, CHD8, and CHD9) are members of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

                         10
                 ....*....|....*.
gi 110611184 484 LRDYQLEGLNWLAHSW 499
Cdd:cd17995    1 LRDYQLEGVNWLLFNW 16

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 110611184 411 PEYLCKWMGLPYSECSWEDEALI 433
Cdd:cd18965   16 LEYLVKWHGLPESENTWEREKDI 38