coiled-coil domain located near the N-terminus of human Excision Repair Cross Complementing 6 ...
97-173
1.25e-33
coiled-coil domain located near the N-terminus of human Excision Repair Cross Complementing 6 (ERCC-6) and related proteins; This model represents a coiled-coil domain located near the N-terminus of ERCC-6 and related proteins. ERCC-6 (also known as Cockayne syndrome group B, CSB) is a DNA-binding protein important in eukaryotic transcription-coupled repair (TCR). TCR is a well-conserved sub-pathway of nucleotide excision repair (NER) that preferentially removes DNA lesions from the template strand blocking translocation of RNA polymerase II (Pol II). In a model for TCR, the processing Pol II encounters the lesion on the transcribed DNA strand and stalls; it is then displaced by the TCR-initiation complex which includes ERCC-6, ERCC-8, UVSSA and USP7; TCR-specific factors then access the lesion for the DNA damage incision process. The N-terminal region, the ATPase domain and the C-terminal region of ERCC-6 all directly contribute to DNA association and catalytic activity. The ATPase domain functions in concert with either the N- or C-terminal region to mediate UV-induced chromatin association. The N-terminal region prevents ERCC-6 from stably associating with chromatin under normal growth conditions, and the C-terminal region of ERCC-6 promotes stable chromatin association in the presence of lesion-stalled transcription. In addition to this coiled-coil domain, the N-terminal region of ERCC-6 includes two lysine residues subject to SUMOylation, a nucleolar localization signal NoLS1, and a nuclear localization signal NLS1. ERCC-6 also includes a SWI/SNF-like ATPase domain, a nucleotide-binding domain and a ubiquitin-binding domain. This coiled-coil domain binds magnesium. This domain family does not include Saccharomyces cerevisiae RAD26, and Schizosaccharomyces pombe Rhp26.
:
Pssm-ID: 411064 [Multi-domain] Cd Length: 77 Bit Score: 124.24 E-value: 1.25e-33
winged-helix domain (WHD) found in cockayne syndrome group B (CSB) and similar proteins; CSB, ...
1473-1546
1.94e-29
winged-helix domain (WHD) found in cockayne syndrome group B (CSB) and similar proteins; CSB, also called cockayne syndrome protein CSB, DNA excision repair protein ERCC-6, ERCC Excision Repair 6, or ATP-dependent helicase ERCC6, is involved in many DNA repair processes and is essential for transcription-coupled repair (TCR). It regulates DNA double-strand break (DSB) repair and checkpoint activation. Upon DNA-binding, it locally modifies DNA conformation by wrapping the DNA around itself, thereby modifying the interface between stalled RNA polymerase II and DNA. It is required for TCR complex formation. CSB also regulates transcription and chromatin remodeling activities that are essential for neuronal differentiation and neuritogenesis. This model corresponds to the winged-helix domain (WHD) of CSB, which is involved in the recruitment of CSB to DSBs. The CSB WHD folds as a single globular domain, defining a class of ubiquitin-binding domains (UBDs) different from other UBD classes.
:
Pssm-ID: 439329 Cd Length: 72 Bit Score: 112.22 E-value: 1.94e-29
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, also known Cockayne syndrome group B (CSB), Rad26 in Saccharomyces cerevisiae, and Rhp26 in Schizosaccharomyces pombe) is a DNA-binding protein that is important in transcription-coupled excision repair. ERCC6 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.
Pssm-ID: 350758 [Multi-domain] Cd Length: 193 Bit Score: 358.17 E-value: 2.31e-114
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
521-823
7.70e-108
SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.
Pssm-ID: 425504 [Multi-domain] Cd Length: 289 Bit Score: 344.28 E-value: 7.70e-108
coiled-coil domain located near the N-terminus of human Excision Repair Cross Complementing 6 ...
97-173
1.25e-33
coiled-coil domain located near the N-terminus of human Excision Repair Cross Complementing 6 (ERCC-6) and related proteins; This model represents a coiled-coil domain located near the N-terminus of ERCC-6 and related proteins. ERCC-6 (also known as Cockayne syndrome group B, CSB) is a DNA-binding protein important in eukaryotic transcription-coupled repair (TCR). TCR is a well-conserved sub-pathway of nucleotide excision repair (NER) that preferentially removes DNA lesions from the template strand blocking translocation of RNA polymerase II (Pol II). In a model for TCR, the processing Pol II encounters the lesion on the transcribed DNA strand and stalls; it is then displaced by the TCR-initiation complex which includes ERCC-6, ERCC-8, UVSSA and USP7; TCR-specific factors then access the lesion for the DNA damage incision process. The N-terminal region, the ATPase domain and the C-terminal region of ERCC-6 all directly contribute to DNA association and catalytic activity. The ATPase domain functions in concert with either the N- or C-terminal region to mediate UV-induced chromatin association. The N-terminal region prevents ERCC-6 from stably associating with chromatin under normal growth conditions, and the C-terminal region of ERCC-6 promotes stable chromatin association in the presence of lesion-stalled transcription. In addition to this coiled-coil domain, the N-terminal region of ERCC-6 includes two lysine residues subject to SUMOylation, a nucleolar localization signal NoLS1, and a nuclear localization signal NLS1. ERCC-6 also includes a SWI/SNF-like ATPase domain, a nucleotide-binding domain and a ubiquitin-binding domain. This coiled-coil domain binds magnesium. This domain family does not include Saccharomyces cerevisiae RAD26, and Schizosaccharomyces pombe Rhp26.
Pssm-ID: 411064 [Multi-domain] Cd Length: 77 Bit Score: 124.24 E-value: 1.25e-33
winged-helix domain (WHD) found in cockayne syndrome group B (CSB) and similar proteins; CSB, ...
1473-1546
1.94e-29
winged-helix domain (WHD) found in cockayne syndrome group B (CSB) and similar proteins; CSB, also called cockayne syndrome protein CSB, DNA excision repair protein ERCC-6, ERCC Excision Repair 6, or ATP-dependent helicase ERCC6, is involved in many DNA repair processes and is essential for transcription-coupled repair (TCR). It regulates DNA double-strand break (DSB) repair and checkpoint activation. Upon DNA-binding, it locally modifies DNA conformation by wrapping the DNA around itself, thereby modifying the interface between stalled RNA polymerase II and DNA. It is required for TCR complex formation. CSB also regulates transcription and chromatin remodeling activities that are essential for neuronal differentiation and neuritogenesis. This model corresponds to the winged-helix domain (WHD) of CSB, which is involved in the recruitment of CSB to DSBs. The CSB WHD folds as a single globular domain, defining a class of ubiquitin-binding domains (UBDs) different from other UBD classes.
Pssm-ID: 439329 Cd Length: 72 Bit Score: 112.22 E-value: 1.94e-29
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, also known Cockayne syndrome group B (CSB), Rad26 in Saccharomyces cerevisiae, and Rhp26 in Schizosaccharomyces pombe) is a DNA-binding protein that is important in transcription-coupled excision repair. ERCC6 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.
Pssm-ID: 350758 [Multi-domain] Cd Length: 193 Bit Score: 358.17 E-value: 2.31e-114
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
521-823
7.70e-108
SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.
Pssm-ID: 425504 [Multi-domain] Cd Length: 289 Bit Score: 344.28 E-value: 7.70e-108
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
518-705
4.03e-72
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350677 [Multi-domain] Cd Length: 182 Bit Score: 238.62 E-value: 4.03e-72
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint helicase (ERCC6L, also known as RAD26L) is an essential component of the mitotic spindle assembly checkpoint, by acting as a tension sensor that associates with catenated DNA which is stretched under tension until it is resolved during anaphase. ERCC6L is proposed to stimulate cancer cell proliferation by promoting cell cycle through a way of RAB31-MAPK-CDK2. ERCC6L 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.
Pssm-ID: 350759 [Multi-domain] Cd Length: 232 Bit Score: 235.73 E-value: 2.00e-70
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ...
518-758
3.27e-64
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging to SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprises a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. Archaeal SWI2 and SNF2 are members 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.
Pssm-ID: 350770 [Multi-domain] Cd Length: 218 Bit Score: 217.43 E-value: 3.27e-64
DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in ...
518-756
2.79e-61
DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in eukaryotes) regulates transcription in association with TATA binding protein (TBP). Mot1, Ino80C, and NC2 function coordinately to regulate pervasive transcription in yeast and mammals. Mot1 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.
Pssm-ID: 350757 [Multi-domain] Cd Length: 232 Bit Score: 209.51 E-value: 2.79e-61
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ...
518-756
3.63e-60
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as RAD26L) may play a role in DNA repair and mitochondrial function. In humans, mutations in the ERCC6L2 gene are associated with bone marrow failure syndrome 2. ERCC6L2 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.
Pssm-ID: 350763 [Multi-domain] Cd Length: 245 Bit Score: 206.85 E-value: 3.63e-60
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
848-975
6.85e-58
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350180 [Multi-domain] Cd Length: 135 Bit Score: 195.77 E-value: 6.85e-58
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ...
518-740
9.13e-47
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) which is involved in transcriptional regulation and chromatin remodeling, and ARIP4 (also called androgen receptor-interacting protein 4, RAD54 like 2 or RAD54L2) which modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. They are members 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.
Pssm-ID: 350765 [Multi-domain] Cd Length: 239 Bit Score: 168.24 E-value: 9.13e-47
DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin ...
517-758
2.15e-46
DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, members 2 and 4 (SMARCA2 and SMARCA4) are members 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.
Pssm-ID: 350754 [Multi-domain] Cd Length: 233 Bit Score: 166.78 E-value: 2.15e-46
DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or ...
518-756
3.41e-46
DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or DOMO1) is the core catalytic component of the multiprotein chromatin-remodeling SRCAP complex, that is necessary for the incorporation of the histone variant H2A.Z into nucleosomes. SRCAP 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.
Pssm-ID: 350761 [Multi-domain] Cd Length: 223 Bit Score: 165.99 E-value: 3.41e-46
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ...
517-758
1.45e-45
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or SMARCA6) is a major epigenetic regulator crucial for normal heterochromatin structure and function. HELLS is part 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.
Pssm-ID: 350767 [Multi-domain] Cd Length: 236 Bit Score: 164.48 E-value: 1.45e-45
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ...
517-758
1.88e-45
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 and 5 (SMARCA1 and SMARCA5) are members 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.
Pssm-ID: 350755 [Multi-domain] Cd Length: 222 Bit Score: 163.65 E-value: 1.88e-45
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ...
518-756
1.87e-43
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are members 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.
Pssm-ID: 350762 [Multi-domain] Cd Length: 240 Bit Score: 158.60 E-value: 1.87e-43
DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; ...
521-756
3.77e-43
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.
Pssm-ID: 350753 [Multi-domain] Cd Length: 223 Bit Score: 157.02 E-value: 3.77e-43
DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and ...
517-756
1.29e-39
DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and similar proteins; Chromodomain-helicase-DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin-remodeling factor which functions as the substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. It regulates polymerase II transcription and is also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. It is not only involved in transcription-related chromatin-remodeling, but is also required to maintain a specific chromatin configuration across the genome. CHD1 is also associated with histone deacetylase (HDAC) activity. 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. Both are members 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.
Pssm-ID: 350751 [Multi-domain] Cd Length: 218 Bit Score: 146.73 E-value: 1.29e-39
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ...
518-756
4.82e-39
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to 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.
Pssm-ID: 350766 [Multi-domain] Cd Length: 241 Bit Score: 145.89 E-value: 4.82e-39
DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, ...
518-756
1.11e-38
DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, also known as ALC1) is involved in DNA repair by regulating chromatin relaxation following DNA damage. CHD1L 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.
Pssm-ID: 350764 [Multi-domain] Cd Length: 216 Bit Score: 144.12 E-value: 1.11e-38
DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent ...
518-705
5.42e-38
DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 (SMARCAD1, also known as ATP-dependent helicase 1 or Hel1) possesses intrinsic ATP-dependent nucleosome-remodeling activity and is required for both DNA repair and heterochromatin organization. SMARCAD1 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.
Pssm-ID: 350756 [Multi-domain] Cd Length: 187 Bit Score: 140.98 E-value: 5.42e-38
DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 (SMARCA5, also called SNF2H) is the catalytic subunit of the four known chromatin-remodeling complexes: CHRAC, RSF, ACF/WCRF, and WICH. SMARCA5 plays a major role organising arrays of nucleosomes adjacent to the binding sites for the architectural transcription factor CTCF sites and acts to promote CTCF binding SMARCA5 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.
Pssm-ID: 350822 [Multi-domain] Cd Length: 244 Bit Score: 140.57 E-value: 4.91e-37
DEXH-box helicase domain of ARIP4; Androgen receptor-interacting protein 4 (ARIP4, also called ...
521-736
6.44e-36
DEXH-box helicase domain of ARIP4; Androgen receptor-interacting protein 4 (ARIP4, also called RAD54 like 2 or RAD54L2 ) modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. ARIP4 is part 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.
Pssm-ID: 350827 [Multi-domain] Cd Length: 227 Bit Score: 136.48 E-value: 6.44e-36
DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 (SMARCA4, also known as transcription activator BRG1) is a component of the CREST-BRG1 complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders. SMARCA4 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.
Pssm-ID: 350820 [Multi-domain] Cd Length: 251 Bit Score: 136.33 E-value: 1.58e-35
DEXH-box helicase domain of SMARCA2; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 (SMARCA2, also known as brahma homolog) is a component of the BAF complex. SMARCA2 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.
Pssm-ID: 350821 [Multi-domain] Cd Length: 251 Bit Score: 134.81 E-value: 6.10e-35
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; ...
517-756
4.07e-34
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.
Pssm-ID: 350812 [Multi-domain] Cd Length: 237 Bit Score: 131.67 E-value: 4.07e-34
coiled-coil domain located near the N-terminus of human Excision Repair Cross Complementing 6 ...
97-173
1.25e-33
coiled-coil domain located near the N-terminus of human Excision Repair Cross Complementing 6 (ERCC-6) and related proteins; This model represents a coiled-coil domain located near the N-terminus of ERCC-6 and related proteins. ERCC-6 (also known as Cockayne syndrome group B, CSB) is a DNA-binding protein important in eukaryotic transcription-coupled repair (TCR). TCR is a well-conserved sub-pathway of nucleotide excision repair (NER) that preferentially removes DNA lesions from the template strand blocking translocation of RNA polymerase II (Pol II). In a model for TCR, the processing Pol II encounters the lesion on the transcribed DNA strand and stalls; it is then displaced by the TCR-initiation complex which includes ERCC-6, ERCC-8, UVSSA and USP7; TCR-specific factors then access the lesion for the DNA damage incision process. The N-terminal region, the ATPase domain and the C-terminal region of ERCC-6 all directly contribute to DNA association and catalytic activity. The ATPase domain functions in concert with either the N- or C-terminal region to mediate UV-induced chromatin association. The N-terminal region prevents ERCC-6 from stably associating with chromatin under normal growth conditions, and the C-terminal region of ERCC-6 promotes stable chromatin association in the presence of lesion-stalled transcription. In addition to this coiled-coil domain, the N-terminal region of ERCC-6 includes two lysine residues subject to SUMOylation, a nucleolar localization signal NoLS1, and a nuclear localization signal NLS1. ERCC-6 also includes a SWI/SNF-like ATPase domain, a nucleotide-binding domain and a ubiquitin-binding domain. This coiled-coil domain binds magnesium. This domain family does not include Saccharomyces cerevisiae RAD26, and Schizosaccharomyces pombe Rhp26.
Pssm-ID: 411064 [Multi-domain] Cd Length: 77 Bit Score: 124.24 E-value: 1.25e-33
DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as ...
518-756
6.23e-33
DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as RDH54, binds to double-stranded DNA, displays ATPase activity in the presence of DNA, and may have a role in meiotic and mitotic recombination. RAD54B 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.
Pssm-ID: 350824 [Multi-domain] Cd Length: 235 Bit Score: 128.42 E-value: 6.23e-33
DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 (SMARCA1, also called SNF2L) is a component of NURF (nucleosome-remodeling factor) and CERF (CECR2-containing-remodeling factor) complexes which promote the perturbation of chromatin structure in an ATP-dependent manner. SMARCA1 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.
Pssm-ID: 350823 [Multi-domain] Cd Length: 233 Bit Score: 127.44 E-value: 1.08e-32
DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 ...
518-756
1.68e-32
DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 chromatin remodeling complex. INO80 removes histone H3-containing nucleosomes from associated chromatin, promotes CENP-ACnp1 chromatin assembly at the centromere in a redundant manner with another chromatin-remodeling factor Chd1Hrp1. INO80 mutants have severe defects in oxygen consumption and promiscuous cell division that is no longer coupled with metabolic status. INO80 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.
Pssm-ID: 350760 [Multi-domain] Cd Length: 229 Bit Score: 126.85 E-value: 1.68e-32
DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5; ...
518-756
1.12e-30
DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5; Chromodomain-helicase-DNA-binding protein 3 (CHD3) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. It is required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity. Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Chromodomain-helicase-DNA-binding protein 5 (CHD5) is a chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. It is thought to specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone H3 and plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at 'Lys-27' thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. As a tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa. CHD3, CHD4, and CHD5 are members 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.
Pssm-ID: 350752 [Multi-domain] Cd Length: 196 Bit Score: 120.24 E-value: 1.12e-30
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; ...
518-756
1.78e-29
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; Chromodomain-helicase-DNA-binding protein 3 (CHD3) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. It is required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity. CHD3 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.
Pssm-ID: 350813 [Multi-domain] Cd Length: 232 Bit Score: 118.19 E-value: 1.78e-29
winged-helix domain (WHD) found in cockayne syndrome group B (CSB) and similar proteins; CSB, ...
1473-1546
1.94e-29
winged-helix domain (WHD) found in cockayne syndrome group B (CSB) and similar proteins; CSB, also called cockayne syndrome protein CSB, DNA excision repair protein ERCC-6, ERCC Excision Repair 6, or ATP-dependent helicase ERCC6, is involved in many DNA repair processes and is essential for transcription-coupled repair (TCR). It regulates DNA double-strand break (DSB) repair and checkpoint activation. Upon DNA-binding, it locally modifies DNA conformation by wrapping the DNA around itself, thereby modifying the interface between stalled RNA polymerase II and DNA. It is required for TCR complex formation. CSB also regulates transcription and chromatin remodeling activities that are essential for neuronal differentiation and neuritogenesis. This model corresponds to the winged-helix domain (WHD) of CSB, which is involved in the recruitment of CSB to DSBs. The CSB WHD folds as a single globular domain, defining a class of ubiquitin-binding domains (UBDs) different from other UBD classes.
Pssm-ID: 439329 Cd Length: 72 Bit Score: 112.22 E-value: 1.94e-29
DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as ...
518-756
2.13e-29
DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as RAD54L or RAD54, plays a role in homologous recombination related repair of DNA double-strand breaks. RAD54A 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.
Pssm-ID: 350825 [Multi-domain] Cd Length: 243 Bit Score: 118.34 E-value: 2.13e-29
DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha ...
518-736
7.38e-29
DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) is involved in transcriptional regulation and chromatin remodeling. Mutations in humans cause mental retardation, X-linked, syndromic, with hypotonic facies 1 (MRXSHF1) and alpha-thalassemia myelodysplasia syndrome (ATMDS). ATRX is part of the a DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350826 [Multi-domain] Cd Length: 246 Bit Score: 116.91 E-value: 7.38e-29
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; ...
518-756
2.10e-28
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; Chromodomain-helicase-DNA-binding protein 5 (CHD5) is a chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. It is thought to specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone H3 and plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at 'Lys-27' thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. As a tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa. CHD5 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.
Pssm-ID: 350815 [Multi-domain] Cd Length: 232 Bit Score: 115.16 E-value: 2.10e-28
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1; ...
517-717
3.40e-28
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1; Chromodomain-helicase-DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. It regulates polymerase II transcription and is also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. It is not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome. CHD1 is also associated with histone deacetylase (HDAC) activity. It 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.
Pssm-ID: 350811 [Multi-domain] Cd Length: 237 Bit Score: 114.76 E-value: 3.40e-28
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; ...
518-756
2.15e-27
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. CHD4 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.
Pssm-ID: 350814 [Multi-domain] Cd Length: 232 Bit Score: 112.08 E-value: 2.15e-27
DEXH-box helicase domain of SMARCAL1; SMARCAL1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1, also known as HARP) is recruited to stalled replication forks to promote repair and helps restart replication. It plays a role in DNA repair, telomere maintenance and replication fork stability in response to DNA replication stress. Mutations cause Schimke Immunoosseous Dysplasia. SMARCAL1 is part 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.
Pssm-ID: 350768 [Multi-domain] Cd Length: 213 Bit Score: 109.99 E-value: 6.79e-27
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; ...
518-718
9.99e-26
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; Chromodomain-helicase-DNA-binding protein 6 (CHD6) is a DNA-dependent ATPase that plays a role in chromatin remodeling. It regulates transcription by disrupting nucleosomes in a largely non-sliding manner which strongly increases the accessibility of chromatin. It activates transcription of specific genes in response to oxidative stress through interaction with NFE2L2.2 and acts as a transcriptional repressor of different viruses including influenza virus or papillomavirus. During influenza virus infection, the viral polymerase complex localizes CHD6 to inactive chromatin where it gets degraded in a proteasome independent-manner. CHD6 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.
Pssm-ID: 350816 [Multi-domain] Cd Length: 222 Bit Score: 107.05 E-value: 9.99e-26
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
851-964
5.47e-25
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 100.75 E-value: 5.47e-25
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; ...
518-756
5.49e-25
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; Chromodomain-helicase-DNA-binding protein 7 (CHD7) is a probable transcription regulator. It may be involved in the 45S precursor rRNA production. CHD7 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.
Pssm-ID: 350817 [Multi-domain] Cd Length: 222 Bit Score: 104.73 E-value: 5.49e-25
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as ...
538-725
1.45e-24
DEXH-box helicase domain of HLTF1; Helicase like transcription factor (HLTF1, also known as HIP116 or SMARCA3) has both helicase and E3 ubiquitin ligase activities and ATP-dependent nucleosome-remodeling activity. HLTF1 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.
Pssm-ID: 350829 [Multi-domain] Cd Length: 239 Bit Score: 104.09 E-value: 1.45e-24
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; ...
518-756
3.25e-24
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; Chromodomain-helicase-DNA-binding protein 8 (CHD8) is a DNA helicase that acts as a chromatin remodeling factor and regulates transcription. It also acts as a transcription repressor by remodeling chromatin structure and recruiting histone H1 to target genes. It suppresses p53/TP53-mediated apoptosis by recruiting histone H1 and preventing p53/TP53 transactivation activity and of STAT3 activity by suppressing the LIF-induced STAT3 transcriptional activity. It also acts as a negative regulator of Wnt signaling pathway and CTNNB1-targeted gene expression. CHD8 is also involved in both enhancer blocking and epigenetic remodeling at chromatin boundary via its interaction with CTCF. It also acts as a transcription activator via its interaction with ZNF143 by participating in efficient U6 RNA polymerase III transcription. CHD8 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.
Pssm-ID: 350818 [Multi-domain] Cd Length: 222 Bit Score: 102.82 E-value: 3.25e-24
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; ...
518-756
8.67e-24
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; Chromodomain-helicase-DNA-binding protein 9 (CHD9) acts as a transcriptional coactivator for PPARA and possibly other nuclear receptors. It is proposed to be a ATP-dependent chromatin remodeling protein. CHD9 has DNA-dependent ATPase activity and binds to A/T-rich DNA. It also associates with A/T-rich regulatory regions in promoters of genes that participate in the differentiation of progenitors during osteogenesis. CHD9 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.
Pssm-ID: 350819 [Multi-domain] Cd Length: 222 Bit Score: 101.62 E-value: 8.67e-24
DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called ...
518-703
1.30e-23
DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called Forkhead-box E1/FOXE1 ) is a transcription termination factor that couples ATP hydrolysis with the removal of RNA polymerase II from the DNA template. Single nucleotide polymorphism (SNP) within the 5'-UTR of TTF2 is associated with thyroid cancer risk.TTF2 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.
Pssm-ID: 350830 [Multi-domain] Cd Length: 241 Bit Score: 101.40 E-value: 1.30e-23
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
518-699
5.41e-17
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part 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.
Pssm-ID: 350769 [Multi-domain] Cd Length: 207 Bit Score: 81.18 E-value: 5.41e-17
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously ...
518-702
1.00e-15
DEXQ-box helicase domain of SHPRH; E3 ubiquitin-protein ligase SHPRH is a ubiquitously expressed protein that contains motifs characteristic of several DNA repair proteins, transcription factors, and helicases. SHPRH is a functional homolog of S. cerevisiae RAD5 and is involved in DNA repair. SHPRH 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.
Pssm-ID: 350828 [Multi-domain] Cd Length: 257 Bit Score: 78.92 E-value: 1.00e-15
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350172 [Multi-domain] Cd Length: 77 Bit Score: 50.78 E-value: 1.01e-07
DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 ...
518-728
1.29e-07
DEXQ-box helicase domain of bacterial SNF2 family proteins; Proteins belonging to the SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprise a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. The bacterial SNF2 present in this family are members 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.
Pssm-ID: 350771 [Multi-domain] Cd Length: 218 Bit Score: 53.89 E-value: 1.29e-07
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
of the residues that compose this conserved feature have been mapped to the query sequence.
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