Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
E [auth A]SCOP2B SuperfamilyCore histone-like8041272 3001387 SCOP2B (2021-05-27)
F [auth B]SCOP2B SuperfamilyCore histone-like8042439 3001387 SCOP2B (2021-05-27)
H [auth D]SCOP2 FamilyNucleosome core histones8102298 4000793 SCOP2 (2021-05-27)
H [auth D]SCOP2 SuperfamilyCore histone-like8102299 3001387 SCOP2 (2021-05-27)
H [auth D]SCOP2B SuperfamilyCore histone-like8041279 3001387 SCOP2B (2021-05-27)
J [auth F]SCOP2B SuperfamilyCore histone-like8042439 3001387 SCOP2B (2021-05-27)
K [auth G]SCOP2B SuperfamilyCore histone-like8041278 3001387 SCOP2B (2021-05-27)
L [auth H]SCOP2 FamilyNucleosome core histones8102296 4000793 SCOP2 (2021-05-27)
L [auth H]SCOP2 SuperfamilyCore histone-like8102297 3001387 SCOP2 (2021-05-27)
L [auth H]SCOP2B SuperfamilyCore histone-like8041279 3001387 SCOP2B (2021-05-27)
G [auth C]SCOP2B SuperfamilyCore histone-like8067126 3001387 SCOP2B (2021-05-27)
I [auth E]SCOP2B SuperfamilyCore histone-like8041272 3001387 SCOP2B (2021-05-27)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth K]PF00850e6z6pK1 A: a/b three-layered sandwichesX: HAD domain-likeH: HAD domain-relatedT: Arginase/deacetylaseF: PF00850ECOD (1.6)
A [auth K]PF09757e6z6pK2 A: a/b three-layered sandwichesX: alpha/beta-Hydrolases (From Topology)H: alpha/beta-Hydrolases (From Topology)T: alpha/beta-HydrolasesF: PF09757ECOD (1.6)
B [auth L]PF00850e6z6pL1 A: a/b three-layered sandwichesX: HAD domain-likeH: HAD domain-relatedT: Arginase/deacetylaseF: PF00850ECOD (1.6)
B [auth L]PF09757e6z6pL2 A: a/b three-layered sandwichesX: alpha/beta-Hydrolases (From Topology)H: alpha/beta-Hydrolases (From Topology)T: alpha/beta-HydrolasesF: PF09757ECOD (1.6)
E [auth A]PF00125e6z6pA1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF00125ECOD (1.6)
F [auth B]PF15511e6z6pB1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF15511ECOD (1.6)
H [auth D]PF00125e6z6pD1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF00125ECOD (1.6)
J [auth F]PF15511e6z6pF1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF15511ECOD (1.6)
K [auth G]PF00125,PF16211e6z6pG1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF00125,PF16211ECOD (1.6)
L [auth H]PF00125e6z6pH1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF00125ECOD (1.6)
G [auth C]PF00125,PF16211e6z6pC1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF00125,PF16211ECOD (1.6)
I [auth E]PF00125e6z6pE1 A: alpha arraysX: Histone-likeH: Histone-relatedT: HistoneF: PF00125ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth K]PF00850Histone deacetylase domain (Hist_deacetyl)Histone deacetylase domainHistones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1]. ...Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1].
Domain
A [auth K]PF09757Arb2-like domain (Arb2-like)Arb2-like domainThis domain is found at the C-terminal of Clr3 (Cryptic loci regulator 3) (also known as histone deacetylase clr3) (EC:3.5.1.98) from S. pombe, its orthologue from S. cerevisiae HDA1, and similar sequences. This domain has been defined by sequence ho ...This domain is found at the C-terminal of Clr3 (Cryptic loci regulator 3) (also known as histone deacetylase clr3) (EC:3.5.1.98) from S. pombe, its orthologue from S. cerevisiae HDA1, and similar sequences. This domain has been defined by sequence homology to the Arb2 protein from S. pombe (not included in this entry). Structure analysis reveals that the Arb2 domain has clear homology to alpha/beta-hydrolases but that it is lacking the catalytic triad of these enzymes. Functional studies show that the this domain is necessary for centromeric heterochromatin silencing suggesting a model where the Arb2-like domain, through residues N562 and Y563, acts as an anchor that connects the HDAC activity of Clr3 to the SHREC complex. SHREC (Snf2/Hdac Repressive) complex in fission yeast drives transcriptional gene silencing in heterochromatin [1]. Studies in HDA1 described that two Arb2-like domains form a compact homo-dimer via the arm elements, and assemble as an inverse 'V' shape and that the domain possesses histone binding ability [2,3].
Domain
B [auth L]PF00850Histone deacetylase domain (Hist_deacetyl)Histone deacetylase domainHistones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1]. ...Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyse the removal of the acetyl group. Histone deacetylases are related to other proteins [1].
Domain
B [auth L]PF09757Arb2-like domain (Arb2-like)Arb2-like domainThis domain is found at the C-terminal of Clr3 (Cryptic loci regulator 3) (also known as histone deacetylase clr3) (EC:3.5.1.98) from S. pombe, its orthologue from S. cerevisiae HDA1, and similar sequences. This domain has been defined by sequence ho ...This domain is found at the C-terminal of Clr3 (Cryptic loci regulator 3) (also known as histone deacetylase clr3) (EC:3.5.1.98) from S. pombe, its orthologue from S. cerevisiae HDA1, and similar sequences. This domain has been defined by sequence homology to the Arb2 protein from S. pombe (not included in this entry). Structure analysis reveals that the Arb2 domain has clear homology to alpha/beta-hydrolases but that it is lacking the catalytic triad of these enzymes. Functional studies show that the this domain is necessary for centromeric heterochromatin silencing suggesting a model where the Arb2-like domain, through residues N562 and Y563, acts as an anchor that connects the HDAC activity of Clr3 to the SHREC complex. SHREC (Snf2/Hdac Repressive) complex in fission yeast drives transcriptional gene silencing in heterochromatin [1]. Studies in HDA1 described that two Arb2-like domains form a compact homo-dimer via the arm elements, and assemble as an inverse 'V' shape and that the domain possesses histone binding ability [2,3].
Domain
E [auth A]PF00125Core histone H2A/H2B/H3/H4 (Histone)Core histone H2A/H2B/H3/H4- Domain
F [auth B]PF15511Centromere kinetochore component CENP-T histone fold (CENP-T_C)Centromere kinetochore component CENP-T histone foldCENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].
Domain
H [auth D]PF00125Core histone H2A/H2B/H3/H4 (Histone)Core histone H2A/H2B/H3/H4- Domain
J [auth F]PF15511Centromere kinetochore component CENP-T histone fold (CENP-T_C)Centromere kinetochore component CENP-T histone foldCENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].
Domain
K [auth G]PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
K [auth G]PF00125Core histone H2A/H2B/H3/H4 (Histone)Core histone H2A/H2B/H3/H4- Domain
L [auth H]PF00125Core histone H2A/H2B/H3/H4 (Histone)Core histone H2A/H2B/H3/H4- Domain
C [auth M]PF11496Class II histone deacetylase complex subunits 2 and 3 (HDA2-3)Class II histone deacetylase complex subunits 2 and 3This family of class II histone deacetylase complex subunits HDA2 and HDA3 is found in fungi, The member from S. pombe is referred to as Ccq1 in Swiss:Q10432. These proteins associate with HDA1 to generate the activity of the HDA1 histone deacetylase ...This family of class II histone deacetylase complex subunits HDA2 and HDA3 is found in fungi, The member from S. pombe is referred to as Ccq1 in Swiss:Q10432. These proteins associate with HDA1 to generate the activity of the HDA1 histone deacetylase complex. HDA1 interacts with itself and with the HDA2-HDA3 subcomplex to form a probable tetramer and these interactions are necessary for catalytic activity. The HDA1 histone deacetylase complex is responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. HDA2 and HDA3 have a conserved coiled-coil domain towards their C-terminus [1].
Domain
D [auth N]PF11496Class II histone deacetylase complex subunits 2 and 3 (HDA2-3)Class II histone deacetylase complex subunits 2 and 3This family of class II histone deacetylase complex subunits HDA2 and HDA3 is found in fungi, The member from S. pombe is referred to as Ccq1 in Swiss:Q10432. These proteins associate with HDA1 to generate the activity of the HDA1 histone deacetylase ...This family of class II histone deacetylase complex subunits HDA2 and HDA3 is found in fungi, The member from S. pombe is referred to as Ccq1 in Swiss:Q10432. These proteins associate with HDA1 to generate the activity of the HDA1 histone deacetylase complex. HDA1 interacts with itself and with the HDA2-HDA3 subcomplex to form a probable tetramer and these interactions are necessary for catalytic activity. The HDA1 histone deacetylase complex is responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. HDA2 and HDA3 have a conserved coiled-coil domain towards their C-terminus [1].
Domain
G [auth C]PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
G [auth C]PF00125Core histone H2A/H2B/H3/H4 (Histone)Core histone H2A/H2B/H3/H4- Domain
I [auth E]PF00125Core histone H2A/H2B/H3/H4 (Histone)Core histone H2A/H2B/H3/H4- Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth K]Histone deacetylase HDA1
B [auth L]Histone deacetylase HDA1
E [auth A]Histone H3 -
F [auth B]Histone H4
H [auth D]Histone H2B -
J [auth F]Histone H4
K [auth G]Histone H2A type 1 -
L [auth H]Histone H2B -
M [auth I]DNA (145-MER)---
N [auth J]DNA (145-MER)---
C [auth M]HDA1 complex subunit 3,HDA1 complex subunit 3
D [auth N]HDA1 complex subunit 2
G [auth C]Histone H2A -
I [auth E]Histone H3.2 -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth K]IPR017321Histone deacetylase class II, yeastFamily
A [auth K]IPR019154Arb2-like domainDomain
A [auth K]IPR000286Histone deacetylase familyFamily
A [auth K]IPR023801Histone deacetylase domainDomain
A [auth K]IPR037138Histone deacetylase domain superfamilyHomologous Superfamily
A [auth K]IPR023696Ureohydrolase domain superfamilyHomologous Superfamily
B [auth L]IPR017321Histone deacetylase class II, yeastFamily
B [auth L]IPR019154Arb2-like domainDomain
B [auth L]IPR000286Histone deacetylase familyFamily
B [auth L]IPR023801Histone deacetylase domainDomain
B [auth L]IPR037138Histone deacetylase domain superfamilyHomologous Superfamily
B [auth L]IPR023696Ureohydrolase domain superfamilyHomologous Superfamily
E [auth A]IPR009072Histone-foldHomologous Superfamily
E [auth A]IPR007125Histone H2A/H2B/H3Domain
E [auth A]IPR000164Histone H3/CENP-AFamily
F [auth B]IPR009072Histone-foldHomologous Superfamily
F [auth B]IPR001951Histone H4Family
F [auth B]IPR035425CENP-T/Histone H4, histone foldDomain
F [auth B]IPR019809Histone H4, conserved siteConserved Site
F [auth B]IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
H [auth D]IPR009072Histone-foldHomologous Superfamily
H [auth D]IPR007125Histone H2A/H2B/H3Domain
H [auth D]IPR000558Histone H2BFamily
J [auth F]IPR009072Histone-foldHomologous Superfamily
J [auth F]IPR001951Histone H4Family
J [auth F]IPR035425CENP-T/Histone H4, histone foldDomain
J [auth F]IPR019809Histone H4, conserved siteConserved Site
J [auth F]IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
K [auth G]IPR009072Histone-foldHomologous Superfamily
K [auth G]IPR007125Histone H2A/H2B/H3Domain
K [auth G]IPR002119Histone H2AFamily
K [auth G]IPR032454Histone H2A, C-terminal domainDomain
K [auth G]IPR032458Histone H2A conserved siteConserved Site
L [auth H]IPR009072Histone-foldHomologous Superfamily
L [auth H]IPR007125Histone H2A/H2B/H3Domain
L [auth H]IPR000558Histone H2BFamily
C [auth M]IPR038609HDA1 complex subunit 2/3 superfamilyHomologous Superfamily
C [auth M]IPR026216HDA1 complex subunit 3Family
C [auth M]IPR021006HDA1 complex subunit 2/3Family
D [auth N]IPR038609HDA1 complex subunit 2/3 superfamilyHomologous Superfamily
D [auth N]IPR021006HDA1 complex subunit 2/3Family
G [auth C]IPR009072Histone-foldHomologous Superfamily
G [auth C]IPR007125Histone H2A/H2B/H3Domain
G [auth C]IPR002119Histone H2AFamily
G [auth C]IPR032454Histone H2A, C-terminal domainDomain
G [auth C]IPR032458Histone H2A conserved siteConserved Site
I [auth E]IPR009072Histone-foldHomologous Superfamily
I [auth E]IPR007125Histone H2A/H2B/H3Domain
I [auth E]IPR000164Histone H3/CENP-AFamily