Annotations: 5J8J

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF09757	e5j8jA1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: PF09757	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF09757	Arb2-like domain (Arb2-like)	Arb2-like domain	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 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Histone deacetylase HDA1	protein-containing complex binding chromatin binding binding deacetylase activity histone deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity histone modifying activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds identical protein binding protein binding	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process protein localization localization cellular macromolecule localization cellular localization negative regulation of transcription by transcription factor localization macromolecule localization positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex protein-DNA complex HDA1 complex nucleus membrane-enclosed lumen nuclear protein-containing complex chromatin chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex protein-DNA complex HDA1 complex nucleus membrane-enclosed lumen nuclear protein-containing complex chromatin chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen histone deacetylase complex intracellular organelle nucleoplasm organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR017321	Histone deacetylase class II, yeast	Family
A	IPR019154	Arb2-like domain	Domain
A	IPR000286	Histone deacetylase family	Family
A	IPR023801	Histone deacetylase domain	Domain
A	IPR037138	Histone deacetylase domain superfamily	Homologous Superfamily
A	IPR023696	Ureohydrolase domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.