1Q1A | pdb_00001q1a

Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP ribose and histone peptide

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1q1aa_	Alpha and beta proteins (a/b)	DHS-like NAD/FAD-binding domain	DHS-like NAD/FAD-binding domain	Sir2 family of transcriptional regulators	Hst2	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Sir2 family of transcriptional regulators	8027152	4003387	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DHS-like NAD/FAD-binding domain	8039531	3001728	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e1q1aA1	A: EF-hand	X: EF-hand-related	H: EF-hand	T: EF-hand_1, EF-hand_6, EF-hand_7	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
A	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02146	Sir2 family (SIR2)	Sir2 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Histone H4	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin identical protein binding	nucleolar large rRNA transcription by RNA polymerase I RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I rRNA transcription nucleolar large rRNA transcription by RNA polymerase I RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I rRNA transcription metabolic process cellular process macromolecule metabolic process rRNA metabolic process protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular component organization or biogenesis nucleosome assembly nucleosome organization regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase I positive regulation of cellular process regulation of transcription by RNA polymerase I positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membraneless organelle transcription regulator complex intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure RNA polymerase I upstream activating factor complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membraneless organelle transcription regulator complex intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure RNA polymerase I upstream activating factor complex RNA polymerase I transcription regulator complex organelle lumen organelle membraneless organelle nuclear lumen protein-DNA complex nucleosome chromatin chromosome
A	HST2 protein	NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein acyltransferase activity histone deacetylase activity, NAD-dependent deacylase activity transferase activity NAD-dependent protein lysine deacylase activity histone deacetylase activity NAD-dependent protein lysine deacetylase activity histone modifying activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity histone H4K16 deacetylase activity, NAD-dependent histone H4K deacetylase activity cation binding metal ion binding	regulation of DNA recombination regulation of cellular process negative regulation of biological process regulation of mitotic recombination regulation of primary metabolic process nucleobase-containing compound metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of mitotic recombination regulation of biological process DNA recombination negative regulation of metabolic process regulation of DNA recombination regulation of cellular process negative regulation of biological process regulation of mitotic recombination regulation of primary metabolic process nucleobase-containing compound metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of mitotic recombination regulation of biological process DNA recombination negative regulation of metabolic process biological regulation mitotic recombination primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process negative regulation of DNA recombination metabolic process cellular process negative regulation of DNA metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process nucleolar chromatin organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling cellular component organization or biogenesis rDNA heterochromatin formation regulation of biosynthetic process heterochromatin formation epigenetic regulation of gene expression heterochromatin organization gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression nucleus organization organelle organization biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleolus organization facultative heterochromatin formation negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR009072	Histone-fold	Homologous Superfamily
B	IPR035425	CENP-T/Histone H4, histone fold	Domain
B	IPR001951	Histone H4	Family
B	IPR019809	Histone H4, conserved site	Conserved Site
A	IPR026590	Sirtuin family, catalytic core domain	Domain
A	IPR050134	NAD-dependent sirtuin protein deacylases	Family
A	IPR017328	Sirtuin, class I	Family
A	IPR026591	Sirtuin, catalytic core small domain superfamily	Homologous Superfamily
A	IPR003000	Sirtuin family	Family
A	IPR029035	DHS-like NAD/FAD-binding domain superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	ALY	Parent Component: LYS RESID: AA0055 PSI-MOD : N6-acetyl-L-lysine MOD:00064

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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.