2OD2 | pdb_00002od2

Crystal Structure of yHst2 I117F mutant bound to carba-NAD+ and an acetylated H4 peptide

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8039531	3001728	SCOP2B (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	MR_MLE_C	e2od2A1	A: alpha bundles	X: Profilin-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: MR_MLE_C	ECOD (develop294)

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
A	NAD-dependent deacetylase HST2	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
B	Acetylated H4 peptide	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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.

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