4IAO

Crystal structure of Sir2 C543S mutant in complex with SID domain of Sir4

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Sir2N regulatory domain-like	8046149	4004909	SCOP2 (2022-06-29)
A	SCOP2 Family	Sir2 family of transcriptional regulators	8092980	4003387	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sir2N regulatory domain-like	8092979	3002652	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DHS-like NAD/FAD-binding domain	8092981	3001728	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8092981	3001728	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sir2N regulatory domain-like	8092979	3002652	SCOP2B (2022-06-29)
C	SCOP2 Family	Sir4 SID domain-like	8046454	4005089	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Sir4 SID domain-like	8092982	3002653	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	DUF592	e4iaoA3	A: alpha arrays	X: Sir2 N-terminal domain (From Topology)	H: Sir2 N-terminal domain (From Topology)	T: Sir2 N-terminal domain	F: DUF592	ECOD (1.6)
A	SIR2_1st	e4iaoA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: SIR2_1st	ECOD (1.6)
A	SIR2_2nd	e4iaoA2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd	ECOD (1.6)
B	DUF592	e4iaoB2	A: alpha arrays	X: Sir2 N-terminal domain (From Topology)	H: Sir2 N-terminal domain (From Topology)	T: Sir2 N-terminal domain	F: DUF592	ECOD (1.6)
B	SIR2_1st	e4iaoB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: SIR2_1st	ECOD (1.6)
B	SIR2_2nd	e4iaoB3	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.1710	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
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)
B	1.20.120.1710	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
B	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
B	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (4.3.0)
C	6.10.140.1820	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
D	6.10.140.1820	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF04574	Protein of unknown function (DUF592) (DUF592)	Protein of unknown function (DUF592)	-	Family
A, B	PF02146	Sir2 family (SIR2)	Sir2 family	-	Family
C, D	PF16991	Sir4 SID domain (SIR4_SID)	Sir4 SID domain	This is the Sir2 interaction domain (SID domain) of silent information regulator 4 (Sir4)[1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	NAD-dependent histone deacetylase SIR2	deacetylase activity NAD-dependent 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 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds histone deacetylase activity NAD-dependent histone H3K14 deacetylase activity histone H3K14 deacetylase activity histone H3K deacetylase activity histone modifying activity NAD-dependent protein lysine deacetylase activity catalytic activity deacetylase activity NAD-dependent 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 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds histone deacetylase activity NAD-dependent histone H3K14 deacetylase activity histone H3K14 deacetylase activity histone H3K deacetylase activity histone modifying activity NAD-dependent protein lysine deacetylase activity catalytic activity NAD-dependent histone H3K9 deacetylase activity histone H3K9 deacetylase activity histone H4K deacetylase activity histone H4K16 deacetylase activity NAD-dependent histone H4K16 deacetylase activity transferase activity NAD+ binding NAD binding binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding cation binding metal ion binding	localization telomere localization telomere tethering at nuclear periphery chromosome localization organelle localization regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process chromatin organization organic substance biosynthetic process localization telomere localization telomere tethering at nuclear periphery chromosome localization organelle localization regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process protein-DNA complex organization cellular component organization organic substance metabolic process chromatin organization organic substance biosynthetic process negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation protein-containing complex organization epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process silent mating-type cassette heterochromatin formation negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process organelle organization chromosome organization sister chromatid cohesion cell cycle cell cycle process regulation of DNA recombination regulation of primary metabolic process nucleobase-containing compound metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process negative regulation of DNA recombination organic cyclic compound metabolic process negative regulation of DNA metabolic process regulation of DNA metabolic process regulatory ncRNA-mediated gene silencing cellular localization establishment of protein-containing complex localization to telomere cellular macromolecule localization macromolecule localization establishment of localization protein-containing complex localization subtelomeric heterochromatin formation telomere organization regulation of DNA amplification regulation of DNA biosynthetic process nucleic acid biosynthetic process negative regulation of DNA amplification DNA amplification nucleobase-containing compound biosynthetic process organic cyclic compound biosynthetic process DNA biosynthetic process negative regulation of DNA biosynthetic process regulation of biological quality regulation of DNA stability nucleolar chromatin organization rDNA heterochromatin formation nucleus organization nucleolus organization facultative heterochromatin formation negative regulation of DNA replication DNA replication regulation of DNA replication cellular response to stimulus double-strand break repair response to stimulus double-strand break repair via nonhomologous end joining cellular response to stress DNA damage response response to stress DNA repair	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle RENT complex protein-containing complex nuclear protein-containing complex chromatin silencing complex protein-DNA complex chromatin chromosome heterochromatin chromosome, telomeric region chromosomal region
C, D	Regulatory protein SIR4	DNA binding double-stranded DNA binding binding organic cyclic compound binding nucleic acid binding molecular adaptor activity protein-containing complex binding chromatin binding nucleosome binding	localization telomere localization telomere tethering at nuclear periphery chromosome localization organelle localization cellular localization establishment of protein-containing complex localization to telomere cellular macromolecule localization macromolecule localization cellular process establishment of localization protein-containing complex localization subtelomeric heterochromatin formation regulation of cellular process localization telomere localization telomere tethering at nuclear periphery chromosome localization organelle localization cellular localization establishment of protein-containing complex localization to telomere cellular macromolecule localization macromolecule localization cellular process establishment of localization protein-containing complex localization subtelomeric heterochromatin formation regulation of cellular process cellular biosynthetic process negative regulation of biological process telomere organization negative regulation of cellular metabolic process cellular component organization protein-DNA complex organization organic substance metabolic process chromatin organization organic substance biosynthetic process negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation protein-containing complex organization epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process biological regulation chromosome organization regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression organelle organization negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process silent mating-type cassette heterochromatin formation cellular response to stimulus double-strand break repair response to stimulus double-strand break repair via nonhomologous end joining primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process cellular response to stress DNA damage response response to stress DNA repair positive regulation of organelle organization cellular component biogenesis regulation of heterochromatin formation regulation of chromatin organization regulation of chromosome organization regulation of organelle organization positive regulation of chromosome organization regulation of cellular component organization positive regulation of cellular component organization positive regulation of biological process positive regulation of heterochromatin formation positive regulation of chromatin organization positive regulation of cellular process positive regulation of cellular component biogenesis regulation of cellular component biogenesis	membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure organelle chromatin silencing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular non-membrane-bounded organelle chromosome chromosome, telomeric region chromosomal region membrane-bounded organelle intracellular organelle protein-containing complex intracellular anatomical structure organelle chromatin silencing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle cellular anatomical entity intracellular non-membrane-bounded organelle chromosome chromosome, telomeric region chromosomal region non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR026590	Sirtuin family, catalytic core domain	Domain
A, B	IPR007654	NAD-dependent histone deacetylase Sir2, N-terminal	Domain
A, B	IPR003000	Sirtuin family	Family
A, B	IPR029035	DHS-like NAD/FAD-binding domain superfamily	Homologous Superfamily
A, B	IPR026591	Sirtuin, catalytic core small domain superfamily	Homologous Superfamily
C, D	IPR031556	Sir4, SID domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.