4IAO | pdb_00004iao

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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e4iaoA1	A: Rubredoxin-like	X: Rubredoxin-related	H: Rubredoxin-related	T:	F:	ECOD (20:10:01)
A		e4iaoA3	A: Alpha-beta plaits	X: Protease propeptides/inhibitors	H: Protease propeptides/inhibitors	T: LPMO_10	F:	ECOD (20:10:01)
B		e4iaoB1	A: Alpha-beta plaits	X: Protease propeptides/inhibitors	H: Protease propeptides/inhibitors	T: RrnaAD	F:	ECOD (20:10:01)
B		e4iaoB3	A: Four-helical up-and-down bundle	X: Glycosyl hydrolase domain	H: Glycosyl hydrolase domain	T: DNA_topoisoIV	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	6.10.140.1820	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
C	6.10.140.1820	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
A, B	PF02146	Sir2 family (SIR2)	Sir2 family	-	Family
A, B	PF04574	Protein of unknown function (DUF592) (DUF592)	Protein of unknown function (DUF592)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Regulatory protein SIR4	DNA binding double-stranded DNA binding 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 establishment of protein-containing complex localization to telomere macromolecule localization establishment of localization subtelomeric heterochromatin formation regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly localization telomere localization telomere tethering at nuclear periphery chromosome localization organelle localization establishment of protein-containing complex localization to telomere macromolecule localization establishment of localization subtelomeric heterochromatin formation regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization 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 epigenetic regulation of gene expression negative regulation of metabolic process biological regulation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule 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 cellular 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 cellular response to stress DNA damage response response to stress DNA repair positive regulation of organelle organization positive regulation of heterochromatin organization 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 chromosome organization regulation of cellular component biogenesis organelle organization regulation of heterochromatin organization	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle chromatin silencing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle chromatin silencing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region
A, B	NAD-dependent histone deacetylase SIR2	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding nucleic acid binding DNA replication origin binding NAD+ binding NAD binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding nucleic acid binding DNA replication origin binding NAD+ binding NAD binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein acyltransferase activity deacylase activity histone deacetylase activity, NAD-dependent histone H3K9 deacetylase activity, NAD-dependent transferase activity NAD-dependent protein lysine deacylase activity histone deacetylase activity histone H3K deacetylase activity histone modifying activity NAD-dependent protein lysine deacetylase activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity histone H3K14 deacetylase activity, NAD-dependent histone H4K16 deacetylase activity, NAD-dependent histone H4K deacetylase activity cation binding metal ion binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process localization telomere localization telomere tethering at nuclear periphery chromosome localization organelle localization developmental process regulation of biological process regulation of developmental process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process localization telomere localization telomere tethering at nuclear periphery chromosome localization organelle localization developmental process regulation of biological process regulation of developmental process regulation of reproductive process reproductive process reproductive process in single-celled organism biological regulation regulation of mating type switching developmental process involved in reproduction mating type switching sex determination mating type determination regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule 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 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 negative regulation of DNA metabolic process regulation of DNA metabolic process regulatory ncRNA-mediated gene silencing establishment of protein-containing complex localization to telomere macromolecule localization establishment of localization subtelomeric heterochromatin formation 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 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 double-strand break repair double-strand break repair via nonhomologous end joining DNA repair	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen RENT complex protein-containing complex nuclear protein-containing complex chromatin silencing complex chromatin chromosome heterochromatin chromosome, telomeric region chromosomal region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR031556	Sir4, SID domain	Domain
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	IPR050134	NAD-dependent sirtuin protein deacylases	Family
A, B	IPR026591	Sirtuin, catalytic core small 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.