5YTK | pdb_00005ytk

Crystal structure of SIRT3 bound to a leucylated AceCS2

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8081956	3001728	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8081956	3001728	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8081956	3001728	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8081956	3001728	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8081956	3001728	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8081956	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)
F	SIR2_1st	e5ytkF2	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)
F	SIR2_2nd_1	e5ytkF1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd_1	ECOD (1.6)
E	SIR2_1st	e5ytkE1	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)
E	SIR2_2nd_1	e5ytkE2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd_1	ECOD (1.6)
D	SIR2_1st	e5ytkD1	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)
D	SIR2_2nd_1	e5ytkD2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd_1	ECOD (1.6)
C	SIR2_1st	e5ytkC2	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)
C	SIR2_2nd_1	e5ytkC1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd_1	ECOD (1.6)
B	SIR2_1st	e5ytkB2	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_1	e5ytkB1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd_1	ECOD (1.6)
A	SIR2_1st	e5ytkA1	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_1	e5ytkA2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SIR2_2nd_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
F	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (4.3.0)
E	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
E	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (4.3.0)
D	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
D	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	CATH (4.3.0)
C	3.40.50.1220	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	TPP-binding domain	CATH (4.3.0)
C	3.30.1600.10	Alpha Beta	2-Layer Sandwich	SIR2/SIRT2 'Small Domain'	SIR2/SIRT2 'Small Domain'	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)
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, B, C, D, E A, B, C, D, E, F	PF02146	Sir2 family (SIR2)	Sir2 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H [auth J], I [auth K], J [auth L]	AceCS2-KLeu	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding CoA-ligase activity propionate-CoA ligase activity fatty acid ligase activity ligase activity, forming carbon-sulfur bonds fatty acid-CoA ligase activity short-chain fatty acid-CoA ligase activity catalytic activity acid-thiol ligase activity ligase activity ATP-dependent activity acetate-CoA ligase activity cation binding AMP binding	monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process acetate metabolic process acetate biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process biosynthetic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process acetate metabolic process acetate biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process biosynthetic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process fatty acid metabolic process short-chain fatty acid metabolic process lipid biosynthetic process primary metabolic process fatty acid biosynthetic process short-chain fatty acid biosynthetic process propionate biosynthetic process lipid metabolic process propionate metabolic process acetyl-CoA metabolic process nucleobase-containing compound metabolic process acyl-CoA metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process acyl-CoA biosynthetic process phosphate-containing compound metabolic process sulfur compound metabolic process amide metabolic process phosphorus metabolic process nucleoside phosphate metabolic process amide biosynthetic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process acetyl-CoA biosynthetic process sulfur compound biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process acetyl-CoA biosynthetic process from acetate alcohol catabolic process catabolic process primary alcohol catabolic process alcohol metabolic process ethanol metabolic process ethanol catabolic process small molecule catabolic process primary alcohol metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen
A, B, C, D, E A, B, C, D, E, F	NAD-dependent protein deacetylase sirtuin-3, mitochondrial	NAD-dependent protein lysine delactylase activity catalytic activity, acting on a protein acyltransferase activity deacylase activity NAD-dependent protein lysine deacetylase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity NAD-dependent protein lysine deacylase activity deacetylase activity protein lysine deacetylase activity sequence-specific DNA binding DNA binding binding NAD-dependent protein lysine delactylase activity catalytic activity, acting on a protein acyltransferase activity deacylase activity NAD-dependent protein lysine deacetylase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity NAD-dependent protein lysine deacylase activity deacetylase activity protein lysine deacetylase activity sequence-specific DNA binding DNA binding binding nucleic acid 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 histone deacetylase activity, NAD-dependent histone deacetylase activity histone modifying activity cation binding transition metal ion binding zinc ion binding metal ion binding protein binding enzyme binding	regulation of molecular function positive regulation of molecular function positive regulation of catalase activity regulation of catalytic activity biological regulation positive regulation of catalytic activity regulation of oxidoreductase activity positive regulation of oxidoreductase activity peptidyl-lysine deacetylation peptidyl-lysine modification primary metabolic process macromolecule deacylation protein deacetylation protein deacylation regulation of molecular function positive regulation of molecular function positive regulation of catalase activity regulation of catalytic activity biological regulation positive regulation of catalytic activity regulation of oxidoreductase activity positive regulation of oxidoreductase activity peptidyl-lysine deacetylation peptidyl-lysine modification primary metabolic process macromolecule deacylation protein deacetylation protein deacylation macromolecule modification peptidyl-amino acid modification metabolic process cellular process protein metabolic process macromolecule metabolic process protein modification process aerobic respiration cellular respiration energy derivation by oxidation of organic compounds generation of precursor metabolites and energy cellular response to stimulus regulation of cellular process response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process signal transduction regulation of biological process regulation of signaling negative regulation of response to stimulus regulation of MAPK cascade negative regulation of signal transduction negative regulation of ERK1 and ERK2 cascade regulation of response to stimulus MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade negative regulation of MAPK cascade cellular response to stress response to stress negative regulation of metabolic process reactive oxygen species metabolic process negative regulation of reactive oxygen species metabolic process regulation of metabolic process regulation of reactive oxygen species metabolic process regulation of superoxide dismutase activity positive regulation of superoxide dismutase activity positive regulation of cell communication regulation of localization establishment of protein localization nitrogen compound transport positive regulation of establishment of protein localization localization positive regulation of insulin secretion intracellular protein localization regulation of biological quality regulation of peptide hormone secretion regulation of hormone levels positive regulation of peptide hormone secretion establishment of protein localization to extracellular region protein secretion establishment of localization regulation of protein secretion regulation of secretion positive regulation of protein localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion transport positive regulation of biological process positive regulation of secretion by cell hormone secretion protein localization to extracellular region positive regulation of protein transport peptide secretion regulation of secretion by cell secretion by cell positive regulation of hormone secretion positive regulation of secretion amide transport signal release positive regulation of cellular process positive regulation of peptide secretion regulation of transport secretion regulation of peptide transport regulation of establishment of protein localization export from cell cell-cell signaling regulation of protein transport positive regulation of protein secretion peptide transport positive regulation of transport protein transport regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport insulin secretion positive regulation of signaling oxidative phosphorylation positive regulation of oxidative phosphorylation regulation of generation of precursor metabolites and energy regulation of cellular respiration regulation of aerobic respiration positive regulation of cellular respiration positive regulation of metabolic process regulation of oxidative phosphorylation regulation of amide metabolic process sphingolipid biosynthetic process regulation of lipid metabolic process positive regulation of ceramide biosynthetic process lipid biosynthetic process positive regulation of sphingolipid biosynthetic process regulation of primary metabolic process cellular component biogenesis regulation of sphingolipid biosynthetic process positive regulation of biosynthetic process positive regulation of lipid metabolic process amide metabolic process cellular component organization or biogenesis regulation of ceramide biosynthetic process regulation of biosynthetic process membrane lipid metabolic process ceramide metabolic process regulation of membrane lipid metabolic process sphingolipid metabolic process amide biosynthetic process regulation of macromolecule metabolic process regulation of cellular component biogenesis macromolecule biosynthetic process biosynthetic process positive regulation of lipid biosynthetic process ceramide biosynthetic process positive regulation of amide metabolic process regulation of macromolecule biosynthetic process regulation of lipid biosynthetic process membrane lipid biosynthetic process lipid metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex mitochondrial matrix

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G, H [auth J], I [auth K], J [auth L]	IPR011904	Acetate-CoA ligase	Family
G, H [auth J], I [auth K], J [auth L]	IPR020845	AMP-binding, conserved site	Conserved Site
G, H [auth J], I [auth K], J [auth L]	IPR045851	AMP-binding enzyme, C-terminal domain superfamily	Homologous Superfamily
G, H [auth J], I [auth K], J [auth L]	IPR042099	ANL, N-terminal domain	Homologous Superfamily
G, H [auth J], I [auth K], J [auth L]	IPR025110	AMP-binding enzyme, C-terminal domain	Domain
G, H [auth J], I [auth K], J [auth L]	IPR000873	AMP-dependent synthetase/ligase domain	Domain
G, H [auth J], I [auth K], J [auth L]	IPR032387	Acetyl-coenzyme A synthetase, N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR026590	Sirtuin family, catalytic core domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003000	Sirtuin family	Family
A, B, C, D, E A, B, C, D, E, F	IPR029035	DHS-like NAD/FAD-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR050134	NAD-dependent sirtuin protein deacylases	Family
A, B, C, D, E A, B, C, D, E, F	IPR026591	Sirtuin, catalytic core small domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
G, H [auth J], I [auth K], J [auth L]	Pharos: Q9NUB1	adrenal cortex carcinoma large cell medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor malignant ependymoma facioscapulohumeral muscular dystrophy medulloblastoma
A, B, C, D, E A, B, C, D, E, F	Pharos: Q9NTG7	obesity disorder squamous cell carcinoma gestational diabetes benign prostatic hyperplasia DOID:0081062 heart disease neurodegenerative disease osteosarcoma type 2 diabetes mellitus brain aneurysm psoriasis uterine corpus leiomyoma breast cancer Hashimoto thyroiditis oral cavity neoplasm

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.