4UTN

Crystal structure of zebrafish Sirtuin 5 in complex with succinylated CPS1-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

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	8063725	4003387	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DHS-like NAD/FAD-binding domain	8063726	3001728	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	DHS-like NAD/FAD-binding domain	8063726	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	PF02146	e4utnA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: PF02146	ECOD (1.6)
A	PF02146	e4utnA2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PF02146	ECOD (1.6)
B	PF02146	e4utnB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: PF02146	ECOD (1.6)
B	F_UNCLASSIFIED	e4utnB1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: F_UNCLASSIFIED	ECOD (1.6)

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)
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
A, B	PF02146	Sir2 family (SIR2)	Sir2 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D]	SUCCINYL-CPS1-PEPTIDE	-	-	-
A, B	NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL	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 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase 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 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity catalytic activity protein-succinyllysine desuccinylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds catalytic activity, acting on a protein protein-glutaryllysine deglutarylase activity protein-malonyllysine demalonylase activity cation binding transition metal ion binding zinc ion binding metal ion binding acyl binding transferase activity NAD-dependent histone deacetylase activity deacetylase activity protein lysine deacetylase activity histone deacetylase activity NAD-dependent protein lysine deacetylase activity histone modifying activity	organonitrogen compound metabolic process protein desuccinylation primary metabolic process macromolecule deacylation protein deacylation organic substance metabolic process macromolecule modification metabolic process protein metabolic process macromolecule metabolic process protein modification process peptidyl-lysine modification peptidyl-lysine desuccinylation peptidyl-amino acid modification organonitrogen compound metabolic process protein desuccinylation primary metabolic process macromolecule deacylation protein deacylation organic substance metabolic process macromolecule modification metabolic process protein metabolic process macromolecule metabolic process protein modification process peptidyl-lysine modification peptidyl-lysine desuccinylation peptidyl-amino acid modification peptidyl-lysine demalonylation protein demalonylation regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of cellular ketone metabolic process small molecule biosynthetic process regulation of ketone biosynthetic process cellular biosynthetic process cellular metabolic process biological regulation regulation of cellular metabolic process regulation of cellular biosynthetic process cellular ketone metabolic process biosynthetic process regulation of small molecule metabolic process organic substance biosynthetic process small molecule metabolic process cellular process regulation of metabolic process ketone biosynthetic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR027546	Sirtuin, class III	Family
A, B	IPR026590	Sirtuin family, catalytic core domain	Domain
A, B	IPR026591	Sirtuin, catalytic core small domain superfamily	Homologous Superfamily
A, B	IPR003000	Sirtuin family	Family
A, B	IPR029035	DHS-like NAD/FAD-binding domain superfamily	Homologous Superfamily

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.