4UU7 | pdb_00004uu7

Crystal structure of zebrafish Sirtuin 5 in complex with 3-methyl- 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
Pharos: Disease Associations

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	8063726	3001728	SCOP2B (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	SIR2	e4uu7A1	A: alpha bundles	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: SIR2	ECOD (develop294)
B	SIR2	e4uu7B1	A: alpha bundles	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: SIR2	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)
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]	CARBAMOYLPHOSPHATE SYNTHETASE I	binding phospholipid binding lipid binding carbon-nitrogen ligase activity, with glutamine as amido-N-donor catalytic activity ligase activity, forming carbon-nitrogen bonds carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity ligase activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding binding phospholipid binding lipid binding carbon-nitrogen ligase activity, with glutamine as amido-N-donor catalytic activity ligase activity, forming carbon-nitrogen bonds carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity ligase activity 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 protein-containing complex binding peptidase activity catalytic activity, acting on a protein hydrolase activity endopeptidase activity cation binding metal ion binding modified amino acid binding calcium ion binding potassium ion binding alkali metal ion binding carbamoyl-phosphate synthase (ammonia) activity organic acid binding amino acid binding carboxylic acid binding glutamate binding	response to stimulus response to chemical response to xenobiotic stimulus developmental process multicellular organism development multicellular organismal process digestive system development tube development midgut development anatomical structure development digestive tract development system development cellular response to stimulus response to lipid response to stimulus response to chemical response to xenobiotic stimulus developmental process multicellular organism development multicellular organismal process digestive system development tube development midgut development anatomical structure development digestive tract development system development cellular response to stimulus response to lipid response to fatty acid response to oxygen-containing compound cellular response to oleic acid cellular response to oxygen-containing compound cellular response to fatty acid cellular response to chemical stimulus response to oleic acid cellular response to lipid cellular process chemical homeostasis homeostatic process monoatomic ion homeostasis monoatomic anion homeostasis response to toxic substance response to fibroblast growth factor cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus response to growth factor cellular response to fibroblast growth factor stimulus response to metal ion response to zinc ion response to ketone response to glucocorticoid response to corticosteroid response to hormone response to steroid hormone response to dexamethasone epithelium development cellular developmental process gland development animal organ development tissue development liver development epithelial cell differentiation cell differentiation hepaticobiliary system development hepatocyte differentiation response to growth hormone response to peptide hormone response to nitrogen compound glutamine metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process metabolic process organic acid metabolic process carbamoyl phosphate metabolic process carbamoyl phosphate biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process phosphorus metabolic process nitrogen cycle metabolic process urea cycle urea metabolic process response to nutrient levels response to stress response to starvation response to acid chemical response to amino acid nitric oxide metabolic process reactive nitrogen species metabolic process cellular response to ammonium ion cellular response to nitrogen compound response to ammonium ion cellular response to peptide hormone stimulus response to glucagon cellular response to glucagon stimulus cellular response to hormone stimulus response to organophosphorus response to purine-containing compound response to cAMP cellular response to cAMP regulation of tube diameter system process regulation of tube size biological regulation circulatory system process vascular process in circulatory system blood vessel diameter maintenance regulation of biological quality vasodilation blood circulation regulation of anatomical structure size homocysteine metabolic process sulfur amino acid metabolic process amino acid metabolic process primary metabolic process alpha-amino acid metabolic process non-proteinogenic amino acid metabolic process sulfur compound metabolic process neutral lipid metabolic process lipid catabolic process catabolic process neutral lipid catabolic process glycerolipid catabolic process acylglycerol catabolic process triglyceride catabolic process triglyceride metabolic process glycerolipid metabolic process acylglycerol metabolic process lipid metabolic process small molecule biosynthetic process organic acid biosynthetic process carboxylic acid biosynthetic process amino acid biosynthetic process citrulline biosynthetic process alpha-amino acid biosynthetic process citrulline metabolic process non-proteinogenic amino acid biosynthetic process pyrimidine-containing compound metabolic process nucleobase biosynthetic process pyrimidine nucleobase biosynthetic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process nucleobase-containing small molecule metabolic process nucleobase metabolic process 'de novo' pyrimidine nucleobase biosynthetic process pyrimidine-containing compound biosynthetic process biological process involved in interspecies interaction between organisms response to other organism response to external stimulus response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin response to amine response to food response to alcohol	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle cell projection sperm principal piece organelle cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection sperm midpiece cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle cell projection sperm principal piece organelle cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection sperm midpiece mitochondrion membrane-enclosed lumen intracellular membraneless organelle nucleoid intracellular membrane-bounded organelle mitochondrial matrix intracellular organelle lumen intracellular organelle organelle lumen membraneless organelle mitochondrial nucleoid mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane nucleus nucleolus nuclear lumen cell periphery plasma membrane protein-containing complex
A, B	NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL	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 catalytic activity, acting on a protein acyltransferase activity deacylase activity 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 catalytic activity, acting on a protein acyltransferase activity deacylase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity protein-succinyllysine desuccinylase activity NAD-dependent protein lysine deacylase activity deacetylase activity protein lysine deacetylase activity histone deacetylase activity, NAD-dependent histone deacetylase activity NAD-dependent protein lysine deacetylase activity histone modifying activity protein-glutaryllysine deglutarylase activity protein-malonyllysine demalonylase activity 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 cation binding transition metal ion binding zinc ion binding metal ion binding acyl binding	protein deacylation macromolecule modification protein desuccinylation metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process macromolecule deacylation protein modification process peptidyl-lysine modification peptidyl-lysine desuccinylation peptidyl-amino acid modification peptidyl-lysine demalonylation protein deacylation macromolecule modification protein desuccinylation metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process macromolecule deacylation 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 small molecule biosynthetic process regulation of ketone biosynthetic process ketone metabolic process biological regulation regulation of ketone metabolic process biosynthetic process regulation of small molecule metabolic process small molecule metabolic process regulation of metabolic process ketone biosynthetic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth D]	IPR029062	Class I glutamine amidotransferase-like	Homologous Superfamily
C [auth D]	IPR005479	Carbamoyl phosphate synthase, ATP-binding domain	Domain
C [auth D]	IPR036897	Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily	Homologous Superfamily
C [auth D]	IPR036914	Methylglyoxal synthase-like domain superfamily	Homologous Superfamily
C [auth D]	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
C [auth D]	IPR005480	Carbamoyl-phosphate synthetase, large subunit oligomerisation domain	Domain
C [auth D]	IPR011607	Methylglyoxal synthase-like domain	Domain
C [auth D]	IPR002474	Carbamoyl-phosphate synthase small subunit, N-terminal domain	Domain
C [auth D]	IPR017926	Glutamine amidotransferase	Domain
C [auth D]	IPR036480	Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily	Homologous Superfamily
C [auth D]	IPR005483	Carbamoyl phosphate synthase, CPSase domain	Domain
C [auth D]	IPR011761	ATP-grasp fold	Domain
C [auth D]	IPR006274	Carbamoyl-phosphate synthase, small subunit	Family
C [auth D]	IPR058047	Carbamoyl phosphate synthase, preATP-grasp domain	Domain
C [auth D]	IPR006275	Carbamoyl-phosphate synthase, large subunit	Family
C [auth D]	IPR016185	Pre-ATP-grasp domain superfamily	Homologous Superfamily
C [auth D]	IPR035686	Carbamoyl-phosphate synthase small subunit, GATase1 domain	Domain
A, B	IPR027546	Sirtuin, class III	Family
A, B	IPR026590	Sirtuin family, catalytic core domain	Domain
A, B	IPR050134	NAD-dependent sirtuin protein deacylases	Family
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth D]	Pharos: P31327	carbamoyl phosphate synthetase I deficiency disease alveolar capillary dysplasia with misalignment of pulmonary veins pulmonary hypertension, neonatal, susceptibility to Liver Cirrhosis, Experimental malignant glioma psoriasis retinal disease cholelithiasis invasive ductal breast carcinoma lung cancer precancerous condition ulcerative colitis atypical teratoid rhabdoid tumor chronic kidney disease glioblastoma carbamoyl phosphate synthetase I deficiency disease alveolar capillary dysplasia with misalignment of pulmonary veins pulmonary hypertension, neonatal, susceptibility to Liver Cirrhosis, Experimental malignant glioma psoriasis retinal disease cholelithiasis invasive ductal breast carcinoma lung cancer precancerous condition ulcerative colitis atypical teratoid rhabdoid tumor chronic kidney disease glioblastoma large cell medulloblastoma malignant ependymoma urea cycle disorder breast cancer drug-induced liver injury intellectual disability