5DOU | pdb_00005dou

Crystal Structure of Human Carbamoyl phosphate synthetase I (CPS1), ligand-bound form

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	CPSase_L_D3	e5douD7	A: alpha arrays	X: HTH	H: HTH	T: winged	F: CPSase_L_D3	ECOD (1.6)
D	ATP-grasp	e5douD2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp	ECOD (1.6)
D	carB	e5douD6	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: carB	ECOD (1.6)
D	GATase	e5douD4	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)
D	CPSase_sm_chain	e5douD8	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: CPSase_sm_chain	ECOD (1.6)
C	CPSase_L_D3	e5douC7	A: alpha arrays	X: HTH	H: HTH	T: winged	F: CPSase_L_D3	ECOD (1.6)
C	ATP-grasp	e5douC2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp	ECOD (1.6)
C	carB	e5douC6	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: carB	ECOD (1.6)
C	GATase	e5douC4	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)
C	CPSase_sm_chain	e5douC8	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: CPSase_sm_chain	ECOD (1.6)
B	CPSase_L_D3	e5douB7	A: alpha arrays	X: HTH	H: HTH	T: winged	F: CPSase_L_D3	ECOD (1.6)
B	ATP-grasp	e5douB2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp	ECOD (1.6)
B	carB	e5douB6	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: carB	ECOD (1.6)
B	GATase	e5douB4	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)
B	CPSase_sm_chain	e5douB8	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: CPSase_sm_chain	ECOD (1.6)
A	CPSase_L_D3	e5douA7	A: alpha arrays	X: HTH	H: HTH	T: winged	F: CPSase_L_D3	ECOD (1.6)
A	ATP-grasp	e5douA2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp	ECOD (1.6)
A	carB	e5douA6	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: carB	ECOD (1.6)
A	GATase	e5douA4	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Class I glutamine amidotransferase-like	F: GATase	ECOD (1.6)
A	CPSase_sm_chain	e5douA8	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: CPSase_sm_chain	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.1030.10	Mainly Alpha	Orthogonal Bundle	Carbamoyl Phosphate Synthetase	Chain A, domain 4	CATH (utative)
D	3.40.50.1380	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Methylglyoxal synthase-like domain	CATH (utative)
C	3.40.50.1380	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Methylglyoxal synthase-like domain	CATH (utative)
B	1.10.1030.10	Mainly Alpha	Orthogonal Bundle	Carbamoyl Phosphate Synthetase	Chain A, domain 4	CATH (utative)
B	3.40.50.1380	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Methylglyoxal synthase-like domain	CATH (utative)
A	1.10.1030.10	Mainly Alpha	Orthogonal Bundle	Carbamoyl Phosphate Synthetase	Chain A, domain 4	CATH (utative)
A	3.40.50.1380	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Methylglyoxal synthase-like domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00117	Glutamine amidotransferase class-I (GATase)	Glutamine amidotransferase class-I		Domain
A, B, C, D	PF00988	Carbamoyl-phosphate synthase small chain, CPSase domain (CPSase_sm_chain)	Carbamoyl-phosphate synthase small chain, CPSase domain	The carbamoyl-phosphate synthase domain is in the amino terminus of protein. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both ...	The carbamoyl-phosphate synthase domain is in the amino terminus of protein. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines [1]. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesise carbamoyl phosphate. See Pfam:PF00289. The small chain has a GATase domain in the carboxyl terminus. See Pfam:PF00117.	Domain
A, B, C, D	PF02142	MGS-like domain (MGS)	MGS-like domain	This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes ino ...	This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes inosicase. The known structures in this family show a common phosphate binding site [1].	Domain
A, B, C, D	PF02786	Carbamoyl-phosphate synthase L chain, ATP binding domain (CPSase_L_D2)	Carbamoyl-phosphate synthase L chain, ATP binding domain	Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines [2]. The c ...	Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines [2]. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesise carbamoyl phosphate. See Pfam:PF00988. The small chain has a GATase domain in the carboxyl terminus. See Pfam:PF00117. The ATP binding domain (this one) has an ATP-grasp fold.	Domain
A, B, C, D	PF02787	Carbamoyl-phosphate synthetase large chain, oligomerisation domain (CPSase_L_D3)	Carbamoyl-phosphate synthetase large chain, oligomerisation domain	Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Carbamoyl-phosphate synthase [ammonia], mitochondrial	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 amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process glutamine family amino acid metabolic process proteinogenic amino acid metabolic process metabolic process small molecule 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 amide biosynthetic process amide metabolic process 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 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	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle mitochondrion membrane-enclosed lumen intracellular membraneless organelle nucleoid intracellular membrane-bounded organelle mitochondrial matrix intracellular organelle lumen intracellular organelle organelle lumen organelle cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle mitochondrion membrane-enclosed lumen intracellular membraneless organelle nucleoid intracellular membrane-bounded organelle mitochondrial matrix intracellular organelle lumen intracellular organelle organelle lumen organelle 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR029062	Class I glutamine amidotransferase-like	Homologous Superfamily
A, B, C, D	IPR005479	Carbamoyl phosphate synthase, ATP-binding domain	Domain
A, B, C, D	IPR036897	Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily	Homologous Superfamily
A, B, C, D	IPR036914	Methylglyoxal synthase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
A, B, C, D	IPR005480	Carbamoyl-phosphate synthetase, large subunit oligomerisation domain	Domain
A, B, C, D	IPR011607	Methylglyoxal synthase-like domain	Domain
A, B, C, D	IPR002474	Carbamoyl-phosphate synthase small subunit, N-terminal domain	Domain
A, B, C, D	IPR017926	Glutamine amidotransferase	Domain
A, B, C, D	IPR036480	Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR005483	Carbamoyl phosphate synthase, CPSase domain	Domain
A, B, C, D	IPR011761	ATP-grasp fold	Domain
A, B, C, D	IPR006274	Carbamoyl-phosphate synthase, small subunit	Family
A, B, C, D	IPR006275	Carbamoyl-phosphate synthase, large subunit	Family
A, B, C, D	IPR016185	Pre-ATP-grasp domain superfamily	Homologous Superfamily
A, B, C, D	IPR035686	Carbamoyl-phosphate synthase small subunit, GATase1 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, 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