1J79

Molecular Structure of Dihydroorotase: A Paradigm for Catalysis Through the Use of a Binuclear Metal Center

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1j79a_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	Dihydroorotase	Dihydroorotase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1j79b_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	Dihydroorotase	Dihydroorotase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Metallo-dependent hydrolases	8033929	3000428	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metallo-dependent hydrolases	8033929	3000428	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	PF01979	e1j79A1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF01979	ECOD (1.6)
B	PF01979	e1j79B1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF01979	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)
B	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01979	Amidohydrolase family (Amidohydro_1)	Amidohydrolase family	This family of enzymes are a a large metal dependent hydrolase superfamily [1]. The family includes Adenine deaminase EC:3.5.4.2 that hydrolyses adenine to form hypoxanthine and ammonia. Adenine deaminases reaction is important for adenine utilisatio ...	This family of enzymes are a a large metal dependent hydrolase superfamily [1]. The family includes Adenine deaminase EC:3.5.4.2 that hydrolyses adenine to form hypoxanthine and ammonia. Adenine deaminases reaction is important for adenine utilisation as a purine and also as a nitrogen source [2]. This family also includes dihydroorotase and N-acetylglucosamine-6-phosphate deacetylases, EC:3.5.1.25 These enzymes catalyse the reaction N-acetyl-D-glucosamine 6-phosphate + H2O <=> D-glucosamine 6-phosphate + acetate. This family includes the catalytic domain of urease alpha subunit [3]. Dihydroorotases (EC:3.5.2.3) are also included [4-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	dihydroorotase	dihydroorotase activity hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds identical protein binding protein binding binding protein homodimerization activity protein dimerization activity cation binding transition metal ion binding zinc ion binding ion binding dihydroorotase activity hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds identical protein binding protein binding binding protein homodimerization activity protein dimerization activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	organonitrogen compound metabolic process pyrimidine-containing compound metabolic process nucleobase biosynthetic process pyrimidine nucleobase biosynthetic process organonitrogen compound biosynthetic process primary metabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process nucleobase-containing small molecule metabolic process nucleobase metabolic process organic cyclic compound biosynthetic process organic substance biosynthetic process organonitrogen compound metabolic process pyrimidine-containing compound metabolic process nucleobase biosynthetic process pyrimidine nucleobase biosynthetic process organonitrogen compound biosynthetic process primary metabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process nucleobase-containing small molecule metabolic process nucleobase metabolic process organic cyclic compound biosynthetic process organic substance biosynthetic process 'de novo' pyrimidine nucleobase biosynthetic process small molecule metabolic process metabolic process pyrimidine-containing compound biosynthetic process nucleotide biosynthetic process pyrimidine nucleotide metabolic process phosphate-containing compound metabolic process phosphorus metabolic process nucleoside phosphate metabolic process cellular metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process cellular process pyrimidine nucleotide biosynthetic process ribose phosphate metabolic process carbohydrate derivative metabolic process 'de novo' UMP biosynthetic process ribonucleotide biosynthetic process UMP biosynthetic process ribonucleotide metabolic process ribonucleoside monophosphate metabolic process UMP metabolic process nucleoside monophosphate metabolic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process carbohydrate derivative biosynthetic process pyrimidine nucleoside monophosphate metabolic process pyrimidine ribonucleoside monophosphate metabolic process nucleoside monophosphate biosynthetic process pyrimidine ribonucleoside monophosphate biosynthetic process pyrimidine nucleoside monophosphate biosynthetic process ribonucleoside monophosphate biosynthetic process pyrimidine ribonucleotide biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR004721	Dihydroorotase homodimeric type	Family
A, B	IPR002195	Dihydroorotase, conserved site	Conserved Site
A, B	IPR006680	Amidohydrolase-related	Domain
A, B	IPR032466	Metal-dependent hydrolase	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	dihydroorotase M-CSA #630	Dihyrdoorotase catalyses the reversible interconversion of carbamoyl aspartate and dihydroorotate. This reaction is an essential part of the pathway for the biosynthesis of pyrimidine nucleotides. Sequence comparisons show that there are two general classes of dihydroorotases. Class II enzymes are all monofunctional proteins from Gram-negative bacteria and yeast. Class I enzymes, found in higher organisms, are much larger and typically contain several enzyme activities as exemplified by CAD, a multifunctional enzyme found in mammals, insects and moulds. This protein combines the first three enzymes of the pyrimidine biosynthesis pathway: carbamoyl phosphate synthetase, aspartate carbamoylase, and dihydroorotase. Sequence homology within each class of enzymes is quite high (>40%) while that between the two classes is much lower. Both classes employ the same mechanism involving a binuclear zinc centre.	Defined by 6 residues: HIS:A-16HIS:A-18LYS:A-102HIS:A-139HIS:A-177ASP:A-250 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.5.2.3 (PDB Primary Data) Search M-CSA Motif + EC 3.5.2.3

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 R01GM133198.