1XRF | pdb_00001xrf

The Crystal Structure of a Novel, Latent Dihydroorotase from Aquifex aeolicus at 1.7 A resolution

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1xrfa1	All beta proteins	Composite domain of metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase)	Two-domain dihydroorotase	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
A	d1xrfa2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase), catalytic domain	Two-domain dihydroorotase	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
A	d1xrfa3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8033870	3000176	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metallo-dependent hydrolases	8033871	3000428	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8033870	3000176	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	D-HYD_C	e1xrfA3	A: beta sandwiches	X: Composite domain of metallo-dependent hydrolases (From Topology)	H: Composite domain of metallo-dependent hydrolases (From Topology)	T: Composite domain of metallo-dependent hydrolases	F: D-HYD_C	ECOD (1.6)
A	DHOase	e1xrfA4	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DHOase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
A	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	PF12890	Dihydro-orotase-like (DHOase)	Dihydro-orotase-like	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	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 allantoinase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	ribose phosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process 'de novo' UMP biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process UMP biosynthetic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process UMP metabolic process small molecule metabolic process pyrimidine-containing compound biosynthetic process ribose phosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process 'de novo' UMP biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process UMP biosynthetic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process UMP metabolic process small molecule metabolic process pyrimidine-containing compound biosynthetic process phosphorus metabolic process nucleoside monophosphate metabolic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine nucleoside monophosphate metabolic process pyrimidine ribonucleoside monophosphate metabolic process pyrimidine-containing compound metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process nucleoside monophosphate biosynthetic process biosynthetic process pyrimidine ribonucleoside monophosphate biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process pyrimidine nucleoside monophosphate biosynthetic process ribonucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process catabolic process purine nucleobase metabolic process purine-containing compound catabolic process purine nucleobase catabolic process purine-containing compound metabolic process nucleobase catabolic process nucleobase metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR050138	Dihydroorotase/Allantoinase hydrolase-like	Family
A	IPR024403	Dihydroorotase, catalytic domain	Domain
A	IPR002195	Dihydroorotase, conserved site	Conserved Site
A	IPR004722	Dihydroorotase	Family
A	IPR011059	Metal-dependent hydrolase, composite domain superfamily	Homologous Superfamily
A	IPR032466	Metal-dependent hydrolase	Homologous Superfamily
A	IPR013108	Amidohydrolase 3	Domain

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.