2FVK | pdb_00002fvk

Crystal structure of dihydropyrimidinase from Saccharomyces kluyveri in complex with the substrate dihydrouracil

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d2fvka1	All beta proteins	Composite domain of metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase)	Dihydropyrimidine amidohydrolase Pyd2	(Lachancea kluyveri ) [TaxId: 4934 ],	SCOPe (2.08)
A	d2fvka2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase), catalytic domain	Dihydropyrimidine amidohydrolase Pyd2	(Lachancea kluyveri ) [TaxId: 4934 ],	SCOPe (2.08)
D	d2fvkd1	All beta proteins	Composite domain of metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase)	Dihydropyrimidine amidohydrolase Pyd2	(Lachancea kluyveri ) [TaxId: 4934 ],	SCOPe (2.08)
D	d2fvkd2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase), catalytic domain	Dihydropyrimidine amidohydrolase Pyd2	(Lachancea kluyveri ) [TaxId: 4934 ],	SCOPe (2.08)
C	d2fvkc1	All beta proteins	Composite domain of metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase)	Dihydropyrimidine amidohydrolase Pyd2	(Lachancea kluyveri ) [TaxId: 4934 ],	SCOPe (2.08)
C	d2fvkc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase), catalytic domain	Dihydropyrimidine amidohydrolase Pyd2	(Lachancea kluyveri ) [TaxId: 4934 ],	SCOPe (2.08)
B	d2fvkb1	All beta proteins	Composite domain of metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase)	Dihydropyrimidine amidohydrolase Pyd2	(Lachancea kluyveri ) [TaxId: 4934 ],	SCOPe (2.08)
B	d2fvkb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase), catalytic domain	Dihydropyrimidine amidohydrolase Pyd2	(Lachancea kluyveri ) [TaxId: 4934 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Hydantoinase (dihydropyrimidinase)	8029014	4002171	SCOP2 (2022-06-29)
A	SCOP2 Family	Hydantoinase (dihydropyrimidinase), catalytic domain	8029016	4002199	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Composite domain of metallo-dependent hydrolases	8041393	3000176	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Metallo-dependent hydrolases	8041395	3000428	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8041393	3000176	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8041393	3000176	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Metallo-dependent hydrolases	8041395	3000428	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Metallo-dependent hydrolases	8041395	3000428	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8041393	3000176	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8041393	3000176	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8041393	3000176	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metallo-dependent hydrolases	8041395	3000428	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8041393	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	Amidohydro_3	e2fvkA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Amidohydro_3	ECOD (v294.1)
D	DUF711	e2fvkD2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)
C	DUF711	e2fvkC2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)
B	DUF711	e2fvkB2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: DUF711	ECOD (v294.1)

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)
D	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
D	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)
C	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
C	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)
B	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
B	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	dihydropyrimidinase	dihydropyrimidinase 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 cation binding ion binding binding metal ion binding small molecule binding	-	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR050378	Metallo-dependent Hydrolases Superfamily	Family
A, B, C, D	IPR011778	Hydantoinase/dihydropyrimidinase	Family
A, B, C, D	IPR006680	Amidohydrolase-related	Domain
A, B, C, D	IPR011059	Metal-dependent hydrolase, composite domain superfamily	Homologous Superfamily
A, B, C, D	IPR032466	Metal-dependent hydrolase	Homologous Superfamily

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.