1GKP

D-Hydantoinase (Dihydropyrimidinase) from Thermus sp. in space group C2221

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	d1gkpa1	All beta proteins	Composite domain of metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase)	D-hydantoinase	(Thermus sp. ) [TaxId: 275 ],	SCOPe (2.08)
A	d1gkpa2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase), catalytic domain	D-hydantoinase	(Thermus sp. ) [TaxId: 275 ],	SCOPe (2.08)
B	d1gkpb1	All beta proteins	Composite domain of metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase)	D-hydantoinase	(Thermus sp. ) [TaxId: 275 ],	SCOPe (2.08)
B	d1gkpb2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase), catalytic domain	D-hydantoinase	(Thermus sp. ) [TaxId: 275 ],	SCOPe (2.08)
C	d1gkpc1	All beta proteins	Composite domain of metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase)	D-hydantoinase	(Thermus sp. ) [TaxId: 275 ],	SCOPe (2.08)
C	d1gkpc2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase), catalytic domain	D-hydantoinase	(Thermus sp. ) [TaxId: 275 ],	SCOPe (2.08)
D	d1gkpd1	All beta proteins	Composite domain of metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase)	D-hydantoinase	(Thermus sp. ) [TaxId: 275 ],	SCOPe (2.08)
D	d1gkpd2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase), catalytic domain	D-hydantoinase	(Thermus sp. ) [TaxId: 275 ],	SCOPe (2.08)
E	d1gkpe1	All beta proteins	Composite domain of metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase)	D-hydantoinase	(Thermus sp. ) [TaxId: 275 ],	SCOPe (2.08)
E	d1gkpe2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase), catalytic domain	D-hydantoinase	(Thermus sp. ) [TaxId: 275 ],	SCOPe (2.08)
F	d1gkpf1	All beta proteins	Composite domain of metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase)	D-hydantoinase	(Thermus sp. ) [TaxId: 275 ],	SCOPe (2.08)
F	d1gkpf2	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Metallo-dependent hydrolases	Hydantoinase (dihydropyrimidinase), catalytic domain	D-hydantoinase	(Thermus sp. ) [TaxId: 275 ],	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)	8026311	4002171	SCOP2 (2022-06-29)
A	SCOP2 Family	Hydantoinase (dihydropyrimidinase), catalytic domain	8026314	4002199	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Composite domain of metallo-dependent hydrolases	8038690	3000176	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Metallo-dependent hydrolases	8038693	3000428	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Metallo-dependent hydrolases	8038693	3000428	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8038690	3000176	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8038690	3000176	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8038690	3000176	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8038690	3000176	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Metallo-dependent hydrolases	8038693	3000428	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8038690	3000176	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8038690	3000176	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Metallo-dependent hydrolases	8038693	3000428	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8038690	3000176	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Metallo-dependent hydrolases	8038693	3000428	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8038690	3000176	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8038690	3000176	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Metallo-dependent hydrolases	8038693	3000428	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Composite domain of metallo-dependent hydrolases	8038690	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	e1gkpA1	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	e1gkpA2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DHOase	ECOD (1.6)
B	D-HYD_C	e1gkpB1	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)
B	DHOase	e1gkpB2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DHOase	ECOD (1.6)
C	D-HYD_C	e1gkpC1	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)
C	DHOase	e1gkpC2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DHOase	ECOD (1.6)
D	D-HYD_C	e1gkpD1	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)
D	DHOase	e1gkpD2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DHOase	ECOD (1.6)
E	D-HYD_C	e1gkpE1	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)
E	DHOase	e1gkpE2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DHOase	ECOD (1.6)
F	D-HYD_C	e1gkpF1	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)
F	DHOase	e1gkpF2	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)
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)
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)
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)
E	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
E	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)
F	2.30.40.10	Mainly Beta	Roll	Urease, subunit C	domain 1	CATH (4.3.0)
F	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, C, D, E A, B, C, D, E, F	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, C, D, E A, B, C, D, E, F	HYDANTOINASE	hydrolase activity 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, E A, B, C, D, E, F	IPR050378	Metallo-dependent Hydrolases Superfamily	Family
A, B, C, D, E A, B, C, D, E, F	IPR011778	Hydantoinase/dihydropyrimidinase	Family
A, B, C, D, E A, B, C, D, E, F	IPR006680	Amidohydrolase-related	Domain
A, B, C, D, E A, B, C, D, E, F	IPR011059	Metal-dependent hydrolase, composite domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	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.