7M31

Dihydropyrimidine Dehydrogenase (DPD) C671S Mutant Soaked with Thymine and NADPH Anaerobically

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	4Fe-4S ferredoxins	8001525	3000020	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	FMN-linked oxidoreductases	8001523	3000014	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	alpha-helical ferredoxin	8001521	3000026	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thioredoxin reductase-like	8017506	3000050	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thioredoxin reductase-like	8017506	3000050	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	FMN-linked oxidoreductases	8001523	3000014	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	alpha-helical ferredoxin	8001521	3000026	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	4Fe-4S ferredoxins	8001525	3000020	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	FMN-linked oxidoreductases	8001523	3000014	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	alpha-helical ferredoxin	8001521	3000026	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	4Fe-4S ferredoxins	8001525	3000020	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thioredoxin reductase-like	8017506	3000050	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	alpha-helical ferredoxin	8001521	3000026	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	FMN-linked oxidoreductases	8001523	3000014	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	4Fe-4S ferredoxins	8001525	3000020	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thioredoxin reductase-like	8017506	3000050	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)
B	Fer4_20	e7m31B2	A: alpha arrays	X: alpha-helical ferredoxin-like	H: alpha-helical ferredoxin (From Topology)	T: alpha-helical ferredoxin	F: Fer4_20	ECOD (1.6)
B	Fer4_21	e7m31B3	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_21	ECOD (1.6)
B	DHO_dh	e7m31B5	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DHO_dh	ECOD (1.6)
B	Pyr_redox_2_3	e7m31B1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2_3	ECOD (1.6)
B	Pyr_redox_2	e7m31B4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: Pyr_redox_2	ECOD (1.6)
C	Fer4_20	e7m31C2	A: alpha arrays	X: alpha-helical ferredoxin-like	H: alpha-helical ferredoxin (From Topology)	T: alpha-helical ferredoxin	F: Fer4_20	ECOD (1.6)
C	Fer4_21	e7m31C1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_21	ECOD (1.6)
C	DHO_dh	e7m31C4	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DHO_dh	ECOD (1.6)
C	Pyr_redox_2_3	e7m31C3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2_3	ECOD (1.6)
C	Pyr_redox_2	e7m31C5	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: Pyr_redox_2	ECOD (1.6)
A	Fer4_20	e7m31A5	A: alpha arrays	X: alpha-helical ferredoxin-like	H: alpha-helical ferredoxin (From Topology)	T: alpha-helical ferredoxin	F: Fer4_20	ECOD (1.6)
A	Fer4_21	e7m31A2	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_21	ECOD (1.6)
A	DHO_dh	e7m31A4	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DHO_dh	ECOD (1.6)
A	Pyr_redox_2_3	e7m31A3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2_3	ECOD (1.6)
A	Pyr_redox_2	e7m31A1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: Pyr_redox_2	ECOD (1.6)
D	Fer4_20	e7m31D4	A: alpha arrays	X: alpha-helical ferredoxin-like	H: alpha-helical ferredoxin (From Topology)	T: alpha-helical ferredoxin	F: Fer4_20	ECOD (1.6)
D	Fer4_21	e7m31D1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_21	ECOD (1.6)
D	DHO_dh	e7m31D5	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DHO_dh	ECOD (1.6)
D	Pyr_redox_2_3	e7m31D3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2_3	ECOD (1.6)
D	Pyr_redox_2	e7m31D2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: Pyr_redox_2	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF07992	Pyridine nucleotide-disulphide oxidoreductase (Pyr_redox_2)	Pyridine nucleotide-disulphide oxidoreductase	This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.	Domain
A, B, C, D	PF01180	Dihydroorotate dehydrogenase (DHO_dh)	Dihydroorotate dehydrogenase	-	Domain
A, B, C, D	PF14691	Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster (Fer4_20)	Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster	Domain II of the enzyme dihydroprymidine dehydrogenase binds FAD. Dihydroprymidine dehydrogenase catalyses the first and rate-limiting step of pyrimidine degradation by converting pyrimidines to the corresponding 5,6- dihydro compounds [1]. This doma ...	Domain II of the enzyme dihydroprymidine dehydrogenase binds FAD. Dihydroprymidine dehydrogenase catalyses the first and rate-limiting step of pyrimidine degradation by converting pyrimidines to the corresponding 5,6- dihydro compounds [1]. This domain carries two Fe4-S4 clusters.	Domain
A, B, C, D	PF14697	4Fe-4S dicluster domain (Fer4_21)	4Fe-4S dicluster domain	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contai ...	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Dihydropyrimidine dehydrogenase [NADP(+)]	dihydropyrimidine dehydrogenase (NADP+) activity oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-CH group of donors catalytic activity binding nucleotide binding FMN binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding dihydropyrimidine dehydrogenase (NADP+) activity oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-CH group of donors catalytic activity binding nucleotide binding FMN binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding purine nucleotide binding adenyl nucleotide binding NADP binding identical protein binding protein binding protein homodimerization activity protein dimerization activity flavin adenine dinucleotide binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding metal ion binding pyrimidine nucleobase binding nucleobase binding uracil binding	pyrimidine-containing compound metabolic process catabolic process thymine catabolic process pyrimidine-containing compound catabolic process primary metabolic process pyrimidine nucleobase catabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process thymine metabolic process nucleobase-containing small molecule metabolic process nucleobase catabolic process nucleobase metabolic process small molecule metabolic process metabolic process pyrimidine-containing compound metabolic process catabolic process thymine catabolic process pyrimidine-containing compound catabolic process primary metabolic process pyrimidine nucleobase catabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process thymine metabolic process nucleobase-containing small molecule metabolic process nucleobase catabolic process nucleobase metabolic process small molecule metabolic process metabolic process cellular process beta-alanine metabolic process oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process beta-alanine biosynthetic process carboxylic acid biosynthetic process non-proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process non-proteinogenic amino acid biosynthetic process glycosyl compound metabolic process deoxyribonucleoside metabolic process thymidine catabolic process carbohydrate derivative metabolic process pyrimidine nucleoside metabolic process carbohydrate derivative catabolic process pyrimidine nucleoside catabolic process glycosyl compound catabolic process nucleoside metabolic process pyrimidine deoxyribonucleoside catabolic process nucleobase-containing compound catabolic process nucleobase-containing small molecule catabolic process nucleoside catabolic process deoxyribonucleoside catabolic process small molecule catabolic process pyrimidine deoxyribonucleoside metabolic process thymidine metabolic process uracil metabolic process uracil catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D	IPR005720	Dihydroorotate dehydrogenase, catalytic	Domain
A, B, C, D	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR009051	Alpha-helical ferredoxin	Homologous Superfamily
A, B, C, D	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
A, B, C, D	IPR028261	Dihydroprymidine dehydrogenase domain II	Domain
A, B, C, D	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
A, B, C, D	IPR023753	FAD/NAD(P)-binding domain	Domain