2XCD | pdb_00002xcd

Structure of YncF,the genomic dUTPase from Bacillus subtilis

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	d2xcda_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d2xcdb_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d2xcdd_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
E	d2xcde_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
F	d2xcdf_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d2xcdc_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	dUTPase-like	8080239	3001957	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	dUTPase-like	8080239	3001957	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	dUTPase-like	8080239	3001957	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	dUTPase-like	8080239	3001957	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	dUTPase-like	8080239	3001957	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	dUTPase-like	8080239	3001957	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	Rhodanese	e2xcdA1	A: alpha bundles	X: Ribonuclease H-like	H: Creatinase/prolidase N-terminal domain	T: Creatinase/prolidase N-terminal domain	F: Rhodanese	ECOD (develop294)
B	F5_F8_type_C	e2xcdB1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: F5_F8_type_C	ECOD (develop294)
D	F5_F8_type_C	e2xcdD1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: F5_F8_type_C	ECOD (develop294)
E	F5_F8_type_C	e2xcdE1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: F5_F8_type_C	ECOD (develop294)
F	F5_F8_type_C	e2xcdF1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: F5_F8_type_C	ECOD (develop294)
C	F5_F8_type_C	e2xcdC1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: F5_F8_type_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
B	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
D	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
E	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
F	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
C	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	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	PF00692	dUTPase (dUTPase)	dUTPase	dUTPase hydrolyses dUTP to dUMP and pyrophosphate.	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	PROBABLE DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YNCF	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding pyrophosphatase activity nucleoside triphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides dUTP diphosphatase activity hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	pyrimidine deoxyribonucleotide catabolic process catabolic process deoxyribonucleotide catabolic process pyrimidine deoxyribonucleotide metabolic process nucleoside triphosphate catabolic process pyrimidine-containing compound catabolic process dUTP metabolic process organophosphate catabolic process carbohydrate derivative metabolic process pyrimidine nucleoside triphosphate catabolic process nucleoside phosphate catabolic process deoxyribose phosphate catabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process pyrimidine nucleotide catabolic process pyrimidine deoxyribonucleotide catabolic process catabolic process deoxyribonucleotide catabolic process pyrimidine deoxyribonucleotide metabolic process nucleoside triphosphate catabolic process pyrimidine-containing compound catabolic process dUTP metabolic process organophosphate catabolic process carbohydrate derivative metabolic process pyrimidine nucleoside triphosphate catabolic process nucleoside phosphate catabolic process deoxyribose phosphate catabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process pyrimidine nucleotide catabolic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process pyrimidine deoxyribonucleoside triphosphate metabolic process small molecule metabolic process dUTP catabolic process phosphorus metabolic process nucleotide catabolic process pyrimidine deoxyribonucleoside triphosphate catabolic process nucleoside phosphate metabolic process carbohydrate derivative catabolic process pyrimidine-containing compound metabolic process pyrimidine nucleoside triphosphate metabolic process 2'-deoxyribonucleotide metabolic process primary metabolic process nucleotide metabolic process nucleobase-containing compound catabolic process organophosphate metabolic process metabolic process cellular process nucleoside triphosphate metabolic process deoxyribose phosphate biosynthetic process nucleotide biosynthetic process pyrimidine deoxyribonucleoside monophosphate metabolic process deoxyribonucleotide biosynthetic process pyrimidine deoxyribonucleotide biosynthetic process deoxyribonucleoside monophosphate biosynthetic process pyrimidine deoxyribonucleoside monophosphate biosynthetic process pyrimidine-containing compound biosynthetic process nucleoside monophosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine nucleoside monophosphate metabolic process 2'-deoxyribonucleotide biosynthetic process nucleobase-containing compound biosynthetic process dUMP biosynthetic process nucleoside monophosphate biosynthetic process dUMP metabolic process biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process pyrimidine nucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR008181	Deoxyuridine triphosphate nucleotidohydrolase	Family
A, B, C, D, E A, B, C, D, E, F	IPR033704	dUTPase, trimeric	Domain
A, B, C, D, E A, B, C, D, E, F	IPR029054	dUTPase-like	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036157	dUTPase-like superfamily	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.