2V9X | pdb_00002v9x

E138D variant of Escherichia coli dCTP deaminase in complex with dUTP

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)
L	d2v9xl_	All beta proteins	beta-clip	dUTPase-like	dUTPase-like	Deoxycytidine triphosphate deaminase (dCTP deaminase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
K	d2v9xk_	All beta proteins	beta-clip	dUTPase-like	dUTPase-like	Deoxycytidine triphosphate deaminase (dCTP deaminase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J	d2v9xj_	All beta proteins	beta-clip	dUTPase-like	dUTPase-like	Deoxycytidine triphosphate deaminase (dCTP deaminase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I	d2v9xi_	All beta proteins	beta-clip	dUTPase-like	dUTPase-like	Deoxycytidine triphosphate deaminase (dCTP deaminase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d2v9xh_	All beta proteins	beta-clip	dUTPase-like	dUTPase-like	Deoxycytidine triphosphate deaminase (dCTP deaminase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d2v9xg_	All beta proteins	beta-clip	dUTPase-like	dUTPase-like	Deoxycytidine triphosphate deaminase (dCTP deaminase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d2v9xf_	All beta proteins	beta-clip	dUTPase-like	dUTPase-like	Deoxycytidine triphosphate deaminase (dCTP deaminase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2v9xe_	All beta proteins	beta-clip	dUTPase-like	dUTPase-like	Deoxycytidine triphosphate deaminase (dCTP deaminase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2v9xd_	All beta proteins	beta-clip	dUTPase-like	dUTPase-like	Deoxycytidine triphosphate deaminase (dCTP deaminase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2v9xc_	All beta proteins	beta-clip	dUTPase-like	dUTPase-like	Deoxycytidine triphosphate deaminase (dCTP deaminase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2v9xb_	All beta proteins	beta-clip	dUTPase-like	dUTPase-like	Deoxycytidine triphosphate deaminase (dCTP deaminase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2v9xa_	All beta proteins	beta-clip	dUTPase-like	dUTPase-like	Deoxycytidine triphosphate deaminase (dCTP deaminase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	dUTPase-like	8044147	3001957	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	dUTPase-like	8044147	3001957	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	dUTPase-like	8044147	3001957	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	dUTPase-like	8044147	3001957	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	dUTPase-like	8044147	3001957	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	dUTPase-like	8044147	3001957	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	dUTPase-like	8044147	3001957	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	dUTPase-like	8044147	3001957	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	dUTPase-like	8044147	3001957	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	dUTPase-like	8044147	3001957	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	dUTPase-like	8044147	3001957	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	dUTPase-like	8044147	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)
L	DCD	e2v9xL1	A: beta barrels	X: beta-clip	H: dUTPase-like (From Topology)	T: dUTPase-like	F: DCD	ECOD (1.6)
K	DCD	e2v9xK1	A: beta barrels	X: beta-clip	H: dUTPase-like (From Topology)	T: dUTPase-like	F: DCD	ECOD (1.6)
J	DCD	e2v9xJ1	A: beta barrels	X: beta-clip	H: dUTPase-like (From Topology)	T: dUTPase-like	F: DCD	ECOD (1.6)
I	DCD	e2v9xI1	A: beta barrels	X: beta-clip	H: dUTPase-like (From Topology)	T: dUTPase-like	F: DCD	ECOD (1.6)
H	DCD	e2v9xH1	A: beta barrels	X: beta-clip	H: dUTPase-like (From Topology)	T: dUTPase-like	F: DCD	ECOD (1.6)
G	DCD	e2v9xG1	A: beta barrels	X: beta-clip	H: dUTPase-like (From Topology)	T: dUTPase-like	F: DCD	ECOD (1.6)
F	DCD	e2v9xF1	A: beta barrels	X: beta-clip	H: dUTPase-like (From Topology)	T: dUTPase-like	F: DCD	ECOD (1.6)
E	DCD	e2v9xE1	A: beta barrels	X: beta-clip	H: dUTPase-like (From Topology)	T: dUTPase-like	F: DCD	ECOD (1.6)
D	DCD	e2v9xD1	A: beta barrels	X: beta-clip	H: dUTPase-like (From Topology)	T: dUTPase-like	F: DCD	ECOD (1.6)
C	DCD	e2v9xC1	A: beta barrels	X: beta-clip	H: dUTPase-like (From Topology)	T: dUTPase-like	F: DCD	ECOD (1.6)
B	DCD	e2v9xB1	A: beta barrels	X: beta-clip	H: dUTPase-like (From Topology)	T: dUTPase-like	F: DCD	ECOD (1.6)
A	DCD	e2v9xA1	A: beta barrels	X: beta-clip	H: dUTPase-like (From Topology)	T: dUTPase-like	F: DCD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
K	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
J	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
I	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
H	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)
G	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)
E	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)
C	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)
A	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, G, H, I, J, K, L	PF22769	dCTP deaminase-like (DCD)	dCTP deaminase-like	This entry represents a dCTP deaminase (DCD) domain found in archaea and bacteria [1-5]. Methanococcus jannaschii, has a bifunctional enzyme DCD-DUT, that harbors both dCTP deaminase and dUTP pyrophosphatase activities [1].	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, G, H, I, J, K, L	DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines hydrolase activity dCTP deaminase activity catalytic activity deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds identical protein binding protein binding	pyrimidine deoxyribonucleotide metabolic process deoxyribose phosphate biosynthetic process nucleotide biosynthetic process dUTP metabolic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process pyrimidine deoxyribonucleoside triphosphate biosynthetic process nucleobase-containing compound metabolic process deoxyribonucleotide biosynthetic process pyrimidine deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process pyrimidine deoxyribonucleoside triphosphate metabolic process pyrimidine deoxyribonucleotide metabolic process deoxyribose phosphate biosynthetic process nucleotide biosynthetic process dUTP metabolic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process pyrimidine deoxyribonucleoside triphosphate biosynthetic process nucleobase-containing compound metabolic process deoxyribonucleotide biosynthetic process pyrimidine deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process pyrimidine deoxyribonucleoside triphosphate metabolic process small molecule metabolic process pyrimidine-containing compound biosynthetic process pyrimidine nucleoside triphosphate biosynthetic process phosphorus metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine-containing compound metabolic process pyrimidine nucleoside triphosphate metabolic process dUTP biosynthetic process nucleoside triphosphate biosynthetic process 2'-deoxyribonucleotide metabolic process 2'-deoxyribonucleotide biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process nucleoside triphosphate metabolic process pyrimidine nucleotide biosynthetic process pyrimidine deoxyribonucleoside monophosphate metabolic process deoxyribonucleoside monophosphate biosynthetic process pyrimidine deoxyribonucleoside monophosphate biosynthetic process nucleoside monophosphate metabolic process pyrimidine nucleoside monophosphate metabolic process dUMP biosynthetic process nucleoside monophosphate biosynthetic process dUMP metabolic process pyrimidine nucleoside monophosphate biosynthetic process nucleobase-containing small molecule interconversion response to stimulus response to radiation response to abiotic stimulus protein-containing complex organization protein trimerization cellular component organization cellular component biogenesis cellular component assembly protein homotrimerization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis dTTP biosynthetic process dTTP metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR033704	dUTPase, trimeric	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR036157	dUTPase-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR011962	dCTP deaminase	Family

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.