2FR5

Crystal Structure of Mouse Cytidine Deaminase Complexed with Tetrahydrouridine

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	d2fr5a_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	Cytidine deaminase	automated matches	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d2fr5b_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	Cytidine deaminase	automated matches	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d2fr5d_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	Cytidine deaminase	automated matches	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d2fr5c_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	Cytidine deaminase	automated matches	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Cytidine deaminase	8028924	4000870	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cytidine deaminase-like	8041303	3001838	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Cytidine deaminase-like	8041303	3001838	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cytidine deaminase-like	8041303	3001838	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cytidine deaminase-like	8041303	3001838	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	dCMP_cyt_deam_1	e2fr5A1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: dCMP_cyt_deam_1	ECOD (1.6)
B	dCMP_cyt_deam_1	e2fr5B1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: dCMP_cyt_deam_1	ECOD (1.6)
D	dCMP_cyt_deam_1	e2fr5D1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: dCMP_cyt_deam_1	ECOD (1.6)
C	dCMP_cyt_deam_1	e2fr5C1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: dCMP_cyt_deam_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
B	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
D	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
C	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00383	Cytidine and deoxycytidylate deaminase zinc-binding region (dCMP_cyt_deam_1)	Cytidine and deoxycytidylate deaminase zinc-binding region	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Cytidine deaminase	binding organic cyclic compound binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines cytidine deaminase activity hydrolase activity catalytic activity binding organic cyclic compound binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines cytidine deaminase activity hydrolase activity catalytic activity deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding transition metal ion binding zinc ion binding ion binding metal ion binding	pyrimidine ribonucleotide catabolic process ribose phosphate metabolic process ribonucleotide catabolic process pyrimidine ribonucleoside monophosphate catabolic process CMP catabolic process catabolic process pyrimidine-containing compound catabolic process organophosphate catabolic process carbohydrate derivative metabolic process nucleoside phosphate catabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process pyrimidine nucleotide catabolic process ribonucleotide metabolic process ribonucleoside monophosphate metabolic process pyrimidine ribonucleotide catabolic process ribose phosphate metabolic process ribonucleotide catabolic process pyrimidine ribonucleoside monophosphate catabolic process CMP catabolic process catabolic process pyrimidine-containing compound catabolic process organophosphate catabolic process carbohydrate derivative metabolic process nucleoside phosphate catabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process pyrimidine nucleotide catabolic process ribonucleotide metabolic process ribonucleoside monophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process ribonucleoside monophosphate catabolic process phosphorus metabolic process nucleoside monophosphate metabolic process pyrimidine ribonucleotide metabolic process nucleotide catabolic process pyrimidine nucleoside monophosphate catabolic process nucleoside phosphate metabolic process pyrimidine nucleoside monophosphate metabolic process carbohydrate derivative catabolic process pyrimidine-containing compound metabolic process pyrimidine ribonucleoside monophosphate metabolic process nucleoside monophosphate catabolic process cellular metabolic process primary metabolic process nucleotide metabolic process nucleobase-containing compound catabolic process CMP metabolic process organophosphate metabolic process metabolic process cellular process pyrimidine deoxyribonucleotide catabolic process pyrimidine deoxyribonucleoside monophosphate catabolic process deoxyribonucleoside monophosphate catabolic process deoxyribonucleotide catabolic process pyrimidine deoxyribonucleotide metabolic process dCMP catabolic process deoxyribose phosphate catabolic process pyrimidine deoxyribonucleoside monophosphate metabolic process deoxyribonucleotide metabolic process dCMP metabolic process 2'-deoxyribonucleotide metabolic process deoxyribose phosphate metabolic process deoxyribonucleoside monophosphate metabolic process glycosyl compound metabolic process pyrimidine nucleoside metabolic process cytidine deamination pyrimidine nucleoside catabolic process cytidine metabolic process glycosyl compound catabolic process nucleoside metabolic process cytidine catabolic process pyrimidine ribonucleoside metabolic process nucleobase-containing small molecule catabolic process nucleoside catabolic process pyrimidine ribonucleoside catabolic process small molecule catabolic process ribonucleoside catabolic process ribonucleoside metabolic process response to ketone response to cycloheximide response to stimulus response to alcohol response to chemical response to oxygen-containing compound response to nitrogen compound response to organic cyclic compound regulation of biological process regulation of growth regulation of cellular component organization regulation of cellular process negative regulation of biological process biological regulation growth negative regulation of cell growth regulation of cell growth cell growth cellular component organization negative regulation of growth negative regulation of cellular process cellular component organization or biogenesis nucleotide biosynthetic process pyrimidine ribonucleotide salvage pyrimidine-containing compound salvage pyrimidine nucleotide salvage nucleotide salvage ribonucleotide biosynthetic process UMP salvage UMP biosynthetic process UMP metabolic process pyrimidine-containing compound biosynthetic process ribose phosphate biosynthetic process cellular metabolic compound salvage carbohydrate derivative biosynthetic process nucleobase-containing compound biosynthetic process nucleoside monophosphate biosynthetic process biosynthetic process pyrimidine ribonucleoside monophosphate biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process pyrimidine nucleoside monophosphate biosynthetic process ribonucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process negative regulation of small molecule metabolic process negative regulation of phosphate metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of nucleotide metabolic process regulation of small molecule metabolic process regulation of phosphate metabolic process regulation of nucleotide metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of phosphorus metabolic process regulation of phosphorus metabolic process regulation of metabolic process cellular response to biotic stimulus cellular response to stimulus cellular response to external biotic stimulus response to external stimulus response to external biotic stimulus response to biotic stimulus cellular response to external stimulus	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR016193	Cytidine deaminase-like	Homologous Superfamily
A, B, C, D	IPR050202	Cytidine and Deoxycytidylate Deaminase	Family
A, B, C, D	IPR006262	Cytidine deaminase, homotetrameric	Family
A, B, C, D	IPR002125	Cytidine and deoxycytidylate deaminase domain	Domain
A, B, C, D	IPR016192	APOBEC/CMP deaminase, zinc-binding	Binding Site

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.