1R5T

The Crystal Structure of Cytidine Deaminase CDD1, an Orphan C to U editase from Yeast

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1r5ta_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	Cytidine deaminase	mono-domain cytidine deaminase	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1r5tb_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	Cytidine deaminase	mono-domain cytidine deaminase	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1r5tc_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	Cytidine deaminase	mono-domain cytidine deaminase	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d1r5td_	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	Cytidine deaminase	mono-domain cytidine deaminase	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	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	8026373	4000870	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cytidine deaminase-like	8038752	3001838	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Cytidine deaminase-like	8038752	3001838	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cytidine deaminase-like	8038752	3001838	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cytidine deaminase-like	8038752	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	e1r5tA1	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	e1r5tB1	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	e1r5tC1	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	e1r5tD1	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)
C	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)

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	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines deoxycytidine deaminase activity hydrolase activity catalytic activity deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cytidine deaminase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines deoxycytidine deaminase activity hydrolase activity catalytic activity deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cytidine deaminase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding	organonitrogen compound metabolic process pyrimidine-containing compound metabolic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process pyrimidine-containing compound salvage nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process organonitrogen compound metabolic process pyrimidine-containing compound metabolic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process pyrimidine-containing compound salvage nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process cellular process pyrimidine-containing compound biosynthetic process cellular metabolic compound salvage glycosyl compound metabolic process catabolic process pyrimidine-containing compound catabolic process carbohydrate derivative metabolic process pyrimidine nucleoside metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process organonitrogen compound catabolic process cytidine deamination carbohydrate derivative catabolic process pyrimidine nucleoside catabolic process cytidine metabolic process glycosyl compound catabolic process nucleoside metabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic 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 organic substance catabolic process ribonucleoside metabolic process deoxyribonucleoside metabolic process deoxycytidine metabolic process pyrimidine deoxyribonucleoside catabolic process deoxycytidine catabolic process deoxyribonucleoside catabolic process pyrimidine deoxyribonucleoside metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

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	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 National Science Foundation (DBI-1832184), 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 R01GM133198.