4EG2

2.2 Angstrom Crystal Structure of Cytidine deaminase from Vibrio cholerae in Complex with Zinc and Uridine

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
D	d4eg2d1	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	automated matches	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
D	d4eg2d3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
A	d4eg2a1	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	automated matches	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
A	d4eg2a3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
B	d4eg2b1	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	automated matches	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
B	d4eg2b3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
C	d4eg2c1	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	automated matches	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
C	d4eg2c3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
E	d4eg2e1	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	automated matches	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
E	d4eg2e3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
F	d4eg2f1	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	automated matches	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
F	d4eg2f3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
G	d4eg2g1	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	automated matches	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
G	d4eg2g3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
H	d4eg2h1	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	automated matches	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
H	d4eg2h3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	dCMP_cyt_deam_1	e4eg2D3	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_2	e4eg2D4	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_2	ECOD (1.6)
A	dCMP_cyt_deam_1	e4eg2A3	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)
A	dCMP_cyt_deam_2	e4eg2A4	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_2	ECOD (1.6)
B	dCMP_cyt_deam_1	e4eg2B3	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_2	e4eg2B4	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_2	ECOD (1.6)
C	dCMP_cyt_deam_1	e4eg2C3	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_2	e4eg2C4	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_2	ECOD (1.6)
E	dCMP_cyt_deam_1	e4eg2E3	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)
E	dCMP_cyt_deam_2	e4eg2E4	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_2	ECOD (1.6)
F	dCMP_cyt_deam_1	e4eg2F3	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)
F	dCMP_cyt_deam_2	e4eg2F4	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_2	ECOD (1.6)
G	dCMP_cyt_deam_1	e4eg2G3	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)
G	dCMP_cyt_deam_2	e4eg2G4	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_2	ECOD (1.6)
H	dCMP_cyt_deam_1	e4eg2H3	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)
H	dCMP_cyt_deam_2	e4eg2H4	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_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
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)
E	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
F	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
G	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
H	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, E A, B, C, D, E, F, G, H	PF08211	Cytidine and deoxycytidylate deaminase zinc-binding region (dCMP_cyt_deam_2)	Cytidine and deoxycytidylate deaminase zinc-binding region	-	Family
A, B, C, D, E A, B, C, D, E, F, G, H	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, E A, B, C, D, E, F, G, H	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 cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding cytidine deaminase activity 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 cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding cytidine deaminase activity identical protein binding protein binding	glycosyl compound metabolic process catabolic process pyrimidine-containing compound catabolic process carbohydrate derivative metabolic process pyrimidine nucleoside metabolic process nucleobase-containing compound metabolic process organic substance metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process organonitrogen compound catabolic process cytidine deamination carbohydrate derivative catabolic process organonitrogen compound metabolic process pyrimidine-containing compound metabolic process glycosyl compound metabolic process catabolic process pyrimidine-containing compound catabolic process carbohydrate derivative metabolic process pyrimidine nucleoside metabolic process nucleobase-containing compound metabolic process organic substance metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process organonitrogen compound catabolic process cytidine deamination carbohydrate derivative catabolic process organonitrogen compound metabolic process pyrimidine-containing compound metabolic process pyrimidine nucleoside catabolic process cytidine metabolic process primary metabolic process glycosyl compound catabolic process nucleoside metabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process cytidine catabolic process organic cyclic compound metabolic process pyrimidine ribonucleoside metabolic process nucleobase-containing small molecule catabolic process nucleoside catabolic process metabolic process pyrimidine ribonucleoside catabolic process small molecule catabolic process ribonucleoside catabolic process organic substance catabolic process ribonucleoside metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006263	Cytidine deaminase, homodimeric	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR020797	Cytidine deaminase, bacteria	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR002125	Cytidine and deoxycytidylate deaminase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR016192	APOBEC/CMP deaminase, zinc-binding	Binding Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013171	Cytidine/deoxycytidylate deaminase, zinc-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR016193	Cytidine deaminase-like	Homologous Superfamily

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.