ID   CDD_ECOLI               Reviewed;         294 AA.
AC   P0ABF6; P13652; Q2MAT6;
DT   25-OCT-2005, integrated into UniProtKB/Swiss-Prot.
DT   25-OCT-2005, sequence version 1.
DT   02-SEP-2026, entry version 146.
DE   RecName: Full=Cytidine deaminase {ECO:0000255|HAMAP-Rule:MF_01558};
DE            EC=3.5.4.5 {ECO:0000255|HAMAP-Rule:MF_01558};
DE   AltName: Full=Cytidine aminohydrolase {ECO:0000255|HAMAP-Rule:MF_01558};
DE            Short=CDA {ECO:0000255|HAMAP-Rule:MF_01558};
GN   Name=cdd {ECO:0000255|HAMAP-Rule:MF_01558};
GN   OrderedLocusNames=b2143, JW2131;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
OC   Enterobacterales; Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PARTIAL PROTEIN SEQUENCE.
RC   STRAIN=K12;
RX   PubMed=1567863; DOI=10.1021/bi00132a003;
RA   Yang C., Carlow D., Wolfenden R., Short S.A.;
RT   "Cloning and nucleotide sequence of the Escherichia coli cytidine deaminase
RT   (ccd) gene.";
RL   Biochemistry 31:4168-4174(1992).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=K12;
RA   Montgomery D.S., Drake C., Purvis I.J.;
RT   "Complete sequence of Escherichia coli cytidine deaminase gene.";
RL   Submitted (NOV-1991) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=K12 / BHB2600;
RA   Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K.,
RA   Church G.M.;
RT   "Automated multiplex sequencing of the E.coli genome.";
RL   Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA   Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA   Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA   Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA   Shao Y.;
RT   "The complete genome sequence of Escherichia coli K-12.";
RL   Science 277:1453-1462(1997).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=16738553; DOI=10.1038/msb4100049;
RA   Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA   Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT   "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT   and W3110.";
RL   Mol. Syst. Biol. 2:E1-E5(2006).
RN   [6]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-77.
RC   STRAIN=K12;
RX   PubMed=2575702; DOI=10.1111/j.1365-2958.1989.tb00120.x;
RA   Valentin-Hansen P., Holst B., Josephsen J., Hammer K., Albrechtsen B.;
RT   "CRP/cAMP- and CytR-regulated promoters in Escherichia coli K12: the cdd
RT   promoter.";
RL   Mol. Microbiol. 3:1385-1390(1989).
RN   [7]
RP   PROTEIN SEQUENCE OF 1-22, AND CHARACTERIZATION.
RX   PubMed=2692708; DOI=10.1021/bi00450a027;
RA   Frick L., Yang C., Marquez V.E., Wolfenden R.;
RT   "Binding of pyrimidin-2-one ribonucleoside by cytidine deaminase as the
RT   transition-state analogue 3,4-dihydrouridine and the contribution of the 4-
RT   hydroxyl group to its binding affinity.";
RL   Biochemistry 28:9423-9430(1989).
RN   [8]
RP   PROTEIN SEQUENCE OF 1-17.
RX   PubMed=8506346; DOI=10.1073/pnas.90.11.5011;
RA   Henzel W.J., Billeci T.M., Stults J.T., Wong S.C., Grimley C., Watanabe C.;
RT   "Identifying proteins from two-dimensional gels by molecular mass searching
RT   of peptide fragments in protein sequence databases.";
RL   Proc. Natl. Acad. Sci. U.S.A. 90:5011-5015(1993).
RN   [9]
RP   PROTEIN SEQUENCE OF 1-15.
RC   STRAIN=K12;
RX   PubMed=8899705; DOI=10.1111/j.1365-2958.1996.tb02652.x;
RA   Gonzalez-Gil G., Bringmann P., Kahmann R.;
RT   "FIS is a regulator of metabolism in Escherichia coli.";
RL   Mol. Microbiol. 22:21-29(1996).
RN   [10]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 256-294.
RC   STRAIN=K12;
RX   PubMed=8550448; DOI=10.1128/jb.178.1.94-102.1996;
RA   Rida S., Caillet J., Alix J.-H.;
RT   "Amplification of a novel gene, sanA, abolishes a vancomycin-sensitive
RT   defect in Escherichia coli.";
RL   J. Bacteriol. 178:94-102(1996).
RN   [11]
RP   X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG AND
RP   ZINC IONS, COFACTOR, AND ACTIVE SITE.
RX   PubMed=8289286; DOI=10.1006/jmbi.1994.1018;
RA   Betts L., Xiang S., Short S.A., Wolfenden R., Carter C.W. Jr.;
RT   "Cytidine deaminase. The 2.3 A crystal structure of an enzyme: transition-
RT   state analog complex.";
RL   J. Mol. Biol. 235:635-656(1994).
RN   [12]
RP   X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG AND
RP   ZINC IONS, COFACTOR, AND ACTIVE SITE.
RX   PubMed=8634261; DOI=10.1021/bi9525583;
RA   Xiang S., Short S.A., Wolfenden R., Carter C.W. Jr.;
RT   "Cytidine deaminase complexed to 3-deazacytidine: a 'valence buffer' in
RT   zinc enzyme catalysis.";
RL   Biochemistry 35:1335-1341(1996).
RN   [13]
RP   X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH URIDINE AND ZINC
RP   IONS, COFACTOR, AND ACTIVE SITE.
RX   PubMed=9125497; DOI=10.1021/bi963091e;
RA   Xiang S., Short S.A., Wolfenden R., Carter C.W. Jr.;
RT   "The structure of the cytidine deaminase-product complex provides evidence
RT   for efficient proton transfer and ground-state destabilization.";
RL   Biochemistry 36:4768-4774(1997).
CC   -!- FUNCTION: This enzyme scavenges exogenous and endogenous cytidine and
CC       2'-deoxycytidine for UMP synthesis.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=cytidine + H2O + H(+) = uridine + NH4(+);
CC         Xref=Rhea:RHEA:16069, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC         ChEBI:CHEBI:16704, ChEBI:CHEBI:17562, ChEBI:CHEBI:28938; EC=3.5.4.5;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_01558};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=2'-deoxycytidine + H2O + H(+) = 2'-deoxyuridine + NH4(+);
CC         Xref=Rhea:RHEA:13433, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC         ChEBI:CHEBI:15698, ChEBI:CHEBI:16450, ChEBI:CHEBI:28938; EC=3.5.4.5;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_01558};
CC   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC         Evidence={ECO:0000269|PubMed:8289286, ECO:0000269|PubMed:8634261,
CC         ECO:0000269|PubMed:9125497};
CC       Note=Binds 1 zinc ion. {ECO:0000269|PubMed:8289286,
CC       ECO:0000269|PubMed:8634261, ECO:0000269|PubMed:9125497};
CC   -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01558,
CC       ECO:0000269|PubMed:8289286, ECO:0000269|PubMed:8634261,
CC       ECO:0000269|PubMed:9125497}.
CC   -!- INTERACTION:
CC       P0ABF6; P0ABF6: cdd; NbExp=2; IntAct=EBI-550703, EBI-550703;
CC   -!- DOMAIN: Each monomer is composed of a small N-terminal alpha-helical
CC       domain and two larger core domains that have nearly identical tertiary
CC       structures and are related by approximate two-fold symmetry, but lack
CC       homology.
CC   -!- SIMILARITY: Belongs to the cytidine and deoxycytidylate deaminase
CC       family. {ECO:0000255|HAMAP-Rule:MF_01558}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=CAA44849.1; Type=Frameshift; Evidence={ECO:0000305};
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DR   EMBL; M60916; AAA23542.1; -; Genomic_DNA.
DR   EMBL; X63144; CAA44849.1; ALT_FRAME; Genomic_DNA.
DR   EMBL; U00007; AAA60533.1; -; Genomic_DNA.
DR   EMBL; U00096; AAC75204.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAE76620.1; -; Genomic_DNA.
DR   EMBL; X16419; CAA34441.1; -; Genomic_DNA.
DR   EMBL; Z47804; CAA87765.1; -; Genomic_DNA.
DR   PIR; F64982; F64982.
DR   RefSeq; NP_416648.1; NC_000913.3.
DR   RefSeq; WP_000553555.1; NZ_CP009789.1.
DR   PDB; 1AF2; X-ray; 2.30 A; A=1-294.
DR   PDB; 1ALN; X-ray; 2.30 A; A=1-294.
DR   PDB; 1CTT; X-ray; 2.20 A; A=1-294.
DR   PDB; 1CTU; X-ray; 2.30 A; A=1-294.
DR   AlphaFoldDB; P0ABF6; -.
DR   MDposit; P0ABF6; -.
DR   MDRepo; P0ABF6; -.
DR   SMR; P0ABF6; -.
DR   BioGRID; 4263038; 10.
DR   BioGRID; 851005; 2.
DR   DIP; DIP-36169N; -.
DR   FunCoup; P0ABF6; 345.
DR   IntAct; P0ABF6; 2.
DR   STRING; 511145.b2143; -.
DR   DrugBank; DB04385; 3-Deazacytidine.
DR   DrugBank; DB03068; Zebularine.
DR   jPOST; P0ABF6; -.
DR   PaxDb; 511145-b2143; -.
DR   EnsemblBacteria; AAC75204; AAC75204; b2143.
DR   GeneID; 93775039; -.
DR   GeneID; 946663; -.
DR   KEGG; ecj:JW2131; -.
DR   KEGG; eco:b2143; -.
DR   KEGG; ecoc:C3026_12010; -.
DR   PATRIC; fig|1411691.4.peg.99; -.
DR   EchoBASE; EB0135; -.
DR   eggNOG; COG0295; Bacteria.
DR   HOGENOM; CLU_052424_0_0_6; -.
DR   InParanoid; P0ABF6; -.
DR   OMA; NYSPCGH; -.
DR   OrthoDB; 9795347at2; -.
DR   PhylomeDB; P0ABF6; -.
DR   BioCyc; EcoCyc:CYTIDEAM-MONOMER; -.
DR   BioCyc; MetaCyc:CYTIDEAM-MONOMER; -.
DR   BRENDA; 3.5.4.5; 2026.
DR   EvolutionaryTrace; P0ABF6; -.
DR   PRO; PR:P0ABF6; -.
DR   Proteomes; UP000000625; Chromosome.
DR   AbasyAtlas; P0ABF6; -.
DR   GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR   GO; GO:0004126; F:cytidine deaminase activity; IDA:EcoCyc.
DR   GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR   GO; GO:0042803; F:protein homodimerization activity; IDA:EcoCyc.
DR   GO; GO:0001884; F:pyrimidine nucleoside binding; IDA:EcoliWiki.
DR   GO; GO:0008270; F:zinc ion binding; IDA:EcoCyc.
DR   GO; GO:0006217; P:deoxycytidine catabolic process; IDA:EcoCyc.
DR   GO; GO:0015949; P:nucleobase-containing small molecule interconversion; IDA:EcoliWiki.
DR   GO; GO:0046109; P:uridine biosynthetic process; IBA:GO_Central.
DR   CDD; cd01283; cytidine_deaminase; 2.
DR   FunFam; 3.40.140.10:FF:000006; Cytidine deaminase; 1.
DR   FunFam; 3.40.140.10:FF:000007; Cytidine deaminase; 1.
DR   Gene3D; 3.40.140.10; Cytidine Deaminase, domain 2; 2.
DR   HAMAP; MF_01558; Cyt_deam; 1.
DR   InterPro; IPR016192; APOBEC/CMP_deaminase_Zn-bd.
DR   InterPro; IPR002125; CMP_dCMP_dom.
DR   InterPro; IPR013171; Cyd/dCyd_deaminase_Zn-bd.
DR   InterPro; IPR050202; Cyt/Deoxycyt_deaminase.
DR   InterPro; IPR006263; Cyt_deam_dimer.
DR   InterPro; IPR016193; Cytidine_deaminase-like.
DR   InterPro; IPR020797; Cytidine_deaminase_bacteria.
DR   NCBIfam; TIGR01355; cyt_deam_dimer; 1.
DR   NCBIfam; NF006537; PRK09027.1; 1.
DR   PANTHER; PTHR11644; CYTIDINE DEAMINASE; 1.
DR   PANTHER; PTHR11644:SF2; CYTIDINE DEAMINASE; 1.
DR   Pfam; PF00383; dCMP_cyt_deam_1; 1.
DR   Pfam; PF08211; dCMP_cyt_deam_2; 1.
DR   PIRSF; PIRSF006334; Cdd_plus_pseudo; 1.
DR   SUPFAM; SSF53927; Cytidine deaminase-like; 2.
DR   PROSITE; PS00903; CYT_DCMP_DEAMINASES_1; 1.
DR   PROSITE; PS51747; CYT_DCMP_DEAMINASES_2; 2.
DR   PDBsum; 1AF2; -.
DR   PDBsum; 1ALN; -.
DR   PDBsum; 1CTT; -.
DR   PDBsum; 1CTU; -.
PE   1: Evidence at protein level;
KW   3D-structure; Direct protein sequencing; Hydrolase; Metal-binding;
KW   Reference proteome; Zinc.
FT   CHAIN           1..294
FT                   /note="Cytidine deaminase"
FT                   /id="PRO_0000171649"
FT   DOMAIN          48..168
FT                   /note="CMP/dCMP-type deaminase 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01083"
FT   DOMAIN          186..294
FT                   /note="CMP/dCMP-type deaminase 2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01083"
FT   ACT_SITE        104
FT                   /note="Proton donor"
FT                   /evidence="ECO:0000305|PubMed:8289286,
FT                   ECO:0000305|PubMed:8634261, ECO:0000305|PubMed:9125497"
FT   BINDING         89..91
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000305|PubMed:8289286,
FT                   ECO:0000305|PubMed:8634261, ECO:0000305|PubMed:9125497"
FT   BINDING         102
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000305|PubMed:8289286,
FT                   ECO:0000305|PubMed:8634261, ECO:0000305|PubMed:9125497"
FT   BINDING         129
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000305|PubMed:8289286,
FT                   ECO:0000305|PubMed:8634261, ECO:0000305|PubMed:9125497"
FT   BINDING         132
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000305|PubMed:8289286,
FT                   ECO:0000305|PubMed:8634261, ECO:0000305|PubMed:9125497"
FT   CONFLICT        4
FT                   /note="R -> I (in Ref. 9; AA sequence)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        58..77
FT                   /note="PLAAACARTPLSNFNVGAIA -> RWRRPVRVRHCRILMLAQLR (in
FT                   Ref. 6)"
FT                   /evidence="ECO:0000305"
FT   HELIX           3..5
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   HELIX           6..10
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   HELIX           14..20
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   TURN            21..25
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   STRAND          31..33
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   HELIX           35..44
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   HELIX           49..62
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   TURN            67..69
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   STRAND          74..79
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   STRAND          84..88
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   HELIX           97..99
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   HELIX           103..113
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   STRAND          119..126
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   HELIX           127..129
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   HELIX           130..136
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   HELIX           142..144
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   STRAND          146..148
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   HELIX           157..160
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   HELIX           167..170
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   HELIX           184..186
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   HELIX           190..200
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   TURN            205..207
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   STRAND          211..217
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   STRAND          222..226
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   HELIX           239..249
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   HELIX           254..256
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   STRAND          257..264
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   HELIX           273..283
FT                   /evidence="ECO:0007829|PDB:1CTT"
FT   STRAND          288..292
FT                   /evidence="ECO:0007829|PDB:1CTT"
SQ   SEQUENCE   294 AA;  31540 MW;  F0B5CD68AB145D7D CRC64;
     MHPRFQTAFA QLADNLQSAL EPILADKYFP ALLTGEQVSS LKSATGLDED ALAFALLPLA
     AACARTPLSN FNVGAIARGV SGTWYFGANM EFIGATMQQT VHAEQSAISH AWLSGEKALA
     AITVNYTPCG HCRQFMNELN SGLDLRIHLP GREAHALRDY LPDAFGPKDL EIKTLLMDEQ
     DHGYALTGDA LSQAAIAAAN RSHMPYSKSP SGVALECKDG RIFSGSYAEN AAFNPTLPPL
     QGALILLNLK GYDYPDIQRA VLAEKADAPL IQWDATSATL KALGCHSIDR VLLA
//