CDD_ECOLI
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 03-AUG-2022, entry version 129.
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; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC 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 + H(+) + H2O = NH4(+) + uridine;
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 + H(+) + H2O = 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_SSZK01000011.1.
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 PDBsum; 1AF2; -.
DR PDBsum; 1ALN; -.
DR PDBsum; 1CTT; -.
DR PDBsum; 1CTU; -.
DR AlphaFoldDB; P0ABF6; -.
DR SMR; P0ABF6; -.
DR BioGRID; 4263038; 10.
DR BioGRID; 851005; 2.
DR DIP; DIP-36169N; -.
DR IntAct; P0ABF6; 2.
DR STRING; 511145.b2143; -.
DR DrugBank; DB04385; 3-Deazacytidine.
DR DrugBank; DB03068; Zebularine.
DR SWISS-2DPAGE; P0ABF6; -.
DR jPOST; P0ABF6; -.
DR PaxDb; P0ABF6; -.
DR PRIDE; P0ABF6; -.
DR EnsemblBacteria; AAC75204; AAC75204; b2143.
DR EnsemblBacteria; BAE76620; BAE76620; BAE76620.
DR GeneID; 58388962; -.
DR GeneID; 946663; -.
DR KEGG; ecj:JW2131; -.
DR KEGG; eco:b2143; -.
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 PhylomeDB; P0ABF6; -.
DR BioCyc; EcoCyc:CYTIDEAM-MON; -.
DR BioCyc; MetaCyc:CYTIDEAM-MON; -.
DR BRENDA; 3.5.4.5; 2026.
DR EvolutionaryTrace; P0ABF6; -.
DR PRO; PR:P0ABF6; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0004126; F:cytidine deaminase activity; IDA:EcoCyc.
DR GO; GO:0047844; F:deoxycytidine deaminase activity; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0001884; F:pyrimidine nucleoside binding; IDA:EcoliWiki.
DR GO; GO:0008270; F:zinc ion binding; IDA:EcoCyc.
DR GO; GO:0009972; P:cytidine deamination; IMP:EcoCyc.
DR GO; GO:0006217; P:deoxycytidine catabolic process; IDA:EcoCyc.
DR GO; GO:0015949; P:nucleobase-containing small molecule interconversion; IDA:EcoliWiki.
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; IPR006263; Cyt_deam_dimer.
DR InterPro; IPR016193; Cytidine_deaminase-like.
DR InterPro; IPR020797; Cytidine_deaminase_bacteria.
DR Pfam; PF00383; dCMP_cyt_deam_1; 1.
DR Pfam; PF08211; dCMP_cyt_deam_2; 1.
DR SUPFAM; SSF53927; SSF53927; 2.
DR TIGRFAMs; TIGR01355; cyt_deam_dimer; 1.
DR PROSITE; PS00903; CYT_DCMP_DEAMINASES_1; 1.
DR PROSITE; PS51747; CYT_DCMP_DEAMINASES_2; 2.
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 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 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
