ID   CDD_BACSU               Reviewed;         136 AA.
AC   P19079;
DT   01-NOV-1990, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1990, sequence version 1.
DT   27-MAR-2024, entry version 162.
DE   RecName: Full=Cytidine deaminase;
DE            Short=CDA;
DE            EC=3.5.4.5;
DE   AltName: Full=Cytidine aminohydrolase;
GN   Name=cdd; OrderedLocusNames=BSU25300;
OS   Bacillus subtilis (strain 168).
OC   Bacteria; Bacillota; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX   NCBI_TaxID=224308;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=168;
RX   PubMed=2526291; DOI=10.1007/bf00334391;
RA   Song B.-H., Neuhard J.;
RT   "Chromosomal location, cloning and nucleotide sequence of the Bacillus
RT   subtilis cdd gene encoding cytidine/deoxycytidine deaminase.";
RL   Mol. Gen. Genet. 216:462-468(1989).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=168 / JH642;
RX   PubMed=8969508; DOI=10.1099/13500872-142-11-3103;
RA   Mizuno M., Masuda S., Takemaru K., Hosono S., Sato T., Takeuchi M.,
RA   Kobayashi Y.;
RT   "Systematic sequencing of the 283 kb 210 degrees-232 degrees region of the
RT   Bacillus subtilis genome containing the skin element and many sporulation
RT   genes.";
RL   Microbiology 142:3103-3111(1996).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=168;
RX   PubMed=9384377; DOI=10.1038/36786;
RA   Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA   Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA   Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA   Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA   Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA   Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA   Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA   Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA   Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA   Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA   Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA   Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA   Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA   Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA   Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA   Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA   Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA   Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA   Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA   Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA   Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA   Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA   Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA   Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA   Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA   Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA   Yoshikawa H., Danchin A.;
RT   "The complete genome sequence of the Gram-positive bacterium Bacillus
RT   subtilis.";
RL   Nature 390:249-256(1997).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-10.
RC   STRAIN=ED40;
RA   Kim K., Hwang S., Suh J., Song B.-H., Hong S., Kim J.;
RT   "Nucleotide sequence upstream of the cdd locus in Bacillus subtilis.";
RL   Submitted (JUL-1995) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG AND
RP   ZINC IONS, AND SUBUNIT.
RX   PubMed=11851403; DOI=10.1021/bi011849a;
RA   Johansson E., Mejlhede N., Neuhard J., Larsen S.;
RT   "Crystal structure of the tetrameric cytidine deaminase from Bacillus
RT   subtilis at 2.0 A resolution.";
RL   Biochemistry 41:2563-2570(2002).
RN   [6]
RP   X-RAY CRYSTALLOGRAPHY (1.99 ANGSTROMS) OF MUTANTS IN COMPLEX WITH SUBSTRATE
RP   ANALOG AND ZINC IONS, SUBUNIT, AND MUTAGENESIS OF CYS-53 AND ARG-56.
RX   PubMed=15147186; DOI=10.1021/bi035893x;
RA   Johansson E., Neuhard J., Willemoes M., Larsen S.;
RT   "Structural, kinetic, and mutational studies of the zinc ion environment in
RT   tetrameric cytidine deaminase.";
RL   Biochemistry 43:6020-6029(2004).
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   -!- 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   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC       Note=Binds 1 zinc ion per subunit.;
CC   -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:11851403,
CC       ECO:0000269|PubMed:15147186}.
CC   -!- SIMILARITY: Belongs to the cytidine and deoxycytidylate deaminase
CC       family. {ECO:0000305}.
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DR   EMBL; U18532; AAB59993.1; -; Genomic_DNA.
DR   EMBL; X17430; CAB57856.1; -; Genomic_DNA.
DR   EMBL; D84432; BAA12481.1; -; Genomic_DNA.
DR   EMBL; K02174; AAB05347.1; -; Genomic_DNA.
DR   EMBL; AL009126; CAB14459.1; -; Genomic_DNA.
DR   EMBL; U29177; AAA70045.1; -; Genomic_DNA.
DR   PIR; JE0022; JE0022.
DR   RefSeq; NP_390408.1; NC_000964.3.
DR   RefSeq; WP_003230049.1; NZ_JNCM01000036.1.
DR   PDB; 1JTK; X-ray; 2.04 A; A/B=1-136.
DR   PDB; 1UWZ; X-ray; 1.99 A; A/B=1-136.
DR   PDB; 1UX0; X-ray; 1.99 A; A/B=1-136.
DR   PDB; 1UX1; X-ray; 2.36 A; A/B/C/D=1-136.
DR   PDBsum; 1JTK; -.
DR   PDBsum; 1UWZ; -.
DR   PDBsum; 1UX0; -.
DR   PDBsum; 1UX1; -.
DR   AlphaFoldDB; P19079; -.
DR   SMR; P19079; -.
DR   STRING; 224308.BSU25300; -.
DR   DrugBank; DB03562; Tetrahydrodeoxyuridine.
DR   PaxDb; 224308-BSU25300; -.
DR   EnsemblBacteria; CAB14459; CAB14459; BSU_25300.
DR   GeneID; 937885; -.
DR   KEGG; bsu:BSU25300; -.
DR   PATRIC; fig|224308.179.peg.2750; -.
DR   eggNOG; COG0295; Bacteria.
DR   InParanoid; P19079; -.
DR   OrthoDB; 9795347at2; -.
DR   PhylomeDB; P19079; -.
DR   BioCyc; BSUB:BSU25300-MONOMER; -.
DR   BioCyc; MetaCyc:BSU25300-MONOMER; -.
DR   BRENDA; 3.5.4.5; 658.
DR   EvolutionaryTrace; P19079; -.
DR   Proteomes; UP000001570; Chromosome.
DR   GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR   GO; GO:0004126; F:cytidine deaminase activity; IBA:GO_Central.
DR   GO; GO:0047844; F:deoxycytidine deaminase activity; IEA:RHEA.
DR   GO; GO:0042802; F:identical protein binding; IEA:UniProt.
DR   GO; GO:0008270; F:zinc ion binding; IBA:GO_Central.
DR   GO; GO:0009972; P:cytidine deamination; IBA:GO_Central.
DR   CDD; cd01283; cytidine_deaminase; 1.
DR   Gene3D; 3.40.140.10; Cytidine Deaminase, domain 2; 1.
DR   InterPro; IPR016192; APOBEC/CMP_deaminase_Zn-bd.
DR   InterPro; IPR002125; CMP_dCMP_dom.
DR   InterPro; IPR006262; Cyt_deam_tetra.
DR   InterPro; IPR016193; Cytidine_deaminase-like.
DR   NCBIfam; TIGR01354; cyt_deam_tetra; 1.
DR   PANTHER; PTHR11644; CYTIDINE DEAMINASE; 1.
DR   PANTHER; PTHR11644:SF2; CYTIDINE DEAMINASE; 1.
DR   Pfam; PF00383; dCMP_cyt_deam_1; 1.
DR   SUPFAM; SSF53927; Cytidine deaminase-like; 1.
DR   PROSITE; PS00903; CYT_DCMP_DEAMINASES_1; 1.
DR   PROSITE; PS51747; CYT_DCMP_DEAMINASES_2; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Hydrolase; Metal-binding; Reference proteome; Zinc.
FT   CHAIN           1..136
FT                   /note="Cytidine deaminase"
FT                   /id="PRO_0000171678"
FT   DOMAIN          1..128
FT                   /note="CMP/dCMP-type deaminase"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01083"
FT   ACT_SITE        55
FT                   /note="Proton donor"
FT   BINDING         42..44
FT                   /ligand="substrate"
FT   BINDING         53
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_note="catalytic"
FT   BINDING         86
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_note="catalytic"
FT   BINDING         89
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_note="catalytic"
FT   MUTAGEN         53
FT                   /note="C->H: Loss of activity. Reduces activity 500-fold,
FT                   without effect on zinc binding; when associated with Q-56."
FT                   /evidence="ECO:0000269|PubMed:15147186"
FT   MUTAGEN         56
FT                   /note="R->A: No effect on zinc binding. Strongly reduces
FT                   Vmax."
FT                   /evidence="ECO:0000269|PubMed:15147186"
FT   MUTAGEN         56
FT                   /note="R->D: Loss of activity. Reduces zinc binding by
FT                   80%."
FT                   /evidence="ECO:0000269|PubMed:15147186"
FT   MUTAGEN         56
FT                   /note="R->Q: No effect on zinc binding. Strongly reduces
FT                   Vmax. Reduces activity 500-fold; when associated with
FT                   H-53."
FT                   /evidence="ECO:0000269|PubMed:15147186"
FT   HELIX           3..14
FT                   /evidence="ECO:0007829|PDB:1UWZ"
FT   TURN            20..22
FT                   /evidence="ECO:0007829|PDB:1UWZ"
FT   STRAND          26..32
FT                   /evidence="ECO:0007829|PDB:1UWZ"
FT   STRAND          37..41
FT                   /evidence="ECO:0007829|PDB:1UWZ"
FT   HELIX           48..50
FT                   /evidence="ECO:0007829|PDB:1UWZ"
FT   HELIX           54..64
FT                   /evidence="ECO:0007829|PDB:1UWZ"
FT   STRAND          70..78
FT                   /evidence="ECO:0007829|PDB:1UWZ"
FT   STRAND          80..82
FT                   /evidence="ECO:0007829|PDB:1UWZ"
FT   HELIX           87..96
FT                   /evidence="ECO:0007829|PDB:1UWZ"
FT   STRAND          102..106
FT                   /evidence="ECO:0007829|PDB:1UWZ"
FT   STRAND          108..110
FT                   /evidence="ECO:0007829|PDB:1UWZ"
FT   STRAND          112..116
FT                   /evidence="ECO:0007829|PDB:1UWZ"
FT   HELIX           117..120
FT                   /evidence="ECO:0007829|PDB:1UWZ"
FT   HELIX           127..129
FT                   /evidence="ECO:0007829|PDB:1UWZ"
SQ   SEQUENCE   136 AA;  14854 MW;  83755B1CDB2A534A CRC64;
     MNRQELITEA LKARDMAYAP YSKFQVGAAL LTKDGKVYRG CNIENAAYSM CNCAERTALF
     KAVSEGDTEF QMLAVAADTP GPVSPCGACR QVISELCTKD VIVVLTNLQG QIKEMTVEEL
     LPGAFSSEDL HDERKL
//