CDD_BACSU
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 03-AUG-2022, entry version 155.
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; Firmicutes; 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; P19079; -.
DR PRIDE; P19079; -.
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 OMA; CGACRQS; -.
DR PhylomeDB; P19079; -.
DR BioCyc; BSUB:BSU25300-MON; -.
DR BioCyc; MetaCyc:BSU25300-MON; -.
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:0008270; F:zinc ion binding; IBA:GO_Central.
DR GO; GO:0009972; P:cytidine deamination; IBA:GO_Central.
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 Pfam; PF00383; dCMP_cyt_deam_1; 1.
DR SUPFAM; SSF53927; SSF53927; 1.
DR TIGRFAMs; TIGR01354; cyt_deam_tetra; 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 H-
FT 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
