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P19079

- CDD_BACSU

UniProt

P19079 - CDD_BACSU

Protein

Cytidine deaminase

Gene

cdd

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
  1. Functioni

    This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.

    Catalytic activityi

    Cytidine + H2O = uridine + NH3.
    2'deoxycytidine + H2O = 2'-deoxyuridine + NH3.

    Cofactori

    Binds 1 zinc ion per subunit.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi53 – 531Zinc; catalytic
    Active sitei55 – 551Proton donor
    Metal bindingi86 – 861Zinc; catalytic
    Metal bindingi89 – 891Zinc; catalytic

    GO - Molecular functioni

    1. cytidine deaminase activity Source: UniProtKB-EC
    2. zinc ion binding Source: InterPro

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciBSUB:BSU25300-MONOMER.
    MetaCyc:BSU25300-MONOMER.
    RETL1328306-WGS:GSTH-198-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Cytidine deaminase (EC:3.5.4.5)
    Short name:
    CDA
    Alternative name(s):
    Cytidine aminohydrolase
    Gene namesi
    Name:cdd
    Ordered Locus Names:BSU25300
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    ProteomesiUP000001570: Chromosome

    Organism-specific databases

    GenoListiBSU25300. [Micado]

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi53 – 531C → H: Loss of activity. Reduces activity 500-fold, without effect on zinc binding; when associated with Q-56. 1 Publication
    Mutagenesisi56 – 561R → A: No effect on zinc binding. Strongly reduces Vmax. 1 Publication
    Mutagenesisi56 – 561R → D: Loss of activity. Reduces zinc binding by 80%. 1 Publication
    Mutagenesisi56 – 561R → Q: No effect on zinc binding. Strongly reduces Vmax. Reduces activity 500-fold; when associated with H-53. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 136136Cytidine deaminasePRO_0000171678Add
    BLAST

    Proteomic databases

    PaxDbiP19079.

    Interactioni

    Subunit structurei

    Homotetramer.2 Publications

    Protein-protein interaction databases

    STRINGi224308.BSU25300.

    Structurei

    Secondary structure

    1
    136
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 1412
    Turni20 – 223
    Beta strandi26 – 327
    Beta strandi37 – 415
    Helixi48 – 503
    Helixi54 – 6411
    Beta strandi70 – 789
    Beta strandi80 – 823
    Helixi87 – 9610
    Beta strandi102 – 1065
    Beta strandi108 – 1103
    Beta strandi112 – 1165
    Helixi117 – 1204
    Helixi127 – 1293

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1JTKX-ray2.04A/B1-136[»]
    1UWZX-ray1.99A/B1-136[»]
    1UX0X-ray1.99A/B1-136[»]
    1UX1X-ray2.36A/B/C/D1-136[»]
    ProteinModelPortaliP19079.
    SMRiP19079. Positions 1-131.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP19079.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini3 – 104102CMP/dCMP deaminase zinc-bindingAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni42 – 443Substrate binding

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0295.
    HOGENOMiHOG000014707.
    KOiK01489.
    OMAiIADTPRP.
    OrthoDBiEOG6XDH25.
    PhylomeDBiP19079.

    Family and domain databases

    InterProiIPR016192. APOBEC/CMP_deaminase_Zn-bd.
    IPR002125. CMP_dCMP_Zn-bd.
    IPR006262. Cyt_deam_tetra.
    IPR016193. Cytidine_deaminase-like.
    [Graphical view]
    PfamiPF00383. dCMP_cyt_deam_1. 1 hit.
    [Graphical view]
    SUPFAMiSSF53927. SSF53927. 1 hit.
    TIGRFAMsiTIGR01354. cyt_deam_tetra. 1 hit.
    PROSITEiPS00903. CYT_DCMP_DEAMINASES. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P19079-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNRQELITEA LKARDMAYAP YSKFQVGAAL LTKDGKVYRG CNIENAAYSM    50
    CNCAERTALF KAVSEGDTEF QMLAVAADTP GPVSPCGACR QVISELCTKD 100
    VIVVLTNLQG QIKEMTVEEL LPGAFSSEDL HDERKL 136
    Length:136
    Mass (Da):14,854
    Last modified:November 1, 1990 - v1
    Checksum:i83755B1CDB2A534A
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U18532 Genomic DNA. Translation: AAB59993.1.
    X17430 Genomic DNA. Translation: CAB57856.1.
    D84432 Genomic DNA. Translation: BAA12481.1.
    K02174 Genomic DNA. Translation: AAB05347.1.
    AL009126 Genomic DNA. Translation: CAB14459.1.
    U29177 Genomic DNA. Translation: AAA70045.1.
    PIRiJE0022.
    RefSeqiNP_390408.1. NC_000964.3.

    Genome annotation databases

    EnsemblBacteriaiCAB14459; CAB14459; BSU25300.
    GeneIDi937885.
    KEGGibsu:BSU25300.
    PATRICi18976898. VBIBacSub10457_2638.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U18532 Genomic DNA. Translation: AAB59993.1 .
    X17430 Genomic DNA. Translation: CAB57856.1 .
    D84432 Genomic DNA. Translation: BAA12481.1 .
    K02174 Genomic DNA. Translation: AAB05347.1 .
    AL009126 Genomic DNA. Translation: CAB14459.1 .
    U29177 Genomic DNA. Translation: AAA70045.1 .
    PIRi JE0022.
    RefSeqi NP_390408.1. NC_000964.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1JTK X-ray 2.04 A/B 1-136 [» ]
    1UWZ X-ray 1.99 A/B 1-136 [» ]
    1UX0 X-ray 1.99 A/B 1-136 [» ]
    1UX1 X-ray 2.36 A/B/C/D 1-136 [» ]
    ProteinModelPortali P19079.
    SMRi P19079. Positions 1-131.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 224308.BSU25300.

    Proteomic databases

    PaxDbi P19079.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAB14459 ; CAB14459 ; BSU25300 .
    GeneIDi 937885.
    KEGGi bsu:BSU25300.
    PATRICi 18976898. VBIBacSub10457_2638.

    Organism-specific databases

    GenoListi BSU25300. [Micado ]

    Phylogenomic databases

    eggNOGi COG0295.
    HOGENOMi HOG000014707.
    KOi K01489.
    OMAi IADTPRP.
    OrthoDBi EOG6XDH25.
    PhylomeDBi P19079.

    Enzyme and pathway databases

    BioCyci BSUB:BSU25300-MONOMER.
    MetaCyc:BSU25300-MONOMER.
    RETL1328306-WGS:GSTH-198-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P19079.

    Family and domain databases

    InterProi IPR016192. APOBEC/CMP_deaminase_Zn-bd.
    IPR002125. CMP_dCMP_Zn-bd.
    IPR006262. Cyt_deam_tetra.
    IPR016193. Cytidine_deaminase-like.
    [Graphical view ]
    Pfami PF00383. dCMP_cyt_deam_1. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53927. SSF53927. 1 hit.
    TIGRFAMsi TIGR01354. cyt_deam_tetra. 1 hit.
    PROSITEi PS00903. CYT_DCMP_DEAMINASES. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Chromosomal location, cloning and nucleotide sequence of the Bacillus subtilis cdd gene encoding cytidine/deoxycytidine deaminase."
      Song B.-H., Neuhard J.
      Mol. Gen. Genet. 216:462-468(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168.
    2. "Systematic sequencing of the 283 kb 210 degrees-232 degrees region of the Bacillus subtilis genome containing the skin element and many sporulation genes."
      Mizuno M., Masuda S., Takemaru K., Hosono S., Sato T., Takeuchi M., Kobayashi Y.
      Microbiology 142:3103-3111(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168 / JH642.
    3. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
      Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
      , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
      Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 168.
    4. "Nucleotide sequence upstream of the cdd locus in Bacillus subtilis."
      Kim K., Hwang S., Suh J., Song B.-H., Hong S., Kim J.
      Submitted (JUL-1995) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-10.
      Strain: ED40.
    5. "Crystal structure of the tetrameric cytidine deaminase from Bacillus subtilis at 2.0 A resolution."
      Johansson E., Mejlhede N., Neuhard J., Larsen S.
      Biochemistry 41:2563-2570(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG AND ZINC IONS, SUBUNIT.
    6. "Structural, kinetic, and mutational studies of the zinc ion environment in tetrameric cytidine deaminase."
      Johansson E., Neuhard J., Willemoes M., Larsen S.
      Biochemistry 43:6020-6029(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.99 ANGSTROMS) OF MUTANTS IN COMPLEX WITH SUBSTRATE ANALOG AND ZINC IONS, SUBUNIT, MUTAGENESIS OF CYS-53 AND ARG-56.

    Entry informationi

    Entry nameiCDD_BACSU
    AccessioniPrimary (citable) accession number: P19079
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1990
    Last sequence update: November 1, 1990
    Last modified: October 1, 2014
    This is version 121 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3