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P0ABF6

- CDD_ECOLI

UniProt

P0ABF6 - CDD_ECOLI

Protein

Cytidine deaminase

Gene

cdd

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 83 (01 Oct 2014)
      Sequence version 1 (25 Oct 2005)
      Previous versions | rss
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    Functioni

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

    Catalytic activityi

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

    Cofactori

    Binds 1 zinc ion.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi102 – 1021Zinc; catalytic
    Active sitei104 – 1041Proton donor
    Metal bindingi129 – 1291Zinc; catalytic
    Metal bindingi132 – 1321Zinc; catalytic

    GO - Molecular functioni

    1. cytidine deaminase activity Source: EcoCyc
    2. deoxycytidine deaminase activity Source: EcoCyc
    3. identical protein binding Source: IntAct
    4. pyrimidine nucleoside binding Source: EcoliWiki
    5. zinc ion binding Source: EcoCyc

    GO - Biological processi

    1. cytidine deamination Source: EcoCyc
    2. deoxycytidine catabolic process Source: EcoCyc
    3. nucleobase-containing small molecule interconversion Source: EcoliWiki

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:CYTIDEAM-MONOMER.
    ECOL316407:JW2131-MONOMER.
    MetaCyc:CYTIDEAM-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Cytidine deaminaseUniRule annotation (EC:3.5.4.5UniRule annotation)
    Alternative name(s):
    Cytidine aminohydrolaseUniRule annotation
    Short name:
    CDAUniRule annotation
    Gene namesi
    Name:cddUniRule annotation
    Ordered Locus Names:b2143, JW2131
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10137. cdd.

    Subcellular locationi

    GO - Cellular componenti

    1. cytosol Source: UniProtKB

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 294294Cytidine deaminasePRO_0000171649Add
    BLAST

    Proteomic databases

    PaxDbiP0ABF6.
    PRIDEiP0ABF6.

    2D gel databases

    SWISS-2DPAGEP0ABF6.

    Expressioni

    Gene expression databases

    GenevestigatoriP0ABF6.

    Interactioni

    Subunit structurei

    Homodimer.3 PublicationsUniRule annotation

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself2EBI-550703,EBI-550703

    Protein-protein interaction databases

    DIPiDIP-36169N.
    IntActiP0ABF6. 2 interactions.
    MINTiMINT-1283574.
    STRINGi511145.b2143.

    Structurei

    Secondary structure

    1
    294
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 53
    Helixi6 – 105
    Helixi14 – 207
    Turni21 – 255
    Beta strandi31 – 333
    Helixi35 – 4410
    Helixi49 – 6214
    Turni67 – 693
    Beta strandi74 – 796
    Beta strandi84 – 885
    Helixi97 – 993
    Helixi103 – 11311
    Beta strandi119 – 1268
    Helixi130 – 1367
    Helixi142 – 1443
    Beta strandi146 – 1483
    Helixi157 – 1604
    Helixi167 – 1704
    Helixi190 – 20011
    Turni205 – 2073
    Beta strandi211 – 2177
    Beta strandi222 – 2265
    Helixi239 – 24911
    Helixi254 – 2563
    Beta strandi257 – 2648
    Helixi273 – 28311
    Beta strandi288 – 2925

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1AF2X-ray2.30A1-294[»]
    1ALNX-ray2.30A1-294[»]
    1CTTX-ray2.20A1-294[»]
    1CTUX-ray2.30A1-294[»]
    ProteinModelPortaliP0ABF6.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0ABF6.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini56 – 13984CMP/dCMP deaminase zinc-bindingAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni89 – 913Substrate binding

    Domaini

    Each monomer is composed of a small N-terminal alpha-helical domain and two larger core domains that have nearly identical tertiary structures and are related by approximate two-fold symmetry, but lack homology.

    Sequence similaritiesi

    Belongs to the cytidine and deoxycytidylate deaminase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0295.
    HOGENOMiHOG000218617.
    KOiK01489.
    OMAiNRSHAPY.
    OrthoDBiEOG6XDH25.
    PhylomeDBiP0ABF6.

    Family and domain databases

    HAMAPiMF_01558. Cyt_deam.
    InterProiIPR016192. APOBEC/CMP_deaminase_Zn-bd.
    IPR002125. CMP_dCMP_Zn-bd.
    IPR013171. Cyd/dCyd_deaminase_Zn-bd.
    IPR006263. Cyt_deam_dimer.
    IPR016193. Cytidine_deaminase-like.
    IPR020797. Cytidine_deaminase_bacteria.
    [Graphical view]
    PfamiPF00383. dCMP_cyt_deam_1. 1 hit.
    PF08211. dCMP_cyt_deam_2. 1 hit.
    [Graphical view]
    PIRSFiPIRSF006334. Cdd_plus_pseudo. 1 hit.
    SUPFAMiSSF53927. SSF53927. 2 hits.
    TIGRFAMsiTIGR01355. cyt_deam_dimer. 1 hit.
    PROSITEiPS00903. CYT_DCMP_DEAMINASES. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P0ABF6-1 [UniParc]FASTAAdd to Basket

    « Hide

    MHPRFQTAFA QLADNLQSAL EPILADKYFP ALLTGEQVSS LKSATGLDED    50
    ALAFALLPLA AACARTPLSN FNVGAIARGV SGTWYFGANM EFIGATMQQT 100
    VHAEQSAISH AWLSGEKALA AITVNYTPCG HCRQFMNELN SGLDLRIHLP 150
    GREAHALRDY LPDAFGPKDL EIKTLLMDEQ DHGYALTGDA LSQAAIAAAN 200
    RSHMPYSKSP SGVALECKDG RIFSGSYAEN AAFNPTLPPL QGALILLNLK 250
    GYDYPDIQRA VLAEKADAPL IQWDATSATL KALGCHSIDR VLLA 294
    Length:294
    Mass (Da):31,540
    Last modified:October 25, 2005 - v1
    Checksum:iF0B5CD68AB145D7D
    GO

    Sequence cautioni

    The sequence CAA44849.1 differs from that shown. Reason: Frameshift at position 255.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti4 – 41R → I AA sequence (PubMed:8899705)Curated
    Sequence conflicti58 – 7720PLAAA…VGAIA → RWRRPVRVRHCRILMLAQLR(PubMed:2575702)CuratedAdd
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M60916 Genomic DNA. Translation: AAA23542.1.
    X63144 Genomic DNA. Translation: CAA44849.1. Frameshift.
    U00007 Genomic DNA. Translation: AAA60533.1.
    U00096 Genomic DNA. Translation: AAC75204.1.
    AP009048 Genomic DNA. Translation: BAE76620.1.
    X16419 Genomic DNA. Translation: CAA34441.1.
    Z47804 Genomic DNA. Translation: CAA87765.1.
    PIRiF64982.
    RefSeqiNP_416648.1. NC_000913.3.
    YP_490382.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75204; AAC75204; b2143.
    BAE76620; BAE76620; BAE76620.
    GeneIDi12934044.
    946663.
    KEGGiecj:Y75_p2105.
    eco:b2143.
    PATRICi32119629. VBIEscCol129921_2225.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M60916 Genomic DNA. Translation: AAA23542.1 .
    X63144 Genomic DNA. Translation: CAA44849.1 . Frameshift.
    U00007 Genomic DNA. Translation: AAA60533.1 .
    U00096 Genomic DNA. Translation: AAC75204.1 .
    AP009048 Genomic DNA. Translation: BAE76620.1 .
    X16419 Genomic DNA. Translation: CAA34441.1 .
    Z47804 Genomic DNA. Translation: CAA87765.1 .
    PIRi F64982.
    RefSeqi NP_416648.1. NC_000913.3.
    YP_490382.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1AF2 X-ray 2.30 A 1-294 [» ]
    1ALN X-ray 2.30 A 1-294 [» ]
    1CTT X-ray 2.20 A 1-294 [» ]
    1CTU X-ray 2.30 A 1-294 [» ]
    ProteinModelPortali P0ABF6.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-36169N.
    IntActi P0ABF6. 2 interactions.
    MINTi MINT-1283574.
    STRINGi 511145.b2143.

    2D gel databases

    SWISS-2DPAGE P0ABF6.

    Proteomic databases

    PaxDbi P0ABF6.
    PRIDEi P0ABF6.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC75204 ; AAC75204 ; b2143 .
    BAE76620 ; BAE76620 ; BAE76620 .
    GeneIDi 12934044.
    946663.
    KEGGi ecj:Y75_p2105.
    eco:b2143.
    PATRICi 32119629. VBIEscCol129921_2225.

    Organism-specific databases

    EchoBASEi EB0135.
    EcoGenei EG10137. cdd.

    Phylogenomic databases

    eggNOGi COG0295.
    HOGENOMi HOG000218617.
    KOi K01489.
    OMAi NRSHAPY.
    OrthoDBi EOG6XDH25.
    PhylomeDBi P0ABF6.

    Enzyme and pathway databases

    BioCyci EcoCyc:CYTIDEAM-MONOMER.
    ECOL316407:JW2131-MONOMER.
    MetaCyc:CYTIDEAM-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P0ABF6.
    PROi P0ABF6.

    Gene expression databases

    Genevestigatori P0ABF6.

    Family and domain databases

    HAMAPi MF_01558. Cyt_deam.
    InterProi IPR016192. APOBEC/CMP_deaminase_Zn-bd.
    IPR002125. CMP_dCMP_Zn-bd.
    IPR013171. Cyd/dCyd_deaminase_Zn-bd.
    IPR006263. Cyt_deam_dimer.
    IPR016193. Cytidine_deaminase-like.
    IPR020797. Cytidine_deaminase_bacteria.
    [Graphical view ]
    Pfami PF00383. dCMP_cyt_deam_1. 1 hit.
    PF08211. dCMP_cyt_deam_2. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF006334. Cdd_plus_pseudo. 1 hit.
    SUPFAMi SSF53927. SSF53927. 2 hits.
    TIGRFAMsi TIGR01355. cyt_deam_dimer. 1 hit.
    PROSITEi PS00903. CYT_DCMP_DEAMINASES. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Cloning and nucleotide sequence of the Escherichia coli cytidine deaminase (ccd) gene."
      Yang C., Carlow D., Wolfenden R., Short S.A.
      Biochemistry 31:4168-4174(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
      Strain: K12.
    2. "Complete sequence of Escherichia coli cytidine deaminase gene."
      Montgomery D.S., Drake C., Purvis I.J.
      Submitted (NOV-1991) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    3. "Automated multiplex sequencing of the E.coli genome."
      Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K., Church G.M.
      Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12 / BHB2600.
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    6. "CRP/cAMP- and CytR-regulated promoters in Escherichia coli K12: the cdd promoter."
      Valentin-Hansen P., Holst B., Josephsen J., Hammer K., Albrechtsen B.
      Mol. Microbiol. 3:1385-1390(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-77.
      Strain: K12.
    7. "Binding of pyrimidin-2-one ribonucleoside by cytidine deaminase as the transition-state analogue 3,4-dihydrouridine and the contribution of the 4-hydroxyl group to its binding affinity."
      Frick L., Yang C., Marquez V.E., Wolfenden R.
      Biochemistry 28:9423-9430(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-22, CHARACTERIZATION.
    8. "Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases."
      Henzel W.J., Billeci T.M., Stults J.T., Wong S.C., Grimley C., Watanabe C.
      Proc. Natl. Acad. Sci. U.S.A. 90:5011-5015(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-17.
    9. "FIS is a regulator of metabolism in Escherichia coli."
      Gonzalez-Gil G., Bringmann P., Kahmann R.
      Mol. Microbiol. 22:21-29(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-15.
      Strain: K12.
    10. "Amplification of a novel gene, sanA, abolishes a vancomycin-sensitive defect in Escherichia coli."
      Rida S., Caillet J., Alix J.-H.
      J. Bacteriol. 178:94-102(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 256-294.
      Strain: K12.
    11. "Cytidine deaminase. The 2.3 A crystal structure of an enzyme: transition-state analog complex."
      Betts L., Xiang S., Short S.A., Wolfenden R., Carter C.W. Jr.
      J. Mol. Biol. 235:635-656(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG AND ZINC IONS.
    12. "Cytidine deaminase complexed to 3-deazacytidine: a 'valence buffer' in zinc enzyme catalysis."
      Xiang S., Short S.A., Wolfenden R., Carter C.W. Jr.
      Biochemistry 35:1335-1341(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG AND ZINC IONS.
    13. "The structure of the cytidine deaminase-product complex provides evidence for efficient proton transfer and ground-state destabilization."
      Xiang S., Short S.A., Wolfenden R., Carter C.W. Jr.
      Biochemistry 36:4768-4774(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH URIDINE AND ZINC IONS.

    Entry informationi

    Entry nameiCDD_ECOLI
    AccessioniPrimary (citable) accession number: P0ABF6
    Secondary accession number(s): P13652, Q2MAT6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 25, 2005
    Last sequence update: October 25, 2005
    Last modified: October 1, 2014
    This is version 83 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, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    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