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Protein

Cytosine deaminase

Gene

codA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the hydrolytic deamination of cytosine to uracil. Is involved in the pyrimidine salvage pathway, which allows the cell to utilize cytosine for pyrimidine nucleotide synthesis. Is also able to catalyze deamination of isoguanine, a mutagenic oxidation product of adenine in DNA, and of isocytosine. To a lesser extent, also catalyzes the conversion of 5-fluorocytosine (5FC) to 5-fluorouracil (5FU); this activity allows the formation of a cytotoxic chemotherapeutic agent from a non-cytotoxic precursor.4 Publications

Catalytic activityi

Cytosine + H2O = uracil + NH3.4 Publications
Isoguanine + H2O = xanthine + NH3.1 Publication

Cofactori

Fe2+2 Publications, Mn2+1 Publication, Zn2+2 PublicationsNote: The purified enzyme contains a mixture of Fe2+ and Zn2+ bound in the active site, and a single equivalent of metal is required for full catalytic activity. After removal of the metal, the reconstitution of the enzyme with Fe2+ gives the highest activity, followed by Mn2+, and, to a much lesser extent, Co2+ and Zn2+.2 Publications

Enzyme regulationi

Fe2+-CDase is rapidly inactivated by H2O2, whereas Mn2+-CDase, Co2+-CDase, and Zn2+-CDase are not inactivated by H2O2. CDase is also inhibited by excess divalent cations (PubMed:8226944). Phosphonocytosine, a mimic of the tetrahedral reaction intermediate, inhibits the deamination of cytosine with a Ki of 52 nM (PubMed:21545144).2 Publications

Kineticsi

kcat is 185 sec(-1) for the deamination of cytosine using Fe2+ as cofactor, kcat is 92 sec(-1) using Mn2+ as cofactor, kcat is 52 sec(-1) using Co2+ as cofactor, and kcat is 32 sec(-1) using Zn2+ as cofactor (PubMed:8226944). kcat is 165 sec(-1) for the deamination of cytosine and 75.6 sec(-1) for the deamination of 5-fluorocytosine (PubMed:15381761). kcat is 132 sec(-1) for the deamination of cytosine, 5.1 sec(-1) for the deamination of isocytosine, 5.6 sec(-1) for the deamination of creatinine and 2.3 sec(-1) for the hydrolysis of 3-oxauracil (PubMed:21545144). kcat is 45 sec(-1) for the deamination of cytosine and 49 sec(-1) for the deamination of isoguanine at pH 7.7 (PubMed:21604715).4 Publications

Manual assertion based on experiment ini

  1. KM=0.22 mM for cytosine1 Publication
  2. KM=0.2 mM for cytosine1 Publication
  3. KM=3.3 mM for 5-fluorocytosine1 Publication
  4. KM=0.97 mM for cytosine1 Publication
  5. KM=0.46 mM for isocytosine1 Publication
  6. KM=25 mM for creatinine1 Publication
  7. KM=4.1 mM for 3-oxauracil1 Publication
  8. KM=72 µM for isoguanine1 Publication
  9. KM=302 µM for cytosine1 Publication

    pH dependencei

    Activity is lost under pH 5 but not affected up to pH 10.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi62Iron or zinc; catalytic6 Publications1
    Metal bindingi64Iron or zinc; catalytic6 Publications1
    Binding sitei157Substrate4 Publications1
    Metal bindingi215Iron or zinc; catalytic6 Publications1
    Active sitei218Proton donor3 Publications1
    Sitei247Activates the nucleophilic water2 Publications1
    Metal bindingi314Iron or zinc; catalytic6 Publications1
    Binding sitei320Substrate3 Publications1

    GO - Molecular functioni

    • cytosine deaminase activity Source: EcoCyc
    • ferrous iron binding Source: EcoCyc
    • identical protein binding Source: EcoCyc
    • isoguanine deaminase activity Source: EcoCyc
    • zinc ion binding Source: EcoCyc

    GO - Biological processi

    • cytosine catabolic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Cytosine metabolism

    Keywords - Ligandi

    Iron, Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:CYTDEAM-MONOMER.
    ECOL316407:JW0328-MONOMER.
    MetaCyc:CYTDEAM-MONOMER.
    BRENDAi3.5.4.1. 2026.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Cytosine deaminase2 Publications (EC:3.5.4.14 Publications)
    Short name:
    CD1 Publication
    Short name:
    CDA1 Publication
    Short name:
    CDase1 Publication
    Alternative name(s):
    Cytosine aminohydrolase
    Isoguanine deaminase1 Publication (EC:3.5.4.-1 Publication)
    Gene namesi
    Name:codA
    Ordered Locus Names:b0337, JW0328
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11326. codA.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: UniProtKB
    Complete GO annotation...

    Pathology & Biotechi

    Biotechnological usei

    Cytosine deaminase is being explored for use as a suicide gene for cancer gene therapy. The cytosine deaminase/5-fluorouracil combined therapy has been used successfully for a variety of animal tumor models and is currently under investigation for the treatment of human cancers.1 Publication1 Publication1 Publication

    Disruption phenotypei

    Cells lacking this gene have less than 1% of the isoguanine deaminase activity of the wild-type strain.1 Publication

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi157Q → A or N: Less than 0.01% of wild-type enzymatic activity. 1 Publication1
    Mutagenesisi218E → A or Q: Less than 0.01% of wild-type enzymatic activity. 1 Publication1
    Mutagenesisi247H → A or N: Less than 0.01% of wild-type enzymatic activity. 1 Publication1
    Mutagenesisi247H → Q: 200-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi314D → A: 17-fold decrease in catalytic efficiency with cytosine as substrate and 2-fold increase in that with 5FC as substrate. Shows increased sensitivity to 5FC. 1 Publication1
    Mutagenesisi314D → A: Less than 0.01% of wild-type enzymatic activity. 1 Publication1
    Mutagenesisi314D → G or S: Still active towards cytosine. Shows increased sensitivity to 5FC. 1 Publication1
    Mutagenesisi314D → K, R or H: Loss of enzymatic activity. 1 Publication1
    Mutagenesisi314D → N: 35000-fold decrease in catalytic efficiency. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved1 Publication
    ChainiPRO_00000900022 – 427Cytosine deaminaseAdd BLAST426

    Proteomic databases

    PaxDbiP25524.
    PRIDEiP25524.

    Interactioni

    Subunit structurei

    Homohexamer.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself3EBI-559181,EBI-559181

    GO - Molecular functioni

    • identical protein binding Source: EcoCyc

    Protein-protein interaction databases

    BioGridi4259813. 4 interactors.
    DIPiDIP-9306N.
    IntActiP25524. 6 interactors.
    MINTiMINT-1307853.
    STRINGi511145.b0337.

    Structurei

    Secondary structure

    1427
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi8 – 13Combined sources6
    Beta strandi19 – 26Combined sources8
    Beta strandi29 – 38Combined sources10
    Beta strandi46 – 48Combined sources3
    Beta strandi53 – 56Combined sources4
    Beta strandi58 – 63Combined sources6
    Turni65 – 69Combined sources5
    Beta strandi73 – 75Combined sources3
    Helixi82 – 93Combined sources12
    Helixi98 – 114Combined sources17
    Beta strandi117 – 125Combined sources9
    Helixi132 – 144Combined sources13
    Turni145 – 147Combined sources3
    Beta strandi149 – 155Combined sources7
    Beta strandi160 – 163Combined sources4
    Helixi166 – 175Combined sources10
    Beta strandi179 – 181Combined sources3
    Helixi185 – 187Combined sources3
    Beta strandi188 – 190Combined sources3
    Helixi191 – 208Combined sources18
    Beta strandi211 – 216Combined sources6
    Helixi226 – 237Combined sources12
    Helixi240 – 242Combined sources3
    Beta strandi243 – 247Combined sources5
    Helixi249 – 253Combined sources5
    Helixi256 – 269Combined sources14
    Beta strandi272 – 275Combined sources4
    Helixi277 – 283Combined sources7
    Turni284 – 287Combined sources4
    Helixi299 – 304Combined sources6
    Beta strandi309 – 311Combined sources3
    Beta strandi316 – 318Combined sources3
    Helixi328 – 338Combined sources11
    Helixi344 – 348Combined sources5
    Helixi349 – 354Combined sources6
    Helixi356 – 361Combined sources6
    Beta strandi368 – 370Combined sources3
    Beta strandi373 – 375Combined sources3
    Beta strandi377 – 384Combined sources8
    Helixi385 – 391Combined sources7
    Beta strandi396 – 400Combined sources5
    Beta strandi403 – 407Combined sources5
    Beta strandi413 – 423Combined sources11

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1K6WX-ray1.75A2-427[»]
    1K70X-ray1.80A2-427[»]
    1R9XX-ray1.58A2-427[»]
    1R9YX-ray1.57A2-427[»]
    1R9ZX-ray1.32A2-427[»]
    1RA0X-ray1.12A2-427[»]
    1RA5X-ray1.40A2-427[»]
    1RAKX-ray1.32A2-427[»]
    3G77X-ray1.80A5-427[»]
    3O7UX-ray1.71A1-427[»]
    3R0DX-ray1.50A1-427[»]
    3RN6X-ray2.26A1-427[»]
    ProteinModelPortaliP25524.
    SMRiP25524.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP25524.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the cytosine deaminase family.Curated

    Phylogenomic databases

    eggNOGiENOG4105DZC. Bacteria.
    COG0402. LUCA.
    HOGENOMiHOG000184778.
    InParanoidiP25524.
    KOiK01485.
    OMAiAFPQDGY.
    PhylomeDBiP25524.

    Family and domain databases

    Gene3Di2.30.40.10. 1 hit.
    InterProiIPR013108. Amidohydro_3.
    IPR011059. Metal-dep_hydrolase_composite.
    IPR032466. Metal_Hydrolase.
    [Graphical view]
    PfamiPF07969. Amidohydro_3. 1 hit.
    [Graphical view]
    SUPFAMiSSF51338. SSF51338. 1 hit.
    SSF51556. SSF51556. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P25524-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSNNALQTII NARLPGEEGL WQIHLQDGKI SAIDAQSGVM PITENSLDAE
    60 70 80 90 100
    QGLVIPPFVE PHIHLDTTQT AGQPNWNQSG TLFEGIERWA ERKALLTHDD
    110 120 130 140 150
    VKQRAWQTLK WQIANGIQHV RTHVDVSDAT LTALKAMLEV KQEVAPWIDL
    160 170 180 190 200
    QIVAFPQEGI LSYPNGEALL EEALRLGADV VGAIPHFEFT REYGVESLHK
    210 220 230 240 250
    TFALAQKYDR LIDVHCDEID DEQSRFVETV AALAHHEGMG ARVTASHTTA
    260 270 280 290 300
    MHSYNGAYTS RLFRLLKMSG INFVANPLVN IHLQGRFDTY PKRRGITRVK
    310 320 330 340 350
    EMLESGINVC FGHDDVFDPW YPLGTANMLQ VLHMGLHVCQ LMGYGQINDG
    360 370 380 390 400
    LNLITHHSAR TLNLQDYGIA AGNSANLIIL PAENGFDALR RQVPVRYSVR
    410 420
    GGKVIASTQP AQTTVYLEQP EAIDYKR
    Length:427
    Mass (Da):47,591
    Last modified:January 23, 2007 - v3
    Checksum:i9F91A2C46B3B1E42
    GO

    Sequence cautioni

    The sequence AAB18061 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural varianti13R → W in strain: SO5076. 1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X63656 Genomic DNA. Translation: CAA45196.1.
    S56903 Genomic DNA. Translation: AAB25761.2.
    U73857 Genomic DNA. Translation: AAB18061.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC73440.1.
    AP009048 Genomic DNA. Translation: BAE76119.1.
    PIRiS22662.
    RefSeqiNP_414871.1. NC_000913.3.
    WP_001301240.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73440; AAC73440; b0337.
    BAE76119; BAE76119; BAE76119.
    GeneIDi944996.
    KEGGiecj:JW0328.
    eco:b0337.
    PATRICi32115805. VBIEscCol129921_0344.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X63656 Genomic DNA. Translation: CAA45196.1.
    S56903 Genomic DNA. Translation: AAB25761.2.
    U73857 Genomic DNA. Translation: AAB18061.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC73440.1.
    AP009048 Genomic DNA. Translation: BAE76119.1.
    PIRiS22662.
    RefSeqiNP_414871.1. NC_000913.3.
    WP_001301240.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1K6WX-ray1.75A2-427[»]
    1K70X-ray1.80A2-427[»]
    1R9XX-ray1.58A2-427[»]
    1R9YX-ray1.57A2-427[»]
    1R9ZX-ray1.32A2-427[»]
    1RA0X-ray1.12A2-427[»]
    1RA5X-ray1.40A2-427[»]
    1RAKX-ray1.32A2-427[»]
    3G77X-ray1.80A5-427[»]
    3O7UX-ray1.71A1-427[»]
    3R0DX-ray1.50A1-427[»]
    3RN6X-ray2.26A1-427[»]
    ProteinModelPortaliP25524.
    SMRiP25524.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4259813. 4 interactors.
    DIPiDIP-9306N.
    IntActiP25524. 6 interactors.
    MINTiMINT-1307853.
    STRINGi511145.b0337.

    Proteomic databases

    PaxDbiP25524.
    PRIDEiP25524.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73440; AAC73440; b0337.
    BAE76119; BAE76119; BAE76119.
    GeneIDi944996.
    KEGGiecj:JW0328.
    eco:b0337.
    PATRICi32115805. VBIEscCol129921_0344.

    Organism-specific databases

    EchoBASEiEB1302.
    EcoGeneiEG11326. codA.

    Phylogenomic databases

    eggNOGiENOG4105DZC. Bacteria.
    COG0402. LUCA.
    HOGENOMiHOG000184778.
    InParanoidiP25524.
    KOiK01485.
    OMAiAFPQDGY.
    PhylomeDBiP25524.

    Enzyme and pathway databases

    BioCyciEcoCyc:CYTDEAM-MONOMER.
    ECOL316407:JW0328-MONOMER.
    MetaCyc:CYTDEAM-MONOMER.
    BRENDAi3.5.4.1. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP25524.
    PROiP25524.

    Family and domain databases

    Gene3Di2.30.40.10. 1 hit.
    InterProiIPR013108. Amidohydro_3.
    IPR011059. Metal-dep_hydrolase_composite.
    IPR032466. Metal_Hydrolase.
    [Graphical view]
    PfamiPF07969. Amidohydro_3. 1 hit.
    [Graphical view]
    SUPFAMiSSF51338. SSF51338. 1 hit.
    SSF51556. SSF51556. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiCODA_ECOLI
    AccessioniPrimary (citable) accession number: P25524
    Secondary accession number(s): Q2MC87
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1992
    Last sequence update: January 23, 2007
    Last modified: November 2, 2016
    This is version 137 of the entry and version 3 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

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.