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P08331

- CPDB_ECOLI

UniProt

P08331 - CPDB_ECOLI

Protein

2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase

Gene

cpdB

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 139 (01 Oct 2014)
      Sequence version 2 (01 Feb 1995)
      Previous versions | rss
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    Functioni

    This bifunctional enzyme catalyzes two consecutive reactions during ribonucleic acid degradation. Converts a 2',3'-cyclic nucleotide to a 3'-nucleotide and then the 3'-nucleotide to the corresponding nucleoside and phosphate.1 Publication

    Catalytic activityi

    Nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 3'-phosphate.1 Publication
    A 3'-ribonucleotide + H2O = a ribonucleoside + phosphate.1 Publication

    Cofactori

    Divalent cations.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi31 – 311Divalent metal cation 1By similarity
    Metal bindingi33 – 331Divalent metal cation 1By similarity
    Metal bindingi76 – 761Divalent metal cation 1By similarity
    Metal bindingi76 – 761Divalent metal cation 2By similarity
    Metal bindingi116 – 1161Divalent metal cation 2By similarity
    Metal bindingi225 – 2251Divalent metal cation 2By similarity
    Metal bindingi257 – 2571Divalent metal cation 2By similarity
    Metal bindingi259 – 2591Divalent metal cation 1By similarity
    Binding sitei440 – 4401SubstrateBy similarity

    GO - Molecular functioni

    1. 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity Source: EcoCyc
    2. 3'-nucleotidase activity Source: EcoCyc
    3. metal ion binding Source: UniProtKB-KW
    4. nucleotide binding Source: UniProtKB-KW

    GO - Biological processi

    1. cellular response to DNA damage stimulus Source: EcoliWiki
    2. dephosphorylation Source: GOC
    3. nucleotide catabolic process Source: EcoCyc

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:CPDB-MONOMER.
    ECOL316407:JW4171-MONOMER.
    MetaCyc:CPDB-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase (EC:3.1.3.6, EC:3.1.4.16)
    Gene namesi
    Name:cpdB
    Ordered Locus Names:b4213, JW4171
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10160. cpdB.

    Subcellular locationi

    Periplasm 1 Publication

    GO - Cellular componenti

    1. periplasmic space Source: EcoCyc

    Keywords - Cellular componenti

    Periplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 19191 PublicationAdd
    BLAST
    Chaini20 – 6476282',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidasePRO_0000000035Add
    BLAST

    Proteomic databases

    PaxDbiP08331.
    PRIDEiP08331.

    Expressioni

    Gene expression databases

    GenevestigatoriP08331.

    Interactioni

    Protein-protein interaction databases

    DIPiDIP-9311N.
    IntActiP08331. 2 interactions.
    MINTiMINT-1228170.
    STRINGi511145.b4213.

    Structurei

    3D structure databases

    ProteinModelPortaliP08331.
    SMRiP08331. Positions 19-550.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni544 – 5507Substrate bindingBy similarity

    Sequence similaritiesi

    Belongs to the 5'-nucleotidase family.Curated

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiCOG0737.
    HOGENOMiHOG000248800.
    KOiK01119.
    OMAiEKAQYPM.
    OrthoDBiEOG696BW0.

    Family and domain databases

    Gene3Di3.60.21.10. 1 hit.
    3.90.780.10. 1 hit.
    InterProiIPR008334. 5'-Nucleotdase_C.
    IPR006146. 5'-Nucleotdase_CS.
    IPR006179. 5_nucleotidase/apyrase.
    IPR004843. Calcineurin-like_PHP_apaH.
    IPR006294. Cyc_nuc_PDE_nucleotidase.
    IPR029052. Metallo-depent_PP-like.
    [Graphical view]
    PANTHERiPTHR11575. PTHR11575. 1 hit.
    PfamiPF02872. 5_nucleotid_C. 1 hit.
    PF00149. Metallophos. 1 hit.
    [Graphical view]
    PRINTSiPR01607. APYRASEFAMLY.
    SUPFAMiSSF55816. SSF55816. 1 hit.
    SSF56300. SSF56300. 1 hit.
    TIGRFAMsiTIGR01390. CycNucDiestase. 1 hit.
    PROSITEiPS00785. 5_NUCLEOTIDASE_1. 1 hit.
    PS00786. 5_NUCLEOTIDASE_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P08331-1 [UniParc]FASTAAdd to Basket

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    MIKFSATLLA TLIAASVNAA TVDLRIMETT DLHSNMMDFD YYKDTATEKF    50
    GLVRTASLIN DARNEVKNSV LVDNGDLIQG SPLADYMSAK GLKAGDIHPV 100
    YKALNTLDYT VGTLGNHEFN YGLDYLKNAL AGAKFPYVNA NVIDARTKQP 150
    MFTPYLIKDT EVVDKDGKKQ TLKIGYIGVV PPQIMGWDKA NLSGKVTVND 200
    ITETVRKYVP EMREKGADVV VVLAHSGLSA DPYKVMAENS VYYLSEIPGV 250
    NAIMFGHAHA VFPGKDFADI EGADIAKGTL NGVPAVMPGM WGDHLGVVDL 300
    QLSNDSGKWQ VTQAKAEARP IYDIANKKSL AAEDSKLVET LKADHDATRQ 350
    FVSKPIGKSA DNMYSYLALV QDDPTVQVVN NAQKAYVEHY IQGDPDLAKL 400
    PVLSAAAPFK VGGRKNDPAS YVEVEKGQLT FRNAADLYLY PNTLIVVKAS 450
    GKEVKEWLEC SAGQFNQIDP NSTKPQSLIN WDGFRTYNFD VIDGVNYQID 500
    VTQPARYDGE CQMINANAER IKNLTFNGKP IDPNAMFLVA TNNYRAYGGK 550
    FAGTGDSHIA FASPDENRSV LAAWIADESK RAGEIHPAAD NNWRLAPIAG 600
    DKKLDIRFET SPSDKAAAFI KEKGQYPMNK VATDDIGFAI YQVDLSK 647
    Length:647
    Mass (Da):70,832
    Last modified:February 1, 1995 - v2
    Checksum:i4B26DC3563473827
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti316 – 3161A → G in AAA23597. (PubMed:3005231)Curated
    Sequence conflicti528 – 55225GKPID…GGKFA → ASRLIRTPCSWLPPITIALT GQIC in AAA23597. (PubMed:3005231)CuratedAdd
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M13464 Genomic DNA. Translation: AAA23597.1.
    U14003 Genomic DNA. Translation: AAA97109.1.
    U00096 Genomic DNA. Translation: AAC77170.1.
    AP009048 Genomic DNA. Translation: BAE78214.1.
    X54008 Genomic DNA. Translation: CAA37954.1.
    PIRiH65232. ESECPC.
    RefSeqiNP_418634.1. NC_000913.3.
    YP_492355.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC77170; AAC77170; b4213.
    BAE78214; BAE78214; BAE78214.
    GeneIDi12933725.
    948729.
    KEGGiecj:Y75_p4099.
    eco:b4213.
    PATRICi32124001. VBIEscCol129921_4345.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M13464 Genomic DNA. Translation: AAA23597.1 .
    U14003 Genomic DNA. Translation: AAA97109.1 .
    U00096 Genomic DNA. Translation: AAC77170.1 .
    AP009048 Genomic DNA. Translation: BAE78214.1 .
    X54008 Genomic DNA. Translation: CAA37954.1 .
    PIRi H65232. ESECPC.
    RefSeqi NP_418634.1. NC_000913.3.
    YP_492355.1. NC_007779.1.

    3D structure databases

    ProteinModelPortali P08331.
    SMRi P08331. Positions 19-550.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-9311N.
    IntActi P08331. 2 interactions.
    MINTi MINT-1228170.
    STRINGi 511145.b4213.

    Proteomic databases

    PaxDbi P08331.
    PRIDEi P08331.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC77170 ; AAC77170 ; b4213 .
    BAE78214 ; BAE78214 ; BAE78214 .
    GeneIDi 12933725.
    948729.
    KEGGi ecj:Y75_p4099.
    eco:b4213.
    PATRICi 32124001. VBIEscCol129921_4345.

    Organism-specific databases

    EchoBASEi EB0158.
    EcoGenei EG10160. cpdB.

    Phylogenomic databases

    eggNOGi COG0737.
    HOGENOMi HOG000248800.
    KOi K01119.
    OMAi EKAQYPM.
    OrthoDBi EOG696BW0.

    Enzyme and pathway databases

    BioCyci EcoCyc:CPDB-MONOMER.
    ECOL316407:JW4171-MONOMER.
    MetaCyc:CPDB-MONOMER.

    Miscellaneous databases

    PROi P08331.

    Gene expression databases

    Genevestigatori P08331.

    Family and domain databases

    Gene3Di 3.60.21.10. 1 hit.
    3.90.780.10. 1 hit.
    InterProi IPR008334. 5'-Nucleotdase_C.
    IPR006146. 5'-Nucleotdase_CS.
    IPR006179. 5_nucleotidase/apyrase.
    IPR004843. Calcineurin-like_PHP_apaH.
    IPR006294. Cyc_nuc_PDE_nucleotidase.
    IPR029052. Metallo-depent_PP-like.
    [Graphical view ]
    PANTHERi PTHR11575. PTHR11575. 1 hit.
    Pfami PF02872. 5_nucleotid_C. 1 hit.
    PF00149. Metallophos. 1 hit.
    [Graphical view ]
    PRINTSi PR01607. APYRASEFAMLY.
    SUPFAMi SSF55816. SSF55816. 1 hit.
    SSF56300. SSF56300. 1 hit.
    TIGRFAMsi TIGR01390. CycNucDiestase. 1 hit.
    PROSITEi PS00785. 5_NUCLEOTIDASE_1. 1 hit.
    PS00786. 5_NUCLEOTIDASE_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Isolation and sequence analysis of the gene (cpdB) encoding periplasmic 2',3'-cyclic phosphodiesterase."
      Liu J., Burns D.M., Beacham I.R.
      J. Bacteriol. 165:1002-1010(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION.
    2. "Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
      Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
      Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "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.
    5. "Transcription and regulation of the cpdB gene in Escherichia coli K12 and Salmonella typhimurium LT2: evidence for modulation of constitutive promoters by cyclic AMP-CRP complex."
      Liu J., Beacham I.R.
      Mol. Gen. Genet. 222:161-165(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-20.
      Strain: K12.
    6. "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12."
      Link A.J., Robison K., Church G.M.
      Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 20-31.
      Strain: K12 / EMG2.

    Entry informationi

    Entry nameiCPDB_ECOLI
    AccessioniPrimary (citable) accession number: P08331
    Secondary accession number(s): Q2M692
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1988
    Last sequence update: February 1, 1995
    Last modified: October 1, 2014
    This is version 139 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Two kinetically distinguishable active sites for the two substrates (2',3'-cyclic nucleotides and 3'-nucleotides) have been identified.

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Multifunctional enzyme, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3