1) that is produced during tRNA splicing into ADP-ribose 1"-phosphate (Appr-1"p). Acts also on nucleoside 2',3'-cyclic phosphates." name="description"/>

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Protein

Cyclic phosphodiesterase

Gene

At4g18930

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Hydrolyzes ADP-ribose 1",2"-cyclic phosphate (Appr>1) that is produced during tRNA splicing into ADP-ribose 1"-phosphate (Appr-1"p). Acts also on nucleoside 2',3'-cyclic phosphates.

Enzyme regulationi

Inhibited by Cu2+ and Zn2+ at 0.5 mM by 93 and 87% respectively. Not inhibited by Ca2+, Mg2+, Co2+, Ni2+, and EDTA at 0.5 mM.

Kineticsi

  1. KM=1.35 mM for Appr>p
  2. KM=1.34 mM for A>p
  3. KM=2.38 mM for C>p
  4. KM=16.86 mM for G>p
  5. KM=17.67 mM for U>p

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei42 – 421Proton donor/acceptor
    Binding sitei44 – 441Substrate
    Active sitei119 – 1191Proton donor/acceptor
    Binding sitei121 – 1211Substrate
    Binding sitei124 – 1241Substrate

    GO - Molecular functioni

    GO - Biological processi

    • tRNA splicing, via endonucleolytic cleavage and ligation Source: TAIR
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Cyclic phosphodiesterase (EC:3.1.4.-)
    Short name:
    CPDase
    Gene namesi
    Ordered Locus Names:At4g18930
    ORF Names:F13C5.100, F13C5_100
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548 Componenti: Chromosome 4

    Organism-specific databases

    TAIRiAT4G18930.

    Subcellular locationi

    • Cytoplasm 1 Publication

    GO - Cellular componenti

    • cytoplasm Source: TAIR
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 181181Cyclic phosphodiesterasePRO_0000079285Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi64 ↔ 177
    Disulfide bondi104 ↔ 110

    Keywords - PTMi

    Disulfide bond

    Proteomic databases

    PaxDbiO04147.
    PRIDEiO04147.

    Expressioni

    Tissue specificityi

    Expressed in leaves, stems, roots, floral buds and germinating seeds.1 Publication

    Interactioni

    Protein-protein interaction databases

    STRINGi3702.AT4G18930.1.

    Structurei

    Secondary structure

    1
    181
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi7 – 159Combined sources
    Turni17 – 193Combined sources
    Helixi20 – 3415Combined sources
    Beta strandi43 – 519Combined sources
    Helixi53 – 6513Combined sources
    Beta strandi70 – 8213Combined sources
    Beta strandi85 – 917Combined sources
    Helixi95 – 10713Combined sources
    Beta strandi119 – 1235Combined sources
    Helixi129 – 14214Combined sources
    Helixi144 – 1463Combined sources
    Beta strandi150 – 16011Combined sources
    Beta strandi172 – 1787Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1FSIX-ray2.50A/B/C1-181[»]
    1JH6X-ray1.80A/B1-181[»]
    1JH7X-ray2.40A1-181[»]
    ProteinModelPortaliO04147.
    SMRiO04147. Positions 1-181.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO04147.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiNOG123043.
    HOGENOMiHOG000241544.
    InParanoidiO04147.
    OMAiASDHCCG.
    PhylomeDBiO04147.

    Family and domain databases

    Gene3Di3.90.1140.10. 1 hit.
    InterProiIPR012386. Cyclic-nucl_3Pdiesterase.
    IPR009097. RNA_ligase/cNuc_Pdiesterase.
    [Graphical view]
    PfamiPF07823. CPDase. 1 hit.
    [Graphical view]
    PIRSFiPIRSF017903. CPDase_plant. 1 hit.
    SUPFAMiSSF55144. SSF55144. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    O04147-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MEEVKKDVYS VWALPDEESE PRFKKLMEAL RSEFTGPRFV PHVTVAVSAY
    60 70 80 90 100
    LTADEAKKMF ESACDGLKAY TATVDRVSTG TFFFQCVFLL LQTTPEVMEA
    110 120 130 140 150
    GEHCKNHFNC STTTPYMPHL SLLYAELTEE EKKNAQEKAY TLDSSLDGLS
    160 170 180
    FRLNRLALCK TDTEDKTLET WETVAVCNLN P
    Length:181
    Mass (Da):20,514
    Last modified:July 1, 1997 - v1
    Checksum:i5FFDFC57213BEE34
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    Y11650 mRNA. Translation: CAA72363.1.
    AL021711 Genomic DNA. Translation: CAA16750.1.
    AL161549 Genomic DNA. Translation: CAB78895.1.
    CP002687 Genomic DNA. Translation: AEE84108.1.
    AY062822 mRNA. Translation: AAL32900.1.
    AY081630 mRNA. Translation: AAM10192.1.
    PIRiT05030.
    RefSeqiNP_193628.1. NM_118010.4.
    UniGeneiAt.29.

    Genome annotation databases

    EnsemblPlantsiAT4G18930.1; AT4G18930.1; AT4G18930.
    GeneIDi827628.
    KEGGiath:AT4G18930.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    Y11650 mRNA. Translation: CAA72363.1.
    AL021711 Genomic DNA. Translation: CAA16750.1.
    AL161549 Genomic DNA. Translation: CAB78895.1.
    CP002687 Genomic DNA. Translation: AEE84108.1.
    AY062822 mRNA. Translation: AAL32900.1.
    AY081630 mRNA. Translation: AAM10192.1.
    PIRiT05030.
    RefSeqiNP_193628.1. NM_118010.4.
    UniGeneiAt.29.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1FSIX-ray2.50A/B/C1-181[»]
    1JH6X-ray1.80A/B1-181[»]
    1JH7X-ray2.40A1-181[»]
    ProteinModelPortaliO04147.
    SMRiO04147. Positions 1-181.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi3702.AT4G18930.1.

    Proteomic databases

    PaxDbiO04147.
    PRIDEiO04147.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblPlantsiAT4G18930.1; AT4G18930.1; AT4G18930.
    GeneIDi827628.
    KEGGiath:AT4G18930.

    Organism-specific databases

    GeneFarmi4171.
    TAIRiAT4G18930.

    Phylogenomic databases

    eggNOGiNOG123043.
    HOGENOMiHOG000241544.
    InParanoidiO04147.
    OMAiASDHCCG.
    PhylomeDBiO04147.

    Miscellaneous databases

    EvolutionaryTraceiO04147.
    PROiO04147.

    Family and domain databases

    Gene3Di3.90.1140.10. 1 hit.
    InterProiIPR012386. Cyclic-nucl_3Pdiesterase.
    IPR009097. RNA_ligase/cNuc_Pdiesterase.
    [Graphical view]
    PfamiPF07823. CPDase. 1 hit.
    [Graphical view]
    PIRSFiPIRSF017903. CPDase_plant. 1 hit.
    SUPFAMiSSF55144. SSF55144. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Cloning and characterization of the Arabidopsis cyclic phosphodiesterase which hydrolyzes ADP-ribose 1'',2''-cyclic phosphate and nucleoside 2',3'-cyclic phosphates."
      Genschik P., Hall J., Filipowicz W.
      J. Biol. Chem. 272:13211-13219(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
      Strain: cv. Columbia.
      Tissue: Leaf.
    2. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
      Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
      , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
      Nature 402:769-777(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    3. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    5. "Structure and mechanism of activity of the cyclic phosphodiesterase of Appr>p, a product of the tRNA splicing reaction."
      Hofmann A., Zdanov A., Genschik P., Ruvinov S., Filipowicz W., Wlodawer A.
      EMBO J. 19:6207-6217(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
    6. "Crystal structures of the semireduced and inhibitor-bound forms of cyclic nucleotide phosphodiesterase from Arabidopsis thaliana."
      Hofmann A., Grella M., Botos I., Filipowicz W., Wlodawer A.
      J. Biol. Chem. 277:1419-1425(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH INHIBITOR 2',3'-CYCLIC URIDINE VANADATE.

    Entry informationi

    Entry nameiCPD_ARATH
    AccessioniPrimary (citable) accession number: O04147
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 16, 2004
    Last sequence update: July 1, 1997
    Last modified: June 24, 2015
    This is version 111 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    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

    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 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.