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O04147

- CPD_ARATH

UniProt

O04147 - CPD_ARATH

Protein

Cyclic phosphodiesterase

Gene

At4g18930

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 104 (01 Oct 2014)
      Sequence version 1 (01 Jul 1997)
      Previous versions | rss
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    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

    1. cyclic-nucleotide phosphodiesterase activity Source: InterPro

    GO - Biological processi

    1. tRNA splicing, via endonucleolytic cleavage and ligation Source: TAIR

    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: Chromosome 4

    Organism-specific databases

    TAIRiAT4G18930.

    Subcellular locationi

    Cytoplasm 1 Publication

    GO - Cellular componenti

    1. cytoplasm Source: TAIR

    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

    Gene expression databases

    GenevestigatoriO04147.

    Interactioni

    Protein-protein interaction databases

    STRINGi3702.AT4G18930.1-P.

    Structurei

    Secondary structure

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

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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

    Phylogenomic databases

    eggNOGiNOG123043.
    HOGENOMiHOG000241544.
    InParanoidiO04147.
    OMAiVEASAHC.
    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

    MEEVKKDVYS VWALPDEESE PRFKKLMEAL RSEFTGPRFV PHVTVAVSAY    50
    LTADEAKKMF ESACDGLKAY TATVDRVSTG TFFFQCVFLL LQTTPEVMEA 100
    GEHCKNHFNC STTTPYMPHL SLLYAELTEE EKKNAQEKAY TLDSSLDGLS 150
    FRLNRLALCK TDTEDKTLET WETVAVCNLN P 181
    Length:181
    Mass (Da):20,514
    Last modified:July 1, 1997 - v1
    Checksum:i5FFDFC57213BEE34
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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 .
    PIRi T05030.
    RefSeqi NP_193628.1. NM_118010.4.
    UniGenei At.29.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1FSI X-ray 2.50 A/B/C 1-181 [» ]
    1JH6 X-ray 1.80 A/B 1-181 [» ]
    1JH7 X-ray 2.40 A 1-181 [» ]
    ProteinModelPortali O04147.
    SMRi O04147. Positions 1-181.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 3702.AT4G18930.1-P.

    Proteomic databases

    PaxDbi O04147.
    PRIDEi O04147.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT4G18930.1 ; AT4G18930.1 ; AT4G18930 .
    GeneIDi 827628.
    KEGGi ath:AT4G18930.

    Organism-specific databases

    GeneFarmi 4171.
    TAIRi AT4G18930.

    Phylogenomic databases

    eggNOGi NOG123043.
    HOGENOMi HOG000241544.
    InParanoidi O04147.
    OMAi VEASAHC.
    PhylomeDBi O04147.

    Miscellaneous databases

    EvolutionaryTracei O04147.

    Gene expression databases

    Genevestigatori O04147.

    Family and domain databases

    Gene3Di 3.90.1140.10. 1 hit.
    InterProi IPR012386. Cyclic-nucl_3Pdiesterase.
    IPR009097. RNA_ligase/cNuc_Pdiesterase.
    [Graphical view ]
    Pfami PF07823. CPDase. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF017903. CPDase_plant. 1 hit.
    SUPFAMi SSF55144. SSF55144. 1 hit.
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 104 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

    External Data

    Dasty 3