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O04147 (CPD_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 103. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Cyclic phosphodiesterase

Short name=CPDase
EC=3.1.4.-
Gene names
Ordered Locus Names:At4g18930
ORF Names:F13C5.100, F13C5_100
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length181 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 regulation

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.

Subcellular location

Cytoplasm Ref.1.

Tissue specificity

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

Biophysicochemical properties

Kinetic parameters:

KM=1.35 mM for Appr>p

KM=1.34 mM for A>p

KM=2.38 mM for C>p

KM=16.86 mM for G>p

KM=17.67 mM for U>p

Ontologies

Keywords
   Cellular componentCytoplasm
   Molecular functionHydrolase
   PTMDisulfide bond
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processtRNA splicing, via endonucleolytic cleavage and ligation

Traceable author statement Ref.1. Source: TAIR

   Cellular_componentcytoplasm

Inferred from direct assay Ref.1. Source: TAIR

   Molecular_functioncyclic-nucleotide phosphodiesterase activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 181181Cyclic phosphodiesterase
PRO_0000079285

Sites

Active site421Proton donor/acceptor
Active site1191Proton donor/acceptor
Binding site441Substrate
Binding site1211Substrate
Binding site1241Substrate

Amino acid modifications

Disulfide bond64 ↔ 177
Disulfide bond104 ↔ 110

Secondary structure

.......................... 181
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
O04147 [UniParc].

Last modified July 1, 1997. Version 1.
Checksum: 5FFDFC57213BEE34

FASTA18120,514
        10         20         30         40         50         60 
MEEVKKDVYS VWALPDEESE PRFKKLMEAL RSEFTGPRFV PHVTVAVSAY LTADEAKKMF 

        70         80         90        100        110        120 
ESACDGLKAY TATVDRVSTG TFFFQCVFLL LQTTPEVMEA GEHCKNHFNC STTTPYMPHL 

       130        140        150        160        170        180 
SLLYAELTEE EKKNAQEKAY TLDSSLDGLS FRLNRLALCK TDTEDKTLET WETVAVCNLN 


P 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRT05030.
RefSeqNP_193628.1. NM_118010.4.
UniGeneAt.29.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1FSIX-ray2.50A/B/C1-181[»]
1JH6X-ray1.80A/B1-181[»]
1JH7X-ray2.40A1-181[»]
ProteinModelPortalO04147.
SMRO04147. Positions 1-181.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING3702.AT4G18930.1-P.

Proteomic databases

PaxDbO04147.
PRIDEO04147.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT4G18930.1; AT4G18930.1; AT4G18930.
GeneID827628.
KEGGath:AT4G18930.

Organism-specific databases

GeneFarm4171.
TAIRAT4G18930.

Phylogenomic databases

eggNOGNOG123043.
HOGENOMHOG000241544.
InParanoidO04147.
OMAVEASAHC.
PhylomeDBO04147.

Gene expression databases

GenevestigatorO04147.

Family and domain databases

Gene3D3.90.1140.10. 1 hit.
InterProIPR012386. Cyclic-nucl_3Pdiesterase.
IPR009097. RNA_ligase/cNuc_Pdiesterase.
[Graphical view]
PfamPF07823. CPDase. 1 hit.
[Graphical view]
PIRSFPIRSF017903. CPDase_plant. 1 hit.
SUPFAMSSF55144. SSF55144. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceO04147.

Entry information

Entry nameCPD_ARATH
AccessionPrimary (citable) accession number: O04147
Entry history
Integrated into UniProtKB/Swiss-Prot: August 16, 2004
Last sequence update: July 1, 1997
Last modified: May 14, 2014
This is version 103 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names