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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

  1. cyclic-nucleotide phosphodiesterase activity Source: InterPro

GO - Biological processi

  1. 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

  1. 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

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 – 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[»]
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[»]
SMRiO04147. Positions 1-181.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT4G18930.1-P.

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.

Gene expression databases

GenevestigatoriO04147.

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(1996) [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(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (MAR-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(2002) [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(1999) [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(2001) [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: April 1, 2015
This is version 108 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.