O04147 (CPD_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Cyclic phosphodiesterase
Short name=CPDase
EC=3.1.4.-

Gene names

Ordered Locus Names:	At4g18930
ORF Names:	F13C5.100, F13C5_100

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	181 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Hydrolyzes APD-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 component	Cytoplasm
Molecular function	Hydrolase
PTM	Disulfide bond
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	tRNA splicing, via endonucleolytic cleavage and ligation Traceable author statement Ref.1. Source: TAIR
Cellular_component	cytoplasm Inferred from direct assay Ref.1. Source: TAIR
Molecular_function	cyclic-nucleotide phosphodiesterase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 181

181

Cyclic phosphodiesterase

PRO_0000079285

Sites

Active site

42

1

Proton donor/acceptor

Active site

119

1

Proton donor/acceptor

Binding site

44

1

Substrate

Binding site

121

1

Substrate

Binding site

124

1

Substrate

Amino acid modifications

Disulfide bond

64 ↔ 177

Disulfide bond

104 ↔ 110

Secondary structure

1

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181

Helix Strand Turn

Details...

Beta strand

7 – 15

9

Turn

17 – 19

3

Helix

20 – 34

15

Beta strand

43 – 51

9

Helix

53 – 65

13

Beta strand

70 – 82

13

Beta strand

85 – 91

7

Helix

95 – 107

13

Beta strand

119 – 123

5

Helix

129 – 142

14

Helix

144 – 146

3

Beta strand

150 – 160

11

Beta strand

172 – 178

7

Sequences

	Sequence		Length	Mass (Da)
	O04147 [UniParc]. Last modified July 1, 1997. Version 1. Checksum: 5FFDFC57213BEE34	FASTA	181	20,514
	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

References

	« Hide 'large scale' referencesShow '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. , 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.
+	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.

IPI

IPI00522282.

PIR

T05030.

RefSeq

NP_193628.1. NM_118010.4.

UniGene

At.29.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

O04147.

SMR

O04147. Positions 1-181.

ModBase

Search...

Protein-protein interaction databases

STRING

3702.AT4G18930.1-P.

Proteomic databases

PaxDb

O04147.

PRIDE

O04147.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblPlants

AT4G18930.1; AT4G18930.1; AT4G18930.

GeneID

827628.

KEGG

ath:AT4G18930.

Organism-specific databases

GeneFarm

4171.

TAIR

At4g18930.

Phylogenomic databases

eggNOG

NOG123043.

HOGENOM

HOG000241544.

InParanoid

O04147.

OMA

STPYMPH.

PhylomeDB

O04147.

ProtClustDB

CLSN2685469.

Gene expression databases

Genevestigator

O04147.

GermOnline

AT4G18930. Arabidopsis thaliana.

Family and domain databases

InterPro

IPR012386. Cyclic-nucl_3Pdiesterase.
IPR009097. RNA_ligase/cNuc_Pdiesterase.
[Graphical view]

Pfam

PF07823. CPDase. 1 hit.
[Graphical view]

PIRSF

PIRSF017903. CPDase_plant. 1 hit.

SUPFAM

SSF55144. Cyc_nuc_Pdiester. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

O04147.

Entry information

Entry name

CPD_ARATH

Accession

Primary (citable) accession number: O04147

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 16, 2004
Last sequence update:	July 1, 1997
Last modified:	May 1, 2013
This is version 95 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program