CPD_ARATH
ID CPD_ARATH Reviewed; 181 AA.
AC O04147;
DT 16-AUG-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1997, sequence version 1.
DT 03-AUG-2022, entry version 147.
DE RecName: Full=Cyclic phosphodiesterase;
DE Short=CPDase;
DE EC=3.1.4.-;
GN OrderedLocusNames=At4g18930; ORFNames=F13C5.100, F13C5_100;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia; TISSUE=Leaf;
RX PubMed=9148938; DOI=10.1074/jbc.272.20.13211;
RA Genschik P., Hall J., Filipowicz W.;
RT "Cloning and characterization of the Arabidopsis cyclic phosphodiesterase
RT which hydrolyzes ADP-ribose 1'',2''-cyclic phosphate and nucleoside 2',3'-
RT cyclic phosphates.";
RL J. Biol. Chem. 272:13211-13219(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
RX PubMed=11080166; DOI=10.1093/emboj/19.22.6207;
RA Hofmann A., Zdanov A., Genschik P., Ruvinov S., Filipowicz W., Wlodawer A.;
RT "Structure and mechanism of activity of the cyclic phosphodiesterase of
RT Appr>p, a product of the tRNA splicing reaction.";
RL EMBO J. 19:6207-6217(2000).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH INHIBITOR
RP 2',3'-CYCLIC URIDINE VANADATE.
RX PubMed=11694509; DOI=10.1074/jbc.m107889200;
RA Hofmann A., Grella M., Botos I., Filipowicz W., Wlodawer A.;
RT "Crystal structures of the semireduced and inhibitor-bound forms of cyclic
RT nucleotide phosphodiesterase from Arabidopsis thaliana.";
RL J. Biol. Chem. 277:1419-1425(2002).
CC -!- FUNCTION: Hydrolyzes ADP-ribose 1'',2''-cyclic phosphate (Appr>1) that
CC is produced during tRNA splicing into ADP-ribose 1''-phosphate (Appr-
CC 1''p). Acts also on nucleoside 2',3'-cyclic phosphates.
CC -!- ACTIVITY REGULATION: Inhibited by Cu(2+) and Zn(2+) at 0.5 mM by 93 and
CC 87% respectively. Not inhibited by Ca(2+), Mg(2+), Co(2+), Ni(2+), and
CC EDTA at 0.5 mM.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.35 mM for Appr>p;
CC KM=1.34 mM for A>p;
CC KM=2.38 mM for C>p;
CC KM=16.86 mM for G>p;
CC KM=17.67 mM for U>p;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:9148938}.
CC -!- TISSUE SPECIFICITY: Expressed in leaves, stems, roots, floral buds and
CC germinating seeds. {ECO:0000269|PubMed:9148938}.
CC -!- SIMILARITY: Belongs to the 2H phosphoesterase superfamily. CPD1 family.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; Y11650; CAA72363.1; -; mRNA.
DR EMBL; AL021711; CAA16750.1; -; Genomic_DNA.
DR EMBL; AL161549; CAB78895.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE84108.1; -; Genomic_DNA.
DR EMBL; AY062822; AAL32900.1; -; mRNA.
DR EMBL; AY081630; AAM10192.1; -; mRNA.
DR PIR; T05030; T05030.
DR RefSeq; NP_193628.1; NM_118010.5.
DR PDB; 1FSI; X-ray; 2.50 A; A/B/C=1-181.
DR PDB; 1JH6; X-ray; 1.80 A; A/B=1-181.
DR PDB; 1JH7; X-ray; 2.40 A; A=1-181.
DR PDBsum; 1FSI; -.
DR PDBsum; 1JH6; -.
DR PDBsum; 1JH7; -.
DR AlphaFoldDB; O04147; -.
DR SMR; O04147; -.
DR STRING; 3702.AT4G18930.1; -.
DR SwissPalm; O04147; -.
DR PaxDb; O04147; -.
DR PRIDE; O04147; -.
DR ProteomicsDB; 222616; -.
DR EnsemblPlants; AT4G18930.1; AT4G18930.1; AT4G18930.
DR GeneID; 827628; -.
DR Gramene; AT4G18930.1; AT4G18930.1; AT4G18930.
DR KEGG; ath:AT4G18930; -.
DR Araport; AT4G18930; -.
DR TAIR; locus:2117099; AT4G18930.
DR eggNOG; ENOG502QPX1; Eukaryota.
DR HOGENOM; CLU_081919_1_0_1; -.
DR InParanoid; O04147; -.
DR OMA; IAECTLT; -.
DR OrthoDB; 1620665at2759; -.
DR PhylomeDB; O04147; -.
DR EvolutionaryTrace; O04147; -.
DR PRO; PR:O04147; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; O04147; baseline and differential.
DR Genevisible; O04147; AT.
DR GO; GO:0005737; C:cytoplasm; IDA:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0004113; F:2',3'-cyclic-nucleotide 3'-phosphodiesterase activity; IBA:GO_Central.
DR GO; GO:0009187; P:cyclic nucleotide metabolic process; IBA:GO_Central.
DR GO; GO:0006388; P:tRNA splicing, via endonucleolytic cleavage and ligation; TAS:TAIR.
DR InterPro; IPR012386; Cyclic-nucl_3Pdiesterase.
DR InterPro; IPR009097; Cyclic_Pdiesterase.
DR PANTHER; PTHR28141; PTHR28141; 1.
DR Pfam; PF07823; CPDase; 1.
DR PIRSF; PIRSF017903; CPDase_plant; 1.
DR SUPFAM; SSF55144; SSF55144; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Disulfide bond; Hydrolase; Reference proteome.
FT CHAIN 1..181
FT /note="Cyclic phosphodiesterase"
FT /id="PRO_0000079285"
FT ACT_SITE 42
FT /note="Proton donor/acceptor"
FT ACT_SITE 119
FT /note="Proton donor/acceptor"
FT BINDING 44
FT /ligand="substrate"
FT BINDING 121
FT /ligand="substrate"
FT BINDING 124
FT /ligand="substrate"
FT DISULFID 64..177
FT DISULFID 104..110
FT STRAND 7..15
FT /evidence="ECO:0007829|PDB:1JH6"
FT TURN 17..19
FT /evidence="ECO:0007829|PDB:1JH6"
FT HELIX 20..34
FT /evidence="ECO:0007829|PDB:1JH6"
FT STRAND 43..51
FT /evidence="ECO:0007829|PDB:1JH6"
FT HELIX 53..65
FT /evidence="ECO:0007829|PDB:1JH6"
FT STRAND 70..82
FT /evidence="ECO:0007829|PDB:1JH6"
FT STRAND 85..91
FT /evidence="ECO:0007829|PDB:1JH6"
FT HELIX 95..107
FT /evidence="ECO:0007829|PDB:1JH6"
FT STRAND 119..123
FT /evidence="ECO:0007829|PDB:1JH6"
FT HELIX 129..142
FT /evidence="ECO:0007829|PDB:1JH6"
FT HELIX 144..146
FT /evidence="ECO:0007829|PDB:1FSI"
FT STRAND 150..160
FT /evidence="ECO:0007829|PDB:1JH6"
FT STRAND 172..178
FT /evidence="ECO:0007829|PDB:1JH6"
SQ SEQUENCE 181 AA; 20514 MW; 5FFDFC57213BEE34 CRC64;
MEEVKKDVYS VWALPDEESE PRFKKLMEAL RSEFTGPRFV PHVTVAVSAY LTADEAKKMF
ESACDGLKAY TATVDRVSTG TFFFQCVFLL LQTTPEVMEA GEHCKNHFNC STTTPYMPHL
SLLYAELTEE EKKNAQEKAY TLDSSLDGLS FRLNRLALCK TDTEDKTLET WETVAVCNLN
P
