ID   P2C09_ARATH             Reviewed;         281 AA.
AC   Q9LME4; Q3ED74; Q8LFF8;
DT   14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2000, sequence version 1.
DT   24-JAN-2024, entry version 139.
DE   RecName: Full=Probable protein phosphatase 2C 9;
DE            Short=AtPP2C09;
DE            EC=3.1.3.16;
DE   AltName: Full=Phytochrome-associated protein phosphatase 2C;
DE            Short=PAPP2C;
GN   OrderedLocusNames=At1g22280; ORFNames=T16E15.10;
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 [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=11130712; DOI=10.1038/35048500;
RA   Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA   Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA   Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA   Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA   Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA   Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA   Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA   Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA   Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA   Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA   Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA   Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA   Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA   Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA   Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT   "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL   Nature 408:816-820(2000).
RN   [2]
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   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
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   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC   STRAIN=cv. Columbia;
RX   PubMed=14993207; DOI=10.1101/gr.1515604;
RA   Castelli V., Aury J.-M., Jaillon O., Wincker P., Clepet C., Menard M.,
RA   Cruaud C., Quetier F., Scarpelli C., Schaechter V., Temple G., Caboche M.,
RA   Weissenbach J., Salanoubat M.;
RT   "Whole genome sequence comparisons and 'full-length' cDNA sequences: a
RT   combined approach to evaluate and improve Arabidopsis genome annotation.";
RL   Genome Res. 14:406-413(2004).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RA   Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA   Feldmann K.A.;
RT   "Full-length cDNA from Arabidopsis thaliana.";
RL   Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN   [6]
RP   DISRUPTION PHENOTYPE, INTERACTION WITH PHYTOCHROMES, AND IDENTIFICATION BY
RP   MASS SPECTROMETRY.
RX   PubMed=16705748; DOI=10.1002/pmic.200500222;
RA   Phee B.-K., Shin D.H., Cho J.-H., Kim S.-H., Kim J.-I., Lee Y.-H.,
RA   Jeon J.-S., Bhoo S.H., Hahn T.-R.;
RT   "Identification of phytochrome-interacting protein candidates in
RT   Arabidopsis thaliana by co-immunoprecipitation coupled with MALDI-TOF MS.";
RL   Proteomics 6:3671-3680(2006).
RN   [7]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   TISSUE=Seedling;
RX   PubMed=17586839; DOI=10.1074/mcp.m700164-mcp200;
RA   Niittylae T., Fuglsang A.T., Palmgren M.G., Frommer W.B., Schulze W.X.;
RT   "Temporal analysis of sucrose-induced phosphorylation changes in plasma
RT   membrane proteins of Arabidopsis.";
RL   Mol. Cell. Proteomics 6:1711-1726(2007).
RN   [8]
RP   FUNCTION, AND SUBCELLULAR LOCATION.
RX   PubMed=18564962; DOI=10.1042/bj20071555;
RA   Phee B.-K., Kim J.-I., Shin D.H., Yoo J., Park K.-J., Han Y.-J.,
RA   Kwon Y.-K., Cho M.H., Jeon J.-S., Bhoo S.H., Hahn T.-R.;
RT   "A novel protein phosphatase indirectly regulates phytochrome-interacting
RT   factor 3 via phytochrome.";
RL   Biochem. J. 415:247-255(2008).
RN   [9]
RP   GENE FAMILY, AND NOMENCLATURE.
RX   PubMed=19021904; DOI=10.1186/1471-2164-9-550;
RA   Xue T., Wang D., Zhang S., Ehlting J., Ni F., Jacab S., Zheng C., Zhong Y.;
RT   "Genome-wide and expression analysis of protein phosphatase 2C in rice and
RT   Arabidopsis.";
RL   BMC Genomics 9:550-550(2008).
RN   [10]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   TISSUE=Root;
RX   PubMed=18433157; DOI=10.1021/pr8000173;
RA   de la Fuente van Bentem S., Anrather D., Dohnal I., Roitinger E.,
RA   Csaszar E., Joore J., Buijnink J., Carreri A., Forzani C., Lorkovic Z.J.,
RA   Barta A., Lecourieux D., Verhounig A., Jonak C., Hirt H.;
RT   "Site-specific phosphorylation profiling of Arabidopsis proteins by mass
RT   spectrometry and peptide chip analysis.";
RL   J. Proteome Res. 7:2458-2470(2008).
RN   [11]
RP   SUBCELLULAR LOCATION, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
RP   ANALYSIS].
RC   STRAIN=cv. Columbia;
RX   PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
RA   Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A., Andreasson E.,
RA   Rathjen J.P., Peck S.C.;
RT   "Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis
RT   thaliana.";
RL   J. Proteomics 72:439-451(2009).
RN   [12]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=19376835; DOI=10.1104/pp.109.138677;
RA   Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA   Grossmann J., Gruissem W., Baginsky S.;
RT   "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT   chloroplast kinase substrates and phosphorylation networks.";
RL   Plant Physiol. 150:889-903(2009).
CC   -!- FUNCTION: Involved in the regulation of phytochrome signaling. May
CC       regulate phytochrome-interacting factor 3 (PIF3) through the
CC       dephosphorylation of phytochrome. {ECO:0000269|PubMed:18564962}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] +
CC         phosphate; Xref=Rhea:RHEA:20629, Rhea:RHEA-COMP:9863, Rhea:RHEA-
CC         COMP:11604, ChEBI:CHEBI:15377, ChEBI:CHEBI:29999, ChEBI:CHEBI:43474,
CC         ChEBI:CHEBI:83421; EC=3.1.3.16;
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] +
CC         phosphate; Xref=Rhea:RHEA:47004, Rhea:RHEA-COMP:11060, Rhea:RHEA-
CC         COMP:11605, ChEBI:CHEBI:15377, ChEBI:CHEBI:30013, ChEBI:CHEBI:43474,
CC         ChEBI:CHEBI:61977; EC=3.1.3.16;
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC       Note=Binds 2 magnesium or manganese ions per subunit. {ECO:0000250};
CC   -!- SUBUNIT: Interacts with phytochromes (via N-terminus).
CC       {ECO:0000269|PubMed:16705748}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:18564962,
CC       ECO:0000269|PubMed:19245862}. Note=Localizes in the nucleus upon
CC       illumination.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1;
CC         IsoId=Q9LME4-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q9LME4-2; Sequence=VSP_036759, VSP_036760;
CC   -!- DISRUPTION PHENOTYPE: Abnormal hypocotyl elongation under continuous
CC       red light. {ECO:0000269|PubMed:16705748}.
CC   -!- SIMILARITY: Belongs to the PP2C family. {ECO:0000305}.
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DR   EMBL; AC068562; AAF87263.1; -; Genomic_DNA.
DR   EMBL; CP002684; AEE30220.1; -; Genomic_DNA.
DR   EMBL; CP002684; AEE30221.1; -; Genomic_DNA.
DR   EMBL; AY080735; AAL86005.1; -; mRNA.
DR   EMBL; AY133737; AAM91671.1; -; mRNA.
DR   EMBL; BX813947; -; NOT_ANNOTATED_CDS; mRNA.
DR   EMBL; AY084874; AAM61437.1; -; mRNA.
DR   PIR; F86355; F86355.
DR   RefSeq; NP_564165.1; NM_102079.5. [Q9LME4-1]
DR   RefSeq; NP_973883.1; NM_202154.2. [Q9LME4-2]
DR   AlphaFoldDB; Q9LME4; -.
DR   SMR; Q9LME4; -.
DR   BioGRID; 24074; 3.
DR   IntAct; Q9LME4; 2.
DR   STRING; 3702.Q9LME4; -.
DR   iPTMnet; Q9LME4; -.
DR   SwissPalm; Q9LME4; -.
DR   PaxDb; 3702-AT1G22280-3; -.
DR   ProteomicsDB; 248868; -. [Q9LME4-1]
DR   EnsemblPlants; AT1G22280.1; AT1G22280.1; AT1G22280. [Q9LME4-1]
DR   EnsemblPlants; AT1G22280.2; AT1G22280.2; AT1G22280. [Q9LME4-2]
DR   GeneID; 838835; -.
DR   Gramene; AT1G22280.1; AT1G22280.1; AT1G22280. [Q9LME4-1]
DR   Gramene; AT1G22280.2; AT1G22280.2; AT1G22280. [Q9LME4-2]
DR   KEGG; ath:AT1G22280; -.
DR   Araport; AT1G22280; -.
DR   TAIR; AT1G22280; PAPP2C.
DR   eggNOG; KOG0698; Eukaryota.
DR   HOGENOM; CLU_013173_0_1_1; -.
DR   InParanoid; Q9LME4; -.
DR   PhylomeDB; Q9LME4; -.
DR   PRO; PR:Q9LME4; -.
DR   Proteomes; UP000006548; Chromosome 1.
DR   ExpressionAtlas; Q9LME4; baseline and differential.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0017018; F:myosin phosphatase activity; IEA:UniProtKB-EC.
DR   CDD; cd00143; PP2Cc; 1.
DR   Gene3D; 3.60.40.10; PPM-type phosphatase domain; 1.
DR   InterPro; IPR015655; PP2C.
DR   InterPro; IPR036457; PPM-type-like_dom_sf.
DR   InterPro; IPR001932; PPM-type_phosphatase-like_dom.
DR   PANTHER; PTHR47992:SF36; PPM-TYPE PHOSPHATASE DOMAIN-CONTAINING PROTEIN; 1.
DR   PANTHER; PTHR47992; PROTEIN PHOSPHATASE; 1.
DR   Pfam; PF00481; PP2C; 1.
DR   SMART; SM00331; PP2C_SIG; 1.
DR   SMART; SM00332; PP2Cc; 1.
DR   SUPFAM; SSF81606; PP2C-like; 1.
DR   PROSITE; PS51746; PPM_2; 1.
DR   Genevisible; Q9LME4; AT.
PE   1: Evidence at protein level;
KW   Alternative splicing; Hydrolase; Magnesium; Manganese; Metal-binding;
KW   Nucleus; Protein phosphatase; Reference proteome.
FT   CHAIN           1..281
FT                   /note="Probable protein phosphatase 2C 9"
FT                   /id="PRO_0000367940"
FT   DOMAIN          33..280
FT                   /note="PPM-type phosphatase"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01082"
FT   BINDING         70
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         70
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         71
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         232
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         271
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   VAR_SEQ         186..199
FT                   /note="DVPRVNGQLAVSRA -> KELILSIECLMKIE (in isoform 2)"
FT                   /evidence="ECO:0000303|PubMed:14993207"
FT                   /id="VSP_036759"
FT   VAR_SEQ         200..281
FT                   /note="Missing (in isoform 2)"
FT                   /evidence="ECO:0000303|PubMed:14993207"
FT                   /id="VSP_036760"
FT   CONFLICT        111..112
FT                   /note="DQ -> E (in Ref. 5; AAM61437)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   281 AA;  30722 MW;  2EE90E4F8FB56768 CRC64;
     MGKFCCFTSA SEVVGGQSSS RSGKGRSDEG MIKYGFSLVK GKANHPMEDY HVANFINIQD
     HELGLFAIYD GHMGDSVPAY LQKRLFSNIL KEGEFWVDPR RSIAKAYEKT DQAILSNSSD
     LGRGGSTAVT AILINGRKLW IANVGDSRAV LSHGGAITQM STDHEPRTER SSIEDRGGFV
     SNLPGDVPRV NGQLAVSRAF GDKGLKTHLS SEPDIKEATV DSQTDVLLLA SDGIWKVMTN
     EEAMEIARRV KDPQKAAKEL TAEALRRESK DDISCVVVRF R
//