ID   CPL3_ARATH              Reviewed;        1241 AA.
AC   Q8LL04; O22804;
DT   26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT   26-MAY-2009, sequence version 2.
DT   24-JAN-2024, entry version 118.
DE   RecName: Full=RNA polymerase II C-terminal domain phosphatase-like 3 {ECO:0000303|PubMed:25464831};
DE            Short=FCP-like 3 {ECO:0000305};
DE            EC=3.1.3.16 {ECO:0000269|PubMed:12149434};
DE   AltName: Full=Carboxyl-terminal phosphatase-like 3 {ECO:0000303|PubMed:12149434};
DE            Short=AtCPL3 {ECO:0000303|PubMed:12149434};
DE            Short=CTD phosphatase-like 3 {ECO:0000303|PubMed:16905668};
GN   Name=CPL3 {ECO:0000303|PubMed:12149434};
GN   Synonyms=AGGIE1 {ECO:0000303|PubMed:25464831};
GN   OrderedLocusNames=At2g33540 {ECO:0000312|Araport:AT2G33540};
GN   ORFNames=F4P9.31 {ECO:0000312|EMBL:AAB80671.1};
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], FUNCTION, CATALYTIC ACTIVITY, AND DISRUPTION
RP   PHENOTYPE.
RX   PubMed=12149434; DOI=10.1073/pnas.112276199;
RA   Koiwa H., Barb A.W., Xiong L., Li F., McCully M.G., Lee B.-H.,
RA   Sokolchik I., Zhu J., Gong Z., Reddy M., Sharkhuu A., Manabe Y., Yokoi S.,
RA   Zhu J.-K., Bressan R.A., Hasegawa P.M.;
RT   "C-terminal domain phosphatase-like family members (AtCPLs) differentially
RT   regulate Arabidopsis thaliana abiotic stress signaling, growth, and
RT   development.";
RL   Proc. Natl. Acad. Sci. U.S.A. 99:10893-10898(2002).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=10617197; DOI=10.1038/45471;
RA   Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA   Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA   Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA   Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA   Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA   Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA   Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT   "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL   Nature 402:761-768(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   FUNCTION, INTERACTION WITH RAP74, DISRUPTION PHENOTYPE, INDUCTION BY NACL,
RP   BRCT DOMAIN, AND SUBCELLULAR LOCATION.
RX   PubMed=16905668; DOI=10.1104/pp.106.084939;
RA   Bang W., Kim S., Ueda A., Vikram M., Yun D., Bressan R.A., Hasegawa P.M.,
RA   Bahk J., Koiwa H.;
RT   "Arabidopsis carboxyl-terminal domain phosphatase-like isoforms share
RT   common catalytic and interaction domains but have distinct in planta
RT   functions.";
RL   Plant Physiol. 142:586-594(2006).
RN   [5]
RP   GENE FAMILY.
RX   PubMed=18156295; DOI=10.1104/pp.107.111393;
RA   Kerk D., Templeton G., Moorhead G.B.G.;
RT   "Evolutionary radiation pattern of novel protein phosphatases revealed by
RT   analysis of protein data from the completely sequenced genomes of humans,
RT   green algae, and higher plants.";
RL   Plant Physiol. 146:351-367(2008).
RN   [6]
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).
RN   [7]
RP   FUNCTION, SUBCELLULAR LOCATION, AND MUTAGENESIS OF ASP-933; ASP-1064 AND
RP   ASP-1065.
RX   PubMed=25464831; DOI=10.1016/j.chom.2014.10.018;
RA   Li F., Cheng C., Cui F., de Oliveira M.V., Yu X., Meng X., Intorne A.C.,
RA   Babilonia K., Li M., Li B., Chen S., Ma X., Xiao S., Zheng Y., Fei Z.,
RA   Metz R.P., Johnson C.D., Koiwa H., Sun W., Li Z., de Souza Filho G.A.,
RA   Shan L., He P.;
RT   "Modulation of RNA polymerase II phosphorylation downstream of pathogen
RT   perception orchestrates plant immunity.";
RL   Cell Host Microbe 16:748-758(2014).
RN   [8]
RP   FUNCTION.
RX   PubMed=31076735; DOI=10.1038/s41477-019-0419-7;
RA   Li T., Natran A., Chen Y., Vercruysse J., Wang K., Gonzalez N., Dubois M.,
RA   Inze D.;
RT   "A genetics screen highlights emerging roles for CPL3, RST1 and URT1 in RNA
RT   metabolism and silencing.";
RL   Nat. Plants 5:539-550(2019).
CC   -!- FUNCTION: Completely dephosphorylates 'Ser-2', and partially 'Ser-5'
CC       and 'Ser-7' of the heptad repeats YSPTSPS in the C-terminal domain
CC       (CTD) of the largest RNA polymerase II subunit (RPB1)
CC       (PubMed:25464831). Involved in defense response (PubMed:25464831). Acts
CC       as a negative regulator of immune gene expression and immunity to
CC       pathogen infections (PubMed:25464831). Preferentially dephosphorylates
CC       'Ser-2' of RNA polymerase II CTD (PubMed:25464831). This
CC       counterregulates the MAP kinase (MAPK) or cyclin-dependent kinase C
CC       (CDKC)-mediated phosphorylation of CTD in response to pathogens and
CC       upon perception of microbe-associated molecular patterns (MAMPs)
CC       (PubMed:25464831). MAPKs phosphorylate and activate CDKCs, which are
CC       CTD kinases that positively regulate plant innate immunity
CC       (PubMed:25464831). Acts as a negative regulator of stress gene
CC       transcription involved in abscisic acid (ABA) mediated signaling
CC       pathway and cold resistance (PubMed:12149434, PubMed:16905668). Acts as
CC       a post-transcriptional gene silencing (PTGS) suppressor
CC       (PubMed:31076735). {ECO:0000269|PubMed:12149434,
CC       ECO:0000269|PubMed:16905668, ECO:0000269|PubMed:25464831,
CC       ECO:0000269|PubMed:31076735}.
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         Evidence={ECO:0000269|PubMed:12149434};
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         Evidence={ECO:0000269|PubMed:12149434};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000250|UniProtKB:Q5YDB6};
CC       Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC         Evidence={ECO:0000250|UniProtKB:Q5YDB6};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000250|UniProtKB:Q5YDB6};
CC       Note=Binds Mg(2+), Co(2+) or Mn(2+). {ECO:0000250|UniProtKB:Q5YDB6};
CC   -!- SUBUNIT: Interacts with RAP74. {ECO:0000269|PubMed:16905668}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:16905668,
CC       ECO:0000269|PubMed:25464831}.
CC   -!- INDUCTION: By NaCl. {ECO:0000269|PubMed:16905668}.
CC   -!- DOMAIN: The BRCT domain is required for interaction with RAP74.
CC   -!- DISRUPTION PHENOTYPE: Grows more slowly and flower earlier than wild-
CC       type plants. ABA hyperactivation of stress-inducible genes.
CC       {ECO:0000269|PubMed:12149434, ECO:0000269|PubMed:16905668}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAB80671.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AF486633; AAM94371.1; -; mRNA.
DR   EMBL; AC002332; AAB80671.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CP002685; AEC08850.1; -; Genomic_DNA.
DR   PIR; G84746; G84746.
DR   RefSeq; NP_180912.2; NM_128914.3.
DR   AlphaFoldDB; Q8LL04; -.
DR   SMR; Q8LL04; -.
DR   BioGRID; 3266; 2.
DR   STRING; 3702.Q8LL04; -.
DR   iPTMnet; Q8LL04; -.
DR   PaxDb; 3702-AT2G33540-1; -.
DR   ProteomicsDB; 220439; -.
DR   EnsemblPlants; AT2G33540.1; AT2G33540.1; AT2G33540.
DR   GeneID; 817919; -.
DR   Gramene; AT2G33540.1; AT2G33540.1; AT2G33540.
DR   KEGG; ath:AT2G33540; -.
DR   Araport; AT2G33540; -.
DR   TAIR; AT2G33540; CPL3.
DR   eggNOG; KOG0323; Eukaryota.
DR   HOGENOM; CLU_007943_0_0_1; -.
DR   InParanoid; Q8LL04; -.
DR   OMA; MRDLYKY; -.
DR   OrthoDB; 11699at2759; -.
DR   PhylomeDB; Q8LL04; -.
DR   PRO; PR:Q8LL04; -.
DR   Proteomes; UP000006548; Chromosome 2.
DR   ExpressionAtlas; Q8LL04; baseline and differential.
DR   GO; GO:0005634; C:nucleus; IDA:TAIR.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0017018; F:myosin phosphatase activity; IEA:UniProtKB-EC.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0008420; F:RNA polymerase II CTD heptapeptide repeat phosphatase activity; IEA:InterPro.
DR   GO; GO:0006952; P:defense response; IEA:UniProtKB-KW.
DR   GO; GO:0009788; P:negative regulation of abscisic acid-activated signaling pathway; IMP:UniProtKB.
DR   GO; GO:1900369; P:negative regulation of post-transcriptional gene silencing by regulatory ncRNA; IGI:TAIR.
DR   GO; GO:0009651; P:response to salt stress; IEP:UniProtKB.
DR   CDD; cd17729; BRCT_CTDP1; 1.
DR   CDD; cd07521; HAD_FCP1-like; 1.
DR   Gene3D; 3.40.50.10190; BRCT domain; 1.
DR   Gene3D; 3.40.50.1000; HAD superfamily/HAD-like; 1.
DR   InterPro; IPR001357; BRCT_dom.
DR   InterPro; IPR036420; BRCT_dom_sf.
DR   InterPro; IPR039189; Fcp1.
DR   InterPro; IPR004274; FCP1_dom.
DR   InterPro; IPR011947; FCP1_euk.
DR   InterPro; IPR036412; HAD-like_sf.
DR   InterPro; IPR023214; HAD_sf.
DR   NCBIfam; TIGR02250; FCP1_euk; 1.
DR   PANTHER; PTHR23081:SF2; RNA POLYMERASE II C-TERMINAL DOMAIN PHOSPHATASE-LIKE 3; 1.
DR   PANTHER; PTHR23081; RNA POLYMERASE II CTD PHOSPHATASE; 1.
DR   Pfam; PF00533; BRCT; 1.
DR   Pfam; PF03031; NIF; 1.
DR   SMART; SM00292; BRCT; 1.
DR   SMART; SM00577; CPDc; 1.
DR   SUPFAM; SSF52113; BRCT domain; 1.
DR   SUPFAM; SSF56784; HAD-like; 1.
DR   PROSITE; PS50172; BRCT; 1.
DR   PROSITE; PS50969; FCP1; 1.
DR   Genevisible; Q8LL04; AT.
PE   1: Evidence at protein level;
KW   Hydrolase; Metal-binding; Nucleus; Plant defense; Reference proteome;
KW   Repressor; RNA-binding; Transcription; Transcription regulation.
FT   CHAIN           1..1241
FT                   /note="RNA polymerase II C-terminal domain phosphatase-like
FT                   3"
FT                   /id="PRO_0000376085"
FT   DOMAIN          923..1103
FT                   /note="FCP1 homology"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00336"
FT   DOMAIN          1146..1239
FT                   /note="BRCT"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT   REGION          361..402
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          428..470
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          505..525
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          578..598
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          677..702
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          720..800
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          852..885
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        428..443
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        450..468
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        750..773
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        863..885
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MUTAGEN         933
FT                   /note="D->A: Loss of phosphatase activity."
FT                   /evidence="ECO:0000269|PubMed:25464831"
FT   MUTAGEN         1064
FT                   /note="D->A: Loss of phosphatase activity; when associated
FT                   with A-1065."
FT                   /evidence="ECO:0000269|PubMed:25464831"
FT   MUTAGEN         1065
FT                   /note="D->A: Loss of phosphatase activity; when associated
FT                   with A-1064."
FT                   /evidence="ECO:0000269|PubMed:25464831"
FT   CONFLICT        1010
FT                   /note="A -> V (in Ref. 1; AAM94371)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   1241 AA;  136479 MW;  CEFFBD725719D404 CRC64;
     MLVARSGCSR TLIRMGNDEN LMVMVDVEEG EIPDSVNTEI EVKHKSTTTT ADVGGDVDVG
     VVAGGRGGGG GGSNGNSRVW TMEELISQYP AYRPYANSGL SNLAWARAVQ NKPFNEGLVM
     DYEPRESDKI VIEDSDDEKE EGELEEGEID LVDNASDDNL VEKDTESVVL ISADKVEDDR
     ILKERDLEKK VKLIRGVLES TSLVEAQTGF EGVCSRILGA LESLRELVSD NDDFPKRDTL
     VQLSFASLQT INYVFCSMNN ISKERNKETM SRLLTLVNDH FSQFLSFNQK NEIETMNQDL
     SRSAIAVFAG TSSEENVNQM TQPSNGDSFL AKKLTSESTH RGAAYLRSRL PMLPLLDLHK
     DHDADSLPSP TRETTPSLPV NGRHTMVRPG FPVGRESQTT EGAKVYSYES DARKAVSTYQ
     QKFGLNSVFK TDDLPSPTPS GEPNDGNGDV GGEVSSSVVK SSNPGSHLIY GQDVPLPSNF
     NSRSMPVANS VSSTVPPHHL SIHAISAPTA SDQTVKPSAK SRDPRLRLAK PDAANVTIYS
     YSSGDARNLS KVELSADLVN PRKQKAADEF LIDGPAWKRQ KSDTDAPKAA GTGGWLEDTE
     SSGLLKLESK PRLIENGVTS MTSSVMPTSA VSVSQKVRTA STDTASLQSL LKDIAVNPTM
     LLNLLKMGER QKVPEKAIQK PMDPRRAAQL PGSSVQPGVS TPLSIPASNA LAANSLNSGV
     LQDSSQNAPA AESGSIRMKP RDPRRILHGS TLQRTDSSME KQTKVNDPST LGTLTMKGKA
     EDLETPPQLD PRQNISQNGT SKMKISGELL SGKTPDFSTQ FTKNLKSIAD MVVVSQQLGN
     PPASMHSVQL KTERDVKHNP SNPNAQDEDV SVSAASVTAA AGPTRSMNSW GDVEHLFEGY
     DDIQRVAIQR ERVRRLEEQN KMFASQKLSL VLDIDHTLLN SAKFNEVESR HEEILRKKEE
     QDREKPYRHL FRFLHMGMWT KLRPGIWNFL EKASKLYELH LYTMGNKLYA TEMAKLLDPK
     GVLFNGRVIS KGDDGDPLDG DERVPKSKDL EGVMGMESSV VIIDDSVRVW PQHKMNLIAV
     ERYLYFPCSR RQFGLLGPSL LELDRDEVPE EGTLASSLAV IEKIHQNFFS HTSLDEVDVR
     NILASEQRKI LAGCRIVFSR IIPVGEAKPH LHPLWQTAEQ FGAVCTTQVD EHVTHVVTNS
     LGTDKVNWAL TRGRFVVHPG WVEASAFLYQ RANENLYAIN P
//