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 Genevisible; Q8LL04; AT.
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.
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
//
