ID   CPL2_ARATH              Reviewed;         770 AA.
AC   Q5YDB5; F4K803; Q9LFA9;
DT   26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT   16-NOV-2011, sequence version 3.
DT   24-JAN-2024, entry version 133.
DE   RecName: Full=RNA polymerase II C-terminal domain phosphatase-like 2 {ECO:0000303|PubMed:15388846};
DE            Short=FCP-like 2 {ECO:0000303|PubMed:15388846};
DE            EC=3.1.3.16 {ECO:0000269|PubMed:15388846};
DE   AltName: Full=ASI1-immunoprecipitated protein 4 {ECO:0000303|PubMed:28808009};
DE   AltName: Full=Carboxyl-terminal phosphatase-like 2 {ECO:0000303|PubMed:15388846};
DE            Short=AtCPL2 {ECO:0000303|PubMed:15388846};
DE            Short=CTD phosphatase-like 2 {ECO:0000303|PubMed:15388846};
GN   Name=CPL2 {ECO:0000303|PubMed:15388846};
GN   Synonyms=AIPP4 {ECO:0000303|PubMed:28808009};
GN   OrderedLocusNames=At5g01270 {ECO:0000312|Araport:AT5G01270};
GN   ORFNames=F7J8.250 {ECO:0000312|EMBL:CAB69855.1};
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, DISRUPTION PHENOTYPE, CATALYTIC
RP   ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR LOCATION, AND
RP   COFACTOR.
RX   PubMed=15388846; DOI=10.1073/pnas.0403174101;
RA   Koiwa H., Hausmann S., Bang W.Y., Ueda A., Kondo N., Hiraguri A.,
RA   Fukuhara T., Bahk J.D., Yun D.-J., Bressan R.A., Hasegawa P.M., Shuman S.;
RT   "Arabidopsis C-terminal domain phosphatase-like 1 and 2 are essential Ser-
RT   5-specific C-terminal domain phosphatases.";
RL   Proc. Natl. Acad. Sci. U.S.A. 101:14539-14544(2004).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=11130714; DOI=10.1038/35048507;
RA   Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA   Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA   Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA   Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA   Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA   O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA   Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA   Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA   Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA   Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA   Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA   Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA   Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA   Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA   Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA   Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA   McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA   Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA   Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA   Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA   Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA   Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA   Bevan M., Fransz P.F.;
RT   "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL   Nature 408:823-826(2000).
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, TISSUE SPECIFICITY, AND DISRUPTION PHENOTYPE.
RX   PubMed=18506580; DOI=10.1007/s11103-008-9348-y;
RA   Ueda A., Li P., Feng Y., Vikram M., Kim S., Kang C.H., Kang J.S.,
RA   Bahk J.D., Lee S.Y., Fukuhara T., Staswick P.E., Pepper A.E., Koiwa H.;
RT   "The Arabidopsis thaliana carboxyl-terminal domain phosphatase-like 2
RT   regulates plant growth, stress and auxin responses.";
RL   Plant Mol. Biol. 67:683-697(2008).
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   INTERACTION WITH RCF3.
RX   PubMed=26512101; DOI=10.1073/pnas.1512865112;
RA   Karlsson P., Christie M.D., Seymour D.K., Wang H., Wang X., Hagmann J.,
RA   Kulcheski F., Manavella P.A.;
RT   "KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA
RT   biogenesis cofactor HYL1.";
RL   Proc. Natl. Acad. Sci. U.S.A. 112:14096-14101(2015).
RN   [7]
RP   FUNCTION, DISRUPTION PHENOTYPE, SUBUNIT, AND INTERACTION WITH AIPP2.
RC   STRAIN=cv. Columbia;
RX   PubMed=28808009; DOI=10.1073/pnas.1710683114;
RA   Duan C.-G., Wang X., Zhang L., Xiong X., Zhang Z., Tang K., Pan L.,
RA   Hsu C.-C., Xu H., Tao W.A., Zhang H., Zhu J.-K.;
RT   "A protein complex regulates RNA processing of intronic heterochromatin-
RT   containing genes in Arabidopsis.";
RL   Proc. Natl. Acad. Sci. U.S.A. 114:E7377-E7384(2017).
RN   [8]
RP   FUNCTION, DISRUPTION PHENOTYPE, SUBUNIT, INTERACTION WITH AIPP2 AND PAIPP2,
RP   AND TISSUE SPECIFICITY.
RC   STRAIN=cv. Columbia;
RX   PubMed=33277495; DOI=10.1038/s41467-020-20089-0;
RA   Zhang Y.-Z., Yuan J., Zhang L., Chen C., Wang Y., Zhang G., Peng L.,
RA   Xie S.-S., Jiang J., Zhu J.-K., Du J., Duan C.-G.;
RT   "Coupling of H3K27me3 recognition with transcriptional repression through
RT   the BAH-PHD-CPL2 complex in Arabidopsis.";
RL   Nat. Commun. 11:6212-6212(2020).
RN   [9]
RP   SUBUNIT.
RC   STRAIN=cv. Columbia;
RX   PubMed=33433058; DOI=10.1111/jipb.13067;
RA   Qian F., Zhao Q.-Y., Zhang T.-N., Li Y.-L., Su Y.-N., Li L., Sui J.-H.,
RA   Chen S., He X.-J.;
RT   "A histone H3K27me3 reader cooperates with a family of PHD finger-
RT   containing proteins to regulate flowering time in Arabidopsis.";
RL   J. Integr. Plant Biol. 63:787-802(2021).
CC   -!- FUNCTION: Processively dephosphorylates 'Ser-5' but not 'Ser-2' of the
CC       heptad repeats YSPTSPS in the C-terminal domain of the largest RNA
CC       polymerase II subunit (RPB1). This promotes the activity of RNA
CC       polymerase II. Together with CPL1, required for male gametes fertility.
CC       Multifunctional regulator that modulates plant growth, stress, and
CC       phytohormones responses. Positive transcription regulator of genes
CC       involved in high salinity resistance and auxin mediated signaling
CC       pathway. Prevents the accumulation of intronic heterochromatin-
CC       containing genes (e.g. IBM1, At3g05410 and RPP7) (PubMed:28808009).
CC       Recruited at histone H3 lysine 27 trimethylation (H3K27me3) marks and
CC       low-methylated H3K4 by the BAH-PHD bivalent histone reader complex to
CC       form a BAH-PHD-CPL2 complex (BPC) in order to silence several H3K27me3
CC       and low-methylated H3K4 enriched loci, including AGO5, via the
CC       phosphorylation state-dependent inhibition of Pol II release from the
CC       transcriptional start site (e.g. Ser5P-Pol II dephosphorylation)
CC       (PubMed:33277495). The BPC complex represses flowering by inhibiting
CC       the expression of several genes, including AGL6, FT, FUL and SOC1
CC       (PubMed:33277495). {ECO:0000269|PubMed:15388846,
CC       ECO:0000269|PubMed:18506580, ECO:0000269|PubMed:28808009,
CC       ECO:0000269|PubMed:33277495}.
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:15388846};
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:15388846};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000269|PubMed:15388846};
CC       Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC         Evidence={ECO:0000269|PubMed:15388846};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000269|PubMed:15388846};
CC       Note=Binds Mg(2+), Co(2+) or Mn(2+). {ECO:0000269|PubMed:15388846};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       pH dependence:
CC         Optimum pH is 5.5-6.0. {ECO:0000269|PubMed:15388846};
CC   -!- SUBUNIT: Interacts with RCF3 (PubMed:26512101). Component of the ASI1-
CC       AIPP1-EDM2 (AAE) RNA regulatory complex composed of at least
CC       AIPP1/EDM3, ASI1 and EDM2 and may contain CPL2, AIPP2 and AIPP3/BDT1
CC       (PubMed:28808009). Associates with the BAH-PHD module that contains
CC       AIPP2, PAIPP2 and AIPP3/BDT1 to form the BAH-PHD-CPL2 complex (BPC) for
CC       transcriptional repression (PubMed:33277495, PubMed:33433058). Binds
CC       directly to AIPP2 and PAIPP2 (PubMed:28808009, PubMed:33277495).
CC       {ECO:0000269|PubMed:26512101, ECO:0000269|PubMed:28808009,
CC       ECO:0000269|PubMed:33277495, ECO:0000269|PubMed:33433058}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:15388846}. Cytoplasm
CC       {ECO:0000269|PubMed:15388846}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=1;
CC         Comment=A number of isoforms are produced. According to EST
CC         sequences.;
CC       Name=1;
CC         IsoId=Q5YDB5-1; Sequence=Displayed;
CC   -!- TISSUE SPECIFICITY: Expressed in seedlings, particularly in tissues
CC       undergoing cell division and expansion, petioles, cotyledons
CC       vasculature, leaves, shoot and root meristems, and flowers, especially
CC       in buds and organs vasculatures. {ECO:0000269|PubMed:18506580,
CC       ECO:0000269|PubMed:33277495}.
CC   -!- DISRUPTION PHENOTYPE: The mutant cpl2-2 exhibits multiple developmental
CC       defects, such as a dwarfed size, early flowering, small leaves and poor
CC       fertility (PubMed:33277495). Abnormally up-regulated expression of many
CC       genes localized at H3K27me3 and low-methylated H3K4 enriched loci
CC       associated with an higher accumulation of activated RNA polymerase II
CC       phosphorylated at Ser-5 (Ser5P-Pol II) (PubMed:33277495). Increased
CC       salt (NaCl) sensitivity. Produces shorter hypocotyls than wild-type
CC       plants in the light, but not in the dark. Enhanced accumulation of
CC       intronic heterochromatin (HC)-containing genes functional full-length
CC       transcripts (e.g. IBM1, At3g05410 and RPP7) (PubMed:28808009).
CC       Increased expression of At4g16870, a transposable element (TE) of
CC       Copia-like retrotransposon origin, associated with methylated status
CC       (PubMed:28808009). {ECO:0000269|PubMed:15388846,
CC       ECO:0000269|PubMed:18506580, ECO:0000269|PubMed:28808009,
CC       ECO:0000269|PubMed:33277495}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=CAB69855.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AY557187; AAT52023.1; -; mRNA.
DR   EMBL; AL137189; CAB69855.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CP002688; AED90320.1; -; Genomic_DNA.
DR   PIR; T45967; T45967.
DR   RefSeq; NP_195747.2; NM_120205.5. [Q5YDB5-1]
DR   AlphaFoldDB; Q5YDB5; -.
DR   STRING; 3702.Q5YDB5; -.
DR   PaxDb; 3702-AT5G01270-2; -.
DR   ProteomicsDB; 222635; -. [Q5YDB5-1]
DR   EnsemblPlants; AT5G01270.1; AT5G01270.1; AT5G01270. [Q5YDB5-1]
DR   GeneID; 831743; -.
DR   Gramene; AT5G01270.1; AT5G01270.1; AT5G01270. [Q5YDB5-1]
DR   KEGG; ath:AT5G01270; -.
DR   Araport; AT5G01270; -.
DR   TAIR; AT5G01270; CPL2.
DR   eggNOG; KOG0323; Eukaryota.
DR   HOGENOM; CLU_010333_0_0_1; -.
DR   InParanoid; Q5YDB5; -.
DR   OMA; RSEELCV; -.
DR   PRO; PR:Q5YDB5; -.
DR   Proteomes; UP000006548; Chromosome 5.
DR   ExpressionAtlas; Q5YDB5; baseline and differential.
DR   GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR   GO; GO:0005634; C:nucleus; IDA:UniProtKB.
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:0004722; F:protein serine/threonine phosphatase activity; IDA:UniProtKB.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0008420; F:RNA polymerase II CTD heptapeptide repeat phosphatase activity; IBA:GO_Central.
DR   GO; GO:0009734; P:auxin-activated signaling pathway; IMP:UniProtKB.
DR   GO; GO:0045814; P:negative regulation of gene expression, epigenetic; IDA:UniProtKB.
DR   GO; GO:0034244; P:negative regulation of transcription elongation by RNA polymerase II; IMP:UniProtKB.
DR   GO; GO:0010468; P:regulation of gene expression; IMP:GO_Central.
DR   GO; GO:2000028; P:regulation of photoperiodism, flowering; IMP:UniProtKB.
DR   CDD; cd10845; DSRM_RNAse_III_family; 1.
DR   CDD; cd07521; HAD_FCP1-like; 1.
DR   Gene3D; 3.30.160.20; -; 1.
DR   Gene3D; 3.40.50.1000; HAD superfamily/HAD-like; 1.
DR   InterPro; IPR014720; dsRBD_dom.
DR   InterPro; IPR039189; Fcp1.
DR   InterPro; IPR004274; FCP1_dom.
DR   InterPro; IPR036412; HAD-like_sf.
DR   InterPro; IPR023214; HAD_sf.
DR   PANTHER; PTHR23081:SF24; RNA POLYMERASE II C-TERMINAL DOMAIN PHOSPHATASE-LIKE 2; 1.
DR   PANTHER; PTHR23081; RNA POLYMERASE II CTD PHOSPHATASE; 1.
DR   Pfam; PF00035; dsrm; 1.
DR   Pfam; PF03031; NIF; 1.
DR   SMART; SM00577; CPDc; 1.
DR   SMART; SM00358; DSRM; 1.
DR   SUPFAM; SSF54768; dsRNA-binding domain-like; 1.
DR   SUPFAM; SSF56784; HAD-like; 1.
DR   PROSITE; PS50137; DS_RBD; 1.
DR   PROSITE; PS50969; FCP1; 1.
DR   Genevisible; Q5YDB5; AT.
PE   1: Evidence at protein level;
KW   Activator; Alternative splicing; Auxin signaling pathway; Cytoplasm;
KW   Developmental protein; Hydrolase; Metal-binding; Nucleus;
KW   Reference proteome; RNA-binding; Transcription; Transcription regulation.
FT   CHAIN           1..770
FT                   /note="RNA polymerase II C-terminal domain phosphatase-like
FT                   2"
FT                   /id="PRO_0000376084"
FT   DOMAIN          134..385
FT                   /note="FCP1 homology"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00336"
FT   DOMAIN          656..722
FT                   /note="DRBM"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00266"
FT   REGION          464..484
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          506..525
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          551..602
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          614..653
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          731..770
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        465..480
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        622..637
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        753..770
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   770 AA;  85953 MW;  7672B4F18397CB14 CRC64;
     MNRLGHKSVV YHGDLRLGEL DVNHVSSSHE FRFPNDEIRI HHLSPAGERC PPLAILQTIA
     SFAVRCKLES SAPVKSQELM HLHAVCFHEL KTAVVMLGDE EIHLVAMPSK EKKFPCFWCF
     SVPSGLYDSC LRMLNTRCLS IVFDLDETLI VANTMKSFED RIEALKSWIS REMDPVRING
     MSAELKRYMD DRMLLKQYID NDYAFDNGVL LKAQPEEVRP TSDGQEKVCR PVIRLPEKNT
     VLTRIKPEIR DTSVLVKLRP AWEELRSYLT AKTRKRFEVY VCTMAERDYA LEMWRLLDPE
     AHLISLKELR DRIVCVKPDA KKSLLSVFNG GICHPKMAMV IDDRMKVWED KDQPRVHVVS
     AYLPYYAPQA ETALVVPHLC VARNVACNVR GYFFKEFDES LMSSISLVYY EDDVENLPPS
     PDVSNYVVIE DPGFASNGNI NAPPINEGMC GGEVERRLNQ AAAADHSTLP ATSNAEQKPE
     TPKPQIAVIP NNASTATAAA LLPSHKPSLL GAPRRDGFTF SDGGRPLMMR PGVDIRNQNF
     NQPPILAKIP MQPPSSSMHS PGGWLVDDEN RPSFPGRPSG LYPSQFPHGT PGSAPVGPFA
     HPSHLRSEEV AMDDDLKRQN PSRQTTEGGI SQNHLVSNGR EHHTDGGKSN GGQSHLFVSA
     LQEIGRRCGS KVEFRTVIST NKELQFSVEV LFTGEKIGIG MAKTKKDAHQ QAAENALRSL
     AEKYVAHVAP LARETEKGPE NDNGFLWESS EDVSNKGLEE EAPKENISEL
//