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Protein

RNA polymerase II C-terminal domain phosphatase-like 1

Gene

CPL1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Processively dephosphorylates 'Ser-5' but not 'Ser-2' of the heptad repeats YSPTSPS in the C-terminal domain of the largest RNA polymerase II subunit (RPB1). This promotes the activity of RNA polymerase II. Together with CPL2, required for male gametes fertility. Multifunctional regulator that modulates plant growth, stress, and phytohormones responses. Negative regulator of stress gene transcription involved in abscisic acid (ABA) mediated and jasmonic acid (JA) mediated signaling pathways, NaCl, osmotic stress, wounding, and cold resistance. Regulates negatively the expression of jasmonic acid (JA) biosynthetic genes in response to wounding (PubMed:11874572, PubMed:12149434, PubMed:12149453, PubMed:15388846, PubMed:18506580, PubMed:18764923). Forms a complex with RCF3 that modulates co-transcriptional processes such as mRNA capping and polyadenylation, and functions to repress stress-inducible gene expression (PubMed:23874224). Dephosphorylates RCF3 (PubMed:26227967). Involved in the dephosphorylation of EIF4A3. This dephosphorylation retains EIF4A3 in the nucleus and limits its accumulation in the cytoplasm. Is essential for the degradation of the nonsense-mediated mRNA decay (NMD) transcripts (PubMed:26887918).9 Publications

Catalytic activityi

[a protein]-serine/threonine phosphate + H2O = [a protein]-serine/threonine + phosphate.1 Publication

Cofactori

Mg2+1 Publication, Co2+1 Publication, Mn2+1 PublicationNote: Binds Mg2+, Co2+ or Mn2+.1 Publication

pH dependencei

Optimum pH is 5.5-6.0.1 Publication

GO - Molecular functioni

  • CTD phosphatase activity Source: GO_Central
  • metal ion binding Source: UniProtKB-KW
  • phosphatase activity Source: TAIR
  • phosphoprotein phosphatase activity Source: TAIR
  • phosphoserine phosphatase activity Source: UniProtKB
  • RNA binding Source: UniProtKB-KW

GO - Biological processi

  • abscisic acid-activated signaling pathway Source: TAIR
  • dephosphorylation of RNA polymerase II C-terminal domain Source: GO_Central
  • multicellular organism development Source: UniProtKB-KW
  • negative regulation of transcription, DNA-templated Source: TAIR
  • response to salt stress Source: TAIR
  • response to wounding Source: UniProtKB
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

Molecular functionDevelopmental protein, Hydrolase, Repressor, RNA-binding
Biological processAbscisic acid signaling pathway, Jasmonic acid signaling pathway, Nonsense-mediated mRNA decay, Transcription, Transcription regulation
LigandMetal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase II C-terminal domain phosphatase-like 1Curated (EC:3.1.3.161 Publication)
Short name:
FCP-like 1Curated
Alternative name(s):
Carboxyl-terminal phosphatase-like 1
Short name:
AtCPL11 Publication
Short name:
CTD phosphatase-like 1
Protein FIERY 21 Publication
Protein JASMONATE OVEREXPRESSING 11 Publication
Protein SHINY 41 Publication
Gene namesi
Name:CPL11 Publication
Synonyms:FRY21 Publication, JOE1Curated, SHI41 Publication
Ordered Locus Names:At4g21670Imported
ORF Names:F17L22.130Imported
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 4

Organism-specific databases

AraportiAT4G21670.
TAIRilocus:2119053. AT4G21670.

Subcellular locationi

GO - Cellular componenti

  • DNA-directed RNA polymerase II, holoenzyme Source: GO_Central
  • nuclear speck Source: UniProtKB-SubCell
  • nucleus Source: UniProtKB

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Grows more rapidly and flower later than wild-type plants. Increased tolerance to salt stress and to ABA during seed germination but more sensitive to freezing damage at the seedling stage, by the enhanced expression of abiotic stress-induced genes. Hypersentitivity to MeJA, accumulates high levels of anthocyanin on medium containing MeJA. Confers wound hyperresponsiveness of JA-biosynthetic genes.5 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi116E → K in cpl1-3 and shi4; enhanced expression of abiotic stress-induced genes, and cold-sensitive phenotype. 2 Publications1
Mutagenesisi161D → A: Loss of catalytic activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003760831 – 967RNA polymerase II C-terminal domain phosphatase-like 1Add BLAST967

Proteomic databases

PaxDbiQ5YDB6.
PRIDEiQ5YDB6.

PTM databases

iPTMnetiQ5YDB6.

Expressioni

Tissue specificityi

Expressed at very low levels in roots, leaves, stems, flowers and siliques.1 Publication

Inductioni

Slightly repressed by ABA.1 Publication

Interactioni

Subunit structurei

Interacts with FREE1, ANAC019, MYB3, MYB4 and MYB32. Binds to DMS3 (PubMed:18541146). Interacts with RCF3 (PubMed:23874224, PubMed:24146632, PubMed:24303021, PubMed:26512101). Interacts with RS40 and RS41 (PubMed:24146632). Interacts with EIF4A3 (PubMed:26887918). Interacts with UPF3 (PubMed:26887918).6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
SEQ9ZVD07EBI-1786459,EBI-6553299

Protein-protein interaction databases

BioGridi13543. 13 interactors.
IntActiQ5YDB6. 12 interactors.
STRINGi3702.AT4G21670.1.

Structurei

3D structure databases

ProteinModelPortaliQ5YDB6.
SMRiQ5YDB6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini151 – 401FCP1 homologyPROSITE-ProRule annotationAdd BLAST251
Domaini724 – 792DRBM 1PROSITE-ProRule annotationAdd BLAST69
Domaini855 – 925DRBM 2PROSITE-ProRule annotationAdd BLAST71

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni945 – 967Required for nuclear localization (NLS)1 PublicationAdd BLAST23

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi38 – 41Nuclear localization signal (NLS)1 Publication4
Motifi947 – 951Nuclear localization signal (NLS)1 Publication5

Domaini

DRBM domains are required for interactions with target transcription factors such as ANAC019 and MYB3.

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0323. Eukaryota.
COG5190. LUCA.
HOGENOMiHOG000078695.
InParanoidiQ5YDB6.
KOiK18998.
OMAiKKQPPHP.
OrthoDBiEOG093601BK.
PhylomeDBiQ5YDB6.

Family and domain databases

Gene3Di3.40.50.1000. 1 hit.
InterProiView protein in InterPro
IPR014720. dsRBD_dom.
IPR004274. FCP1_dom.
IPR023214. HAD-like_dom.
PfamiView protein in Pfam
PF00035. dsrm. 2 hits.
PF03031. NIF. 1 hit.
SMARTiView protein in SMART
SM00577. CPDc. 1 hit.
SM00358. DSRM. 2 hits.
SUPFAMiSSF56784. SSF56784. 2 hits.
PROSITEiView protein in PROSITE
PS50137. DS_RBD. 2 hits.
PS50969. FCP1. 1 hit.

Sequencei

Sequence statusi: Complete.

Q5YDB6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYSNNRVEVF HGDGRLGELE IYPSRELNQQ QDDVMKQRKK KQREVMELAK
60 70 80 90 100
MGIRISHFSQ SGERCPPLAI LTTISSCGLC FKLEASPSPA QESLSLFYSS
110 120 130 140 150
CLRDNKTAVM LLGGEELHLV AMYSENIKND RPCFWAFSVA PGIYDSCLVM
160 170 180 190 200
LNLRCLGIVF DLDETLVVAN TMRSFEDKID GFQRRINNEM DPQRLAVIVA
210 220 230 240 250
EMKRYQDDKN LLKQYIESDQ VVENGEVIKV QSEIVPALSD NHQPLVRPLI
260 270 280 290 300
RLQEKNIILT RINPMIRDTS VLVRMRPSWE ELRSYLTAKG RKRFEVYVCT
310 320 330 340 350
MAERDYALEM WRLLDPEGNL INTNDLLARI VCVKSGFKKS LFNVFLDGTC
360 370 380 390 400
HPKMALVIDD RLKVWDEKDQ PRVHVVPAFA PYYSPQAEAA ATPVLCVARN
410 420 430 440 450
VACGVRGGFF RDFDDSLLPR IAEISYENDA EDIPSPPDVS HYLVSEDDTS
460 470 480 490 500
GLNGNKDPLS FDGMADTEVE RRLKEAISAS SAVLPAANID PRIAAPVQFP
510 520 530 540 550
MASASSVSVP VPVQVVQQAI QPSAMAFPSI PFQQPQQPTS IAKHLVPSEP
560 570 580 590 600
SLQSSPAREE GEVPESELDP DTRRRLLILQ HGQDTRDPAP SEPSFPQRPP
610 620 630 640 650
VQAPPSHVQS RNGWFPVEEE MDPAQIRRAV SKEYPLDSEM IHMEKHRPRH
660 670 680 690 700
PSFFSKIDNS TQSDRMLHEN RRPPKESLRR DEQLRSNNNL PDSHPFYGED
710 720 730 740 750
ASWNQSSSRN SDLDFLPERS VSATETSADV LHGIAIKCGA KVEYKPSLVS
760 770 780 790 800
STDLRFSVEA WLSNQKIGEG IGKSRREALH KAAEASIQNL ADGYMRANGD
810 820 830 840 850
PGPSHRDATP FTNENISMGN ANALNNQPFA RDETALPVSS RPTDPRLEGS
860 870 880 890 900
MRHTGSITAL RELCASEGLE MAFQSQRQLP SDMVHRDELH AQVEIDGRVV
910 920 930 940 950
GEGVGSTWDE ARMQAAERAL SSVRSMLGQP LHKRQGSPRS FGGMSNKRLK
960
PDFQRSLQRM PSSGRYS
Length:967
Mass (Da):108,421
Last modified:November 23, 2004 - v1
Checksum:i3FD10F0F3A73154D
GO

Sequence cautioni

The sequence CAB36811 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence CAB81274 differs from that shown. Reason: Erroneous gene model prediction.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti446E → V in BAF01152 (Ref. 4) Curated1
Sequence conflicti669E → V in BAD94401 (Ref. 4) Curated1
Sequence conflicti797A → T in BAD94401 (Ref. 4) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY557186 mRNA. Translation: AAT52022.1.
AL035527 Genomic DNA. Translation: CAB36811.1. Sequence problems.
AL161555 Genomic DNA. Translation: CAB81274.1. Sequence problems.
CP002687 Genomic DNA. Translation: AEE84488.1.
AK221944 mRNA. Translation: BAD94401.1.
AK229289 mRNA. Translation: BAF01152.1.
PIRiT05842.
RefSeqiNP_193898.3. NM_118287.5.
UniGeneiAt.2700.
At.32611.

Genome annotation databases

EnsemblPlantsiAT4G21670.1; AT4G21670.1; AT4G21670.
GeneIDi828254.
GrameneiAT4G21670.1; AT4G21670.1; AT4G21670.
KEGGiath:AT4G21670.

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.

Entry informationi

Entry nameiCPL1_ARATH
AccessioniPrimary (citable) accession number: Q5YDB6
Secondary accession number(s): Q0WNZ7, Q56WT8, Q9SVT0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 26, 2009
Last sequence update: November 23, 2004
Last modified: June 7, 2017
This is version 97 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names