VCS_ARATH
ID VCS_ARATH Reviewed; 1344 AA.
AC Q9LTT8; F4JC94; Q0WLC5; Q56YT1; Q8L7N9;
DT 11-JUL-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 25-MAY-2022, entry version 146.
DE RecName: Full=Enhancer of mRNA-decapping protein 4;
DE AltName: Full=Protein VARICOSE;
GN Name=VCS; Synonyms=EDC4; OrderedLocusNames=At3g13300; ORFNames=MDC11.13;
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=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(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] OF 571-1344 (ISOFORMS 1/2).
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, DISRUPTION PHENOTYPE, DEVELOPMENTAL STAGE, TISSUE SPECIFICITY,
RP AND INDUCTION BY AUXIN.
RC STRAIN=cv. Columbia;
RX PubMed=14660546; DOI=10.1242/dev.00909;
RA Deyholos M.K., Cavaness G.F., Hall B., King E., Punwani J., Van Norman J.,
RA Sieburth L.E.;
RT "VARICOSE, a WD-domain protein, is required for leaf blade development.";
RL Development 130:6577-6588(2003).
RN [6]
RP FUNCTION, INTERACTION WITH DCP2, SUBCELLULAR LOCATION, DISRUPTION
RP PHENOTYPE, AND TISSUE SPECIFICITY.
RX PubMed=17158604; DOI=10.1105/tpc.106.047605;
RA Xu J., Yang J.-Y., Niu Q.-W., Chua N.-H.;
RT "Arabidopsis DCP2, DCP1, and VARICOSE form a decapping complex required for
RT postembryonic development.";
RL Plant Cell 18:3386-3398(2006).
RN [7]
RP FUNCTION, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE, INTERACTION WITH
RP DCP2, AND HOMODIMER.
RC STRAIN=cv. Columbia;
RX PubMed=17513503; DOI=10.1105/tpc.106.047621;
RA Goeres D.C., Van Norman J.M., Zhang W., Fauver N.A., Spencer M.L.,
RA Sieburth L.E.;
RT "Components of the Arabidopsis mRNA decapping complex are required for
RT early seedling development.";
RL Plant Cell 19:1549-1564(2007).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-660 AND SER-692, AND
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 [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-98, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE 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 [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-86; SER-98; SER-660 AND
RP SER-692, AND 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: As a component of the decapping complex, involved in the
CC degradation of mRNAs. Essential for postembryonic development,
CC especially during the formation of the shoot (SAM) and root apical
CC meristems. Required for normal patterning of internal tissues of
CC leaves. {ECO:0000269|PubMed:14660546, ECO:0000269|PubMed:17158604,
CC ECO:0000269|PubMed:17513503}.
CC -!- SUBUNIT: Homodimer. Component of the decapping complex. Interacts with
CC DCP2. {ECO:0000269|PubMed:17158604, ECO:0000269|PubMed:17513503}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm, P-body {ECO:0000269|PubMed:17158604,
CC ECO:0000269|PubMed:17513503}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9LTT8-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9LTT8-2; Sequence=VSP_044027;
CC -!- TISSUE SPECIFICITY: Present in seedlings, roots, hypocotyls,
CC cotyledons, leaves, stems, shoot apex, siliques and flowers. In leaves,
CC particularly present in trichomes, some stomata and vascular tissues.
CC {ECO:0000269|PubMed:14660546, ECO:0000269|PubMed:17158604}.
CC -!- DEVELOPMENTAL STAGE: At early leaf developmental stages, expressed in a
CC spot at the distal end of the organ. As leaf development progresses,
CC present in procambium and differentiating vascular tissues.
CC {ECO:0000269|PubMed:14660546}.
CC -!- INDUCTION: By auxin. {ECO:0000269|PubMed:14660546}.
CC -!- DISRUPTION PHENOTYPE: Lethal phenotype at the seedling cotyledon stage
CC that are small and chlorotic, with disorganized veins, swollen root
CC hairs, and altered epidermal cell morphology as well as leaf and shoot
CC apical meristem defects. Altered RNA decay. These phenotypes are
CC suppressed at low temperature. {ECO:0000269|PubMed:14660546,
CC ECO:0000269|PubMed:17158604, ECO:0000269|PubMed:17513503}.
CC -!- SIMILARITY: Belongs to the WD repeat EDC4 family. {ECO:0000305}.
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DR EMBL; AB024034; BAB02799.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75330.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75331.1; -; Genomic_DNA.
DR EMBL; AY128341; AAM91544.1; -; mRNA.
DR EMBL; AK230280; BAF02082.1; -; mRNA.
DR EMBL; AK221240; BAD93855.1; -; mRNA.
DR RefSeq; NP_187938.2; NM_112175.3. [Q9LTT8-1]
DR RefSeq; NP_850576.1; NM_180245.2. [Q9LTT8-2]
DR AlphaFoldDB; Q9LTT8; -.
DR BioGRID; 5864; 11.
DR DIP; DIP-61422N; -.
DR IntAct; Q9LTT8; 8.
DR MINT; Q9LTT8; -.
DR STRING; 3702.AT3G13300.1; -.
DR iPTMnet; Q9LTT8; -.
DR MetOSite; Q9LTT8; -.
DR PaxDb; Q9LTT8; -.
DR PRIDE; Q9LTT8; -.
DR ProMEX; Q9LTT8; -.
DR ProteomicsDB; 242330; -. [Q9LTT8-1]
DR EnsemblPlants; AT3G13300.1; AT3G13300.1; AT3G13300. [Q9LTT8-1]
DR EnsemblPlants; AT3G13300.2; AT3G13300.2; AT3G13300. [Q9LTT8-2]
DR GeneID; 820530; -.
DR Gramene; AT3G13300.1; AT3G13300.1; AT3G13300. [Q9LTT8-1]
DR Gramene; AT3G13300.2; AT3G13300.2; AT3G13300. [Q9LTT8-2]
DR KEGG; ath:AT3G13300; -.
DR Araport; AT3G13300; -.
DR TAIR; locus:2088165; AT3G13300.
DR eggNOG; KOG1916; Eukaryota.
DR InParanoid; Q9LTT8; -.
DR OMA; ASANHNP; -.
DR OrthoDB; 1424637at2759; -.
DR PhylomeDB; Q9LTT8; -.
DR PRO; PR:Q9LTT8; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LTT8; baseline and differential.
DR Genevisible; Q9LTT8; AT.
DR GO; GO:0000932; C:P-body; IDA:TAIR.
DR GO; GO:0003729; F:mRNA binding; HDA:TAIR.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0071365; P:cellular response to auxin stimulus; IMP:UniProtKB.
DR GO; GO:0031087; P:deadenylation-independent decapping of nuclear-transcribed mRNA; IDA:TAIR.
DR GO; GO:0009965; P:leaf morphogenesis; IMP:TAIR.
DR GO; GO:0006402; P:mRNA catabolic process; IMP:TAIR.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0009791; P:post-embryonic development; IMP:UniProtKB.
DR GO; GO:0010072; P:primary shoot apical meristem specification; IMP:UniProtKB.
DR GO; GO:0010071; P:root meristem specification; IMP:UniProtKB.
DR Gene3D; 1.10.220.100; -; 1.
DR Gene3D; 2.130.10.10; -; 1.
DR InterPro; IPR045152; EDC4-like.
DR InterPro; IPR044938; EDC4_C.
DR InterPro; IPR032401; EDC4_WD40.
DR InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
DR InterPro; IPR001680; WD40_repeat.
DR InterPro; IPR036322; WD40_repeat_dom_sf.
DR PANTHER; PTHR15598; PTHR15598; 1.
DR Pfam; PF16529; Ge1_WD40; 1.
DR SMART; SM00320; WD40; 2.
DR SUPFAM; SSF50978; SSF50978; 1.
DR PROSITE; PS50082; WD_REPEATS_2; 2.
DR PROSITE; PS50294; WD_REPEATS_REGION; 2.
PE 1: Evidence at protein level;
KW Alternative splicing; Coiled coil; Cytoplasm; mRNA processing;
KW Phosphoprotein; Reference proteome; Repeat; WD repeat.
FT CHAIN 1..1344
FT /note="Enhancer of mRNA-decapping protein 4"
FT /id="PRO_0000418337"
FT REPEAT 235..275
FT /note="WD 1"
FT REPEAT 354..394
FT /note="WD 2"
FT REPEAT 397..443
FT /note="WD 3"
FT DOMAIN 1186..1230
FT /note="LEM"
FT REGION 1..88
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 616..649
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 711..735
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 762..815
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 845..896
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 925..946
FT /evidence="ECO:0000255"
FT COILED 1147..1178
FT /evidence="ECO:0000255"
FT COMPBIAS 25..39
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 44..88
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 712..728
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 764..815
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 86
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:19376835"
FT MOD_RES 98
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19245862,
FT ECO:0007744|PubMed:19376835"
FT MOD_RES 660
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18433157,
FT ECO:0007744|PubMed:19376835"
FT MOD_RES 692
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18433157,
FT ECO:0007744|PubMed:19376835"
FT VAR_SEQ 6..40
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_044027"
FT CONFLICT 572
FT /note="S -> C (in Ref. 4; BAF02082)"
FT /evidence="ECO:0000305"
FT CONFLICT 808
FT /note="D -> N (in Ref. 3; AAM91544)"
FT /evidence="ECO:0000305"
FT CONFLICT 1075
FT /note="A -> S (in Ref. 4; BAD93855)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1344 AA; 145720 MW; 5A32D32C46AB5BF4 CRC64;
MASSPGNTNP HNTPPFDLGI LFKPSSNPYP PPAASYPPPT GPFLHNQYDQ QHYAPPGISA
QPSPVTQQQQ DVSSSSAATN LHPQRTLSYP TPPLNLQSPR SNHNPGTHIL ALLNNTNNGA
PVANQEPSHQ LPVVNHNEIA RSFPGGSGPI RVPSCKLPKG RRLIGEHAVY DVDVRLQGEI
QPQLEVTPIT KYGSDPQLVV GRQIAVNKVY ICYGLKGGNI RVLNINTALR SLFRGHSQRV
TDMAFFAEDV DMLASVSLDG KVFVWKISEG SEGEDQPQIT GKIVLALQIL GEEDTKHPRV
CWHCHKQEIL VVSIGKHVLR IDTTKVGRGE VFSAEAPLQC PLDKLIDGVQ IVGKHDGEVT
DLSMCQWMTT RLVSSSVDGT IKIWQDRKAQ PLVVLRPHDG HPVSSATFVT SPERPDHIIL
ITGGPLNREM KIWVSAGEEG WLLPADAESW RCTQTLDLKS STEPRAEEAF FNQVIALSEA
GLLLLANAKR NALYAVHLDY GSSPVGTRMD YLSEFTVTMP ILSFIGTNDP PEEPIVKVYC
VQTLAIQQYT LDLCLCLPPP IENMGLEKSD SSVSREANLV EGMSEPSGLK PTDLPSVDSV
PKPSIIVNRS ESANKLSFPS AEATSQAIVP PNGEPKTSGL PSQTSGAGSA YATLPQLPLS
PRLSSKLSGY HTPVEAIEPV IPHHELGGKT PSADYSVDRQ MDAVGERNLD VSSVEEISRS
KDSNVTPDDD VSGMRSPSAF FKHPTHLVTP SEILMGVSSA EASITTEDRR DRDANIQDVN
NDPRDTEVEV KEISEARSTQ NGEINDHDET ENCTSENREK VFCSQVSNLS TEMARDCYPS
TEGTFIPGES KAYGQPIKAG DESGVDSRGG PAKLLKGKKQ KAKNSQGPGL SSTSSNVANL
ADSFNEQSQS LSHPMTDLLP QLLAMQETMN QVMASQKEMQ RQLSNAATGP IGKESKRLEV
ALGRMIEKSS KSNADALWAR IQEETVKNEK ALRDHAQQIV NATTNFMSKE LNAMFEKTIK
KELAAIGPAL ARSVVPVIEK TVSSAITESF QRGIGDKAVN QLDKSVNIKL EATVARQIQA
QFQTSGKQAL QEGLRSSVES SVIPSFEKAC KAMFDQIDSA FQKGIAEHTN AAQQRFDSGH
SQLAHTLKES ITSASSVAQA LSRELAETQR NLLALAAAGA NSGGSNSLVT QLSGGPLGAL
LEKVEAPMDP TTELSRLISE RKYEESFTSA LQRSDVSIVS WLCSQVDLRG LLAMNPLPLS
QGVLLSLLQQ LACDISKDTS RKLAWMTDVV AAINPSDQMI AVHARPIFEQ VYQILHHHRN
APGSDVSAIR LIMHVINSML MGCK
