DCP2_ARATH
ID DCP2_ARATH Reviewed; 373 AA.
AC Q8GW31; F4K3Z9; Q9FNB6;
DT 11-JUL-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=mRNA-decapping enzyme subunit 2;
DE Short=AtDCP2;
DE Short=Protein DECAPPING 2;
DE EC=3.6.1.62 {ECO:0000269|PubMed:18025047};
DE AltName: Full=M(7)GpppN-mRNA hydrolase DCP2;
DE AltName: Full=Protein TRIDENT;
GN Name=DCP2; Synonyms=TDT; OrderedLocusNames=At5g13570; ORFNames=MSH12.3;
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=9405937; DOI=10.1093/dnares/4.4.291;
RA Kotani H., Nakamura Y., Sato S., Kaneko T., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence
RT features of the regions of 1,044,062 bp covered by thirteen physically
RT assigned P1 clones.";
RL DNA Res. 4:291-300(1997).
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=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [4]
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 [5]
RP FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH DCP1 AND VCS, TISSUE
RP SPECIFICITY, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF GLU-158.
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 [6]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=17485080; DOI=10.1016/j.febslet.2007.04.051;
RA Iwasaki S., Takeda A., Motose H., Watanabe Y.;
RT "Characterization of Arabidopsis decapping proteins AtDCP1 and AtDCP2,
RT which are essential for post-embryonic development.";
RL FEBS Lett. 581:2455-2459(2007).
RN [7]
RP FUNCTION, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE, INTERACTION WITH VCS,
RP 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 CATALYTIC ACTIVITY, FUNCTION, COFACTOR, ACTIVITY REGULATION, MUTAGENESIS OF
RP GLU-154; GLU-158; 222-VAL--LEU-232; GLY-226; LYS-231; LYS-243; LYS-248 AND
RP 372-SER-ALA-373, AND PDZ DOMAIN-BINDING.
RC STRAIN=cv. Columbia;
RX PubMed=18025047; DOI=10.1093/nar/gkm1002;
RA Gunawardana D., Cheng H.-C., Gayler K.R.;
RT "Identification of functional domains in Arabidopsis thaliana mRNA
RT decapping enzyme (AtDcp2).";
RL Nucleic Acids Res. 36:203-216(2008).
RN [9]
RP INTERACTION WITH DCP5, AND DEVELOPMENTAL STAGE.
RX PubMed=19855049; DOI=10.1105/tpc.109.070078;
RA Xu J., Chua N.-H.;
RT "Arabidopsis decapping 5 is required for mRNA decapping, P-body formation,
RT and translational repression during postembryonic development.";
RL Plant Cell 21:3270-3279(2009).
CC -!- FUNCTION: Catalytic component of the decapping complex necessary for
CC the degradation of mRNAs, both in normal mRNA turnover and in nonsense-
CC mediated mRNA decay. Removes the 7-methyl guanine cap structure from
CC mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP.
CC Essential for postembryonic development, especially during the
CC formation of the shoot apical meristem (SAM).
CC {ECO:0000269|PubMed:17158604, ECO:0000269|PubMed:17485080,
CC ECO:0000269|PubMed:17513503, ECO:0000269|PubMed:18025047}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside
CC in mRNA + H2O = a 5'-end phospho-ribonucleoside in mRNA + 2 H(+) +
CC N(7)-methyl-GDP; Xref=Rhea:RHEA:67484, Rhea:RHEA-COMP:15692,
CC Rhea:RHEA-COMP:17167, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:63714, ChEBI:CHEBI:138282, ChEBI:CHEBI:156461;
CC EC=3.6.1.62; Evidence={ECO:0000269|PubMed:18025047};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:67485;
CC Evidence={ECO:0000269|PubMed:18025047};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:18025047};
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:18025047};
CC -!- ACTIVITY REGULATION: Inhibited by the product 7-methyl GDP.
CC {ECO:0000269|PubMed:18025047}.
CC -!- SUBUNIT: Homodimer. Catalytic component of the decapping complex.
CC Interacts with DCP1, DCP5 and VCS. {ECO:0000269|PubMed:17158604,
CC ECO:0000269|PubMed:17513503, ECO:0000269|PubMed:19855049}.
CC -!- INTERACTION:
CC Q8GW31; Q9SJF3: At1g08370; NbExp=2; IntAct=EBI-4425465, EBI-7786643;
CC -!- SUBCELLULAR LOCATION: Cytoplasm, P-body {ECO:0000269|PubMed:17158604,
CC ECO:0000269|PubMed:17485080, ECO:0000269|PubMed:17513503}. Note=The
CC localization to P-body is VCS-dependent.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8GW31-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8GW31-2; Sequence=VSP_044026;
CC -!- TISSUE SPECIFICITY: Expressed in seedlings, mostly in root tips, root
CC hairs, and the vascular system. Also present in roots, leaves, stems,
CC and flowers. {ECO:0000269|PubMed:17158604}.
CC -!- DEVELOPMENTAL STAGE: Gradually accumulates upon germination.
CC {ECO:0000269|PubMed:19855049}.
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. Altered RNA decay.
CC {ECO:0000269|PubMed:17158604, ECO:0000269|PubMed:17513503}.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. DCP2 subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB08683.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB006704; BAB08683.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED91912.1; -; Genomic_DNA.
DR EMBL; CP002688; AED91913.1; -; Genomic_DNA.
DR EMBL; AK119112; BAC43684.1; -; mRNA.
DR EMBL; BT005332; AAO63396.1; -; mRNA.
DR RefSeq; NP_001190304.1; NM_001203375.1. [Q8GW31-2]
DR RefSeq; NP_196861.2; NM_121360.4. [Q8GW31-1]
DR AlphaFoldDB; Q8GW31; -.
DR SMR; Q8GW31; -.
DR BioGRID; 16479; 4.
DR IntAct; Q8GW31; 3.
DR MINT; Q8GW31; -.
DR STRING; 3702.AT5G13570.2; -.
DR iPTMnet; Q8GW31; -.
DR PaxDb; Q8GW31; -.
DR PRIDE; Q8GW31; -.
DR ProteomicsDB; 224691; -. [Q8GW31-1]
DR EnsemblPlants; AT5G13570.1; AT5G13570.1; AT5G13570. [Q8GW31-1]
DR EnsemblPlants; AT5G13570.2; AT5G13570.2; AT5G13570. [Q8GW31-2]
DR GeneID; 831201; -.
DR Gramene; AT5G13570.1; AT5G13570.1; AT5G13570. [Q8GW31-1]
DR Gramene; AT5G13570.2; AT5G13570.2; AT5G13570. [Q8GW31-2]
DR KEGG; ath:AT5G13570; -.
DR Araport; AT5G13570; -.
DR TAIR; locus:2173174; AT5G13570.
DR eggNOG; KOG2937; Eukaryota.
DR InParanoid; Q8GW31; -.
DR OMA; KLNMSAI; -.
DR OrthoDB; 1230808at2759; -.
DR PhylomeDB; Q8GW31; -.
DR PRO; PR:Q8GW31; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q8GW31; baseline and differential.
DR Genevisible; Q8GW31; AT.
DR GO; GO:0005737; C:cytoplasm; IDA:TAIR.
DR GO; GO:0000932; C:P-body; IDA:TAIR.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0050072; F:m7G(5')pppN diphosphatase activity; IDA:TAIR.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0030145; F:manganese ion binding; IDA:UniProtKB.
DR GO; GO:0003729; F:mRNA binding; IDA:TAIR.
DR GO; GO:0042803; F:protein homodimerization activity; IPI:TAIR.
DR GO; GO:0000290; P:deadenylation-dependent decapping of nuclear-transcribed mRNA; IBA:GO_Central.
DR GO; GO:0031087; P:deadenylation-independent decapping of nuclear-transcribed mRNA; IDA:TAIR.
DR GO; GO:0019048; P:modulation by virus of host process; 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:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IEA:InterPro.
DR GO; GO:0009791; P:post-embryonic development; IMP:UniProtKB.
DR GO; GO:0016441; P:post-transcriptional gene silencing; IMP:TAIR.
DR GO; GO:0010072; P:primary shoot apical meristem specification; IMP:UniProtKB.
DR CDD; cd03672; Dcp2p; 1.
DR Gene3D; 1.10.10.1050; -; 1.
DR InterPro; IPR007722; DCP2_BoxA.
DR InterPro; IPR036189; DCP2_BoxA_sf.
DR InterPro; IPR044099; Dcp2_NUDIX.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR020084; NUDIX_hydrolase_CS.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR Pfam; PF05026; DCP2; 1.
DR Pfam; PF00293; NUDIX; 1.
DR SMART; SM01125; DCP2; 1.
DR SUPFAM; SSF140586; SSF140586; 1.
DR SUPFAM; SSF55811; SSF55811; 1.
DR PROSITE; PS51462; NUDIX; 1.
DR PROSITE; PS00893; NUDIX_BOX; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; ATP-binding; Cytoplasm; Hydrolase; Magnesium;
KW Manganese; Metal-binding; mRNA processing; Nucleotide-binding;
KW Reference proteome; RNA-binding.
FT CHAIN 1..373
FT /note="mRNA-decapping enzyme subunit 2"
FT /id="PRO_0000418336"
FT DOMAIN 106..234
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT REGION 233..250
FT /note="RNA binding"
FT REGION 275..342
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 139..160
FT /note="Nudix box"
FT MOTIF 370..373
FT /note="PDZ-binding"
FT COMPBIAS 275..292
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 293..322
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 323..338
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 154
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 158
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 178
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 233
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT VAR_SEQ 154
FT /note="E -> ELSSAILLVNVAFQ (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_044026"
FT MUTAGEN 154
FT /note="E->Q: Loss of mRNA decaping activity."
FT /evidence="ECO:0000269|PubMed:18025047"
FT MUTAGEN 158
FT /note="E->Q: Loss of mRNA decaping activity."
FT /evidence="ECO:0000269|PubMed:17158604,
FT ECO:0000269|PubMed:18025047"
FT MUTAGEN 222..232
FT /note="Missing: Loss of mRNA decaping activity."
FT /evidence="ECO:0000269|PubMed:18025047"
FT MUTAGEN 226
FT /note="G->A: Reduced mRNA decaping activity."
FT /evidence="ECO:0000269|PubMed:18025047"
FT MUTAGEN 231
FT /note="K->A: Reduced mRNA decaping activity."
FT /evidence="ECO:0000269|PubMed:18025047"
FT MUTAGEN 243
FT /note="K->A: Reduced mRNA decaping activity."
FT /evidence="ECO:0000269|PubMed:18025047"
FT MUTAGEN 248
FT /note="K->A: Reduced mRNA decaping activity."
FT /evidence="ECO:0000269|PubMed:18025047"
FT MUTAGEN 372..373
FT /note="SA->PD: Enhanced stability due do reduced
FT proteolysis."
FT /evidence="ECO:0000269|PubMed:18025047"
SQ SEQUENCE 373 AA; 42387 MW; 7BB6FB5727D0085F CRC64;
MSGLHRSSSS SKNIGNCLPS KELLDDLCSR FVLNVPEEDQ QSFERILFLV EYAYWYYEDN
AVENDPKLKS LSLKEFTSLL FNSCDVLRPY VTHIDDIFKD FTSYKCRVPV TGAIILDETY
ERCLLVKGWK GSSWSFPRGK KSKDEEDHAC AIREVLEETG FDVSKLLKRE EYIEFVFRQQ
RVRLYIVAGV TEDTVFAPLT KKEISEITWH RLDHLQPASN EVITHGVSGL KLYMVAPFLS
SLKSWILKHP SPVARRPNKP LKALCVWNAR TSVGGNGTAT VESQNRKSEL RTTTMESNSR
KPELKRTTME SHSTKPELRK GTMESHNTTA TVESHNTKPV VDHSQDIKPG GSFINFKFNQ
SVILQALESG NSA
