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mRNA-decapping enzyme subunit 2 (AtDCP2) (Protein DECAPPING 2) (EC 3.6.1.62) (M(7)GpppN-mRNA hydrolase DCP2) (Protein TRIDENT)

 DCP2_ARATH              Reviewed;         373 AA.
Q8GW31; F4K3Z9; Q9FNB6;
11-JUL-2012, integrated into UniProtKB/Swiss-Prot.
01-MAR-2003, sequence version 1.
05-DEC-2018, entry version 126.
RecName: Full=mRNA-decapping enzyme subunit 2;
Short=AtDCP2;
Short=Protein DECAPPING 2;
EC=3.6.1.62;
AltName: Full=M(7)GpppN-mRNA hydrolase DCP2;
AltName: Full=Protein TRIDENT;
Name=DCP2; Synonyms=TDT; OrderedLocusNames=At5g13570;
ORFNames=MSH12.3;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=9405937; DOI=10.1093/dnares/4.4.291;
Kotani H., Nakamura Y., Sato S., Kaneko T., Asamizu E., Miyajima N.,
Tabata S.;
"Structural analysis of Arabidopsis thaliana chromosome 5. II.
Sequence features of the regions of 1,044,062 bp covered by thirteen
physically assigned P1 clones.";
DNA Res. 4:291-300(1997).
[2]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
STRAIN=cv. Columbia;
PubMed=11910074; DOI=10.1126/science.1071006;
Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M.,
Hayashizaki Y., Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T.,
Shibata K., Shinagawa A., Shinozaki K.;
"Functional annotation of a full-length Arabidopsis cDNA collection.";
Science 296:141-145(2002).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[5]
FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH DCP1 AND VCS, TISSUE
SPECIFICITY, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF GLU-158.
PubMed=17158604; DOI=10.1105/tpc.106.047605;
Xu J., Yang J.-Y., Niu Q.-W., Chua N.-H.;
"Arabidopsis DCP2, DCP1, and VARICOSE form a decapping complex
required for postembryonic development.";
Plant Cell 18:3386-3398(2006).
[6]
FUNCTION, AND SUBCELLULAR LOCATION.
STRAIN=cv. Columbia;
PubMed=17485080; DOI=10.1016/j.febslet.2007.04.051;
Iwasaki S., Takeda A., Motose H., Watanabe Y.;
"Characterization of Arabidopsis decapping proteins AtDCP1 and AtDCP2,
which are essential for post-embryonic development.";
FEBS Lett. 581:2455-2459(2007).
[7]
FUNCTION, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE, INTERACTION WITH
VCS, AND HOMODIMER.
STRAIN=cv. Columbia;
PubMed=17513503; DOI=10.1105/tpc.106.047621;
Goeres D.C., Van Norman J.M., Zhang W., Fauver N.A., Spencer M.L.,
Sieburth L.E.;
"Components of the Arabidopsis mRNA decapping complex are required for
early seedling development.";
Plant Cell 19:1549-1564(2007).
[8]
CATALYTIC ACTIVITY, FUNCTION, COFACTOR, ACTIVITY REGULATION,
MUTAGENESIS OF GLU-154; GLU-158; 222-VAL--LEU-232; GLY-226; LYS-231;
LYS-243; LYS-248 AND 372-SER-ALA-373, AND PDZ DOMAIN-BINDING.
STRAIN=cv. Columbia;
PubMed=18025047; DOI=10.1093/nar/gkm1002;
Gunawardana D., Cheng H.-C., Gayler K.R.;
"Identification of functional domains in Arabidopsis thaliana mRNA
decapping enzyme (AtDcp2).";
Nucleic Acids Res. 36:203-216(2008).
[9]
INTERACTION WITH DCP5, AND DEVELOPMENTAL STAGE.
PubMed=19855049; DOI=10.1105/tpc.109.070078;
Xu J., Chua N.-H.;
"Arabidopsis decapping 5 is required for mRNA decapping, P-body
formation, and translational repression during postembryonic
development.";
Plant Cell 21:3270-3279(2009).
-!- FUNCTION: Catalytic component of the decapping complex necessary
for the degradation of mRNAs, both in normal mRNA turnover and in
nonsense-mediated mRNA decay. Removes the 7-methyl guanine cap
structure from mRNA molecules, yielding a 5'-phosphorylated mRNA
fragment and 7m-GDP. Essential for postembryonic development,
especially during the formation of the shoot apical meristem
(SAM). {ECO:0000269|PubMed:17158604, ECO:0000269|PubMed:17485080,
ECO:0000269|PubMed:17513503, ECO:0000269|PubMed:18025047}.
-!- CATALYTIC ACTIVITY:
Reaction=a 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] + H2O =
a 5'-phospho-[mRNA] + 2 H(+) + N(7)-methylguanosine 5'-
diphosphate; Xref=Rhea:RHEA:37371, Rhea:RHEA-COMP:11471,
Rhea:RHEA-COMP:11474, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
ChEBI:CHEBI:63714, ChEBI:CHEBI:68546, ChEBI:CHEBI:74429;
EC=3.6.1.62; Evidence={ECO:0000269|PubMed:18025047};
-!- COFACTOR:
Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
Evidence={ECO:0000269|PubMed:18025047};
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:18025047};
-!- ACTIVITY REGULATION: Inhibited by the product 7-methyl GDP.
{ECO:0000269|PubMed:18025047}.
-!- SUBUNIT: Homodimer. Catalytic component of the decapping complex.
Interacts with DCP1, DCP5 and VCS. {ECO:0000269|PubMed:17158604,
ECO:0000269|PubMed:17513503, ECO:0000269|PubMed:19855049}.
-!- INTERACTION:
Q9SJF3:At1g08370; NbExp=2; IntAct=EBI-4425465, EBI-7786643;
-!- SUBCELLULAR LOCATION: Cytoplasm, P-body
{ECO:0000269|PubMed:17158604, ECO:0000269|PubMed:17485080,
ECO:0000269|PubMed:17513503}. Note=The localization to P-body is
VCS-dependent.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q8GW31-1; Sequence=Displayed;
Name=2;
IsoId=Q8GW31-2; Sequence=VSP_044026;
Note=Derived from EST data. No experimental confirmation
available.;
-!- TISSUE SPECIFICITY: Expressed in seedlings, mostly in root tips,
root hairs, and the vascular system. Also present in roots,
leaves, stems, and flowers. {ECO:0000269|PubMed:17158604}.
-!- DEVELOPMENTAL STAGE: Gradually accumulates upon germination.
{ECO:0000269|PubMed:19855049}.
-!- DISRUPTION PHENOTYPE: Lethal phenotype at the seedling cotyledon
stage that are small and chlorotic, with disorganized veins,
swollen root hairs, and altered epidermal cell morphology. Altered
RNA decay. {ECO:0000269|PubMed:17158604,
ECO:0000269|PubMed:17513503}.
-!- SIMILARITY: Belongs to the Nudix hydrolase family. DCP2 subfamily.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=BAB08683.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; AB006704; BAB08683.1; ALT_SEQ; Genomic_DNA.
EMBL; CP002688; AED91912.1; -; Genomic_DNA.
EMBL; CP002688; AED91913.1; -; Genomic_DNA.
EMBL; AK119112; BAC43684.1; -; mRNA.
EMBL; BT005332; AAO63396.1; -; mRNA.
RefSeq; NP_001190304.1; NM_001203375.1. [Q8GW31-2]
RefSeq; NP_196861.2; NM_121360.4. [Q8GW31-1]
UniGene; At.32052; -.
ProteinModelPortal; Q8GW31; -.
SMR; Q8GW31; -.
BioGrid; 16479; 4.
IntAct; Q8GW31; 3.
MINT; Q8GW31; -.
STRING; 3702.AT5G13570.2; -.
iPTMnet; Q8GW31; -.
PaxDb; Q8GW31; -.
PRIDE; Q8GW31; -.
EnsemblPlants; AT5G13570.1; AT5G13570.1; AT5G13570. [Q8GW31-1]
EnsemblPlants; AT5G13570.2; AT5G13570.2; AT5G13570. [Q8GW31-2]
GeneID; 831201; -.
Gramene; AT5G13570.1; AT5G13570.1; AT5G13570. [Q8GW31-1]
Gramene; AT5G13570.2; AT5G13570.2; AT5G13570. [Q8GW31-2]
KEGG; ath:AT5G13570; -.
Araport; AT5G13570; -.
TAIR; locus:2173174; AT5G13570.
eggNOG; KOG2937; Eukaryota.
eggNOG; COG0494; LUCA.
HOGENOM; HOG000005974; -.
InParanoid; Q8GW31; -.
KO; K12613; -.
OMA; HACAVRE; -.
PhylomeDB; Q8GW31; -.
Reactome; R-ATH-430039; mRNA decay by 5' to 3' exoribonuclease.
Reactome; R-ATH-450604; KSRP (KHSRP) binds and destabilizes mRNA.
PRO; PR:Q8GW31; -.
Proteomes; UP000006548; Chromosome 5.
ExpressionAtlas; Q8GW31; baseline and differential.
Genevisible; Q8GW31; AT.
GO; GO:0005737; C:cytoplasm; IDA:TAIR.
GO; GO:0000932; C:P-body; IDA:TAIR.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0050072; F:m7G(5')pppN diphosphatase activity; IDA:TAIR.
GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
GO; GO:0030145; F:manganese ion binding; IDA:UniProtKB.
GO; GO:0003729; F:mRNA binding; IDA:TAIR.
GO; GO:0000290; P:deadenylation-dependent decapping of nuclear-transcribed mRNA; IBA:GO_Central.
GO; GO:0031087; P:deadenylation-independent decapping of nuclear-transcribed mRNA; IDA:TAIR.
GO; GO:0019048; P:modulation by virus of host morphology or physiology; IMP:TAIR.
GO; GO:0006402; P:mRNA catabolic process; IMP:TAIR.
GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
GO; GO:0009791; P:post-embryonic development; IMP:UniProtKB.
GO; GO:0016441; P:posttranscriptional gene silencing; IMP:TAIR.
GO; GO:0010072; P:primary shoot apical meristem specification; IMP:UniProtKB.
Gene3D; 1.10.10.1050; -; 1.
InterPro; IPR007722; DCP2_BoxA.
InterPro; IPR036189; DCP2_BoxA_sf.
InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
InterPro; IPR020084; NUDIX_hydrolase_CS.
InterPro; IPR000086; NUDIX_hydrolase_dom.
Pfam; PF05026; DCP2; 1.
Pfam; PF00293; NUDIX; 1.
SMART; SM01125; DCP2; 1.
SUPFAM; SSF140586; SSF140586; 1.
SUPFAM; SSF55811; SSF55811; 1.
PROSITE; PS51462; NUDIX; 1.
PROSITE; PS00893; NUDIX_BOX; 1.
1: Evidence at protein level;
Alternative splicing; ATP-binding; Complete proteome; Cytoplasm;
Hydrolase; Magnesium; Manganese; Metal-binding; mRNA processing;
Nucleotide-binding; Reference proteome; RNA-binding.
CHAIN 1 373 mRNA-decapping enzyme subunit 2.
/FTId=PRO_0000418336.
DOMAIN 106 234 Nudix hydrolase. {ECO:0000255|PROSITE-
ProRule:PRU00794}.
REGION 233 250 RNA binding.
MOTIF 139 160 Nudix box.
MOTIF 370 373 PDZ-binding.
COMPBIAS 7 11 Poly-Ser.
METAL 154 154 Magnesium or manganese. {ECO:0000250}.
METAL 158 158 Magnesium or manganese. {ECO:0000250}.
BINDING 178 178 ATP. {ECO:0000250}.
BINDING 233 233 ATP. {ECO:0000250}.
VAR_SEQ 154 154 E -> ELSSAILLVNVAFQ (in isoform 2).
{ECO:0000305}.
/FTId=VSP_044026.
MUTAGEN 154 154 E->Q: Loss of mRNA decaping activity.
{ECO:0000269|PubMed:18025047}.
MUTAGEN 158 158 E->Q: Loss of mRNA decaping activity.
{ECO:0000269|PubMed:17158604,
ECO:0000269|PubMed:18025047}.
MUTAGEN 222 232 Missing: Loss of mRNA decaping activity.
{ECO:0000269|PubMed:18025047}.
MUTAGEN 226 226 G->A: Reduced mRNA decaping activity.
{ECO:0000269|PubMed:18025047}.
MUTAGEN 231 231 K->A: Reduced mRNA decaping activity.
{ECO:0000269|PubMed:18025047}.
MUTAGEN 243 243 K->A: Reduced mRNA decaping activity.
{ECO:0000269|PubMed:18025047}.
MUTAGEN 248 248 K->A: Reduced mRNA decaping activity.
{ECO:0000269|PubMed:18025047}.
MUTAGEN 372 373 SA->PD: Enhanced stability due do reduced
proteolysis.
{ECO:0000269|PubMed:18025047}.
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


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