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Protein

mRNA-decapping enzyme subunit 2

Gene

DCP2

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

Functioni

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).4 Publications

Catalytic activityi

5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] + H2O = N(7)-methylguanosine 5'-diphosphate + 5'-phospho-[mRNA].1 Publication

Cofactori

Mn2+1 Publication, Mg2+1 Publication

Enzyme regulationi

Inhibited by the product 7-methyl GDP.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi154 – 1541Magnesium or manganeseBy similarity
Metal bindingi158 – 1581Magnesium or manganeseBy similarity
Binding sitei178 – 1781ATPBy similarity
Binding sitei233 – 2331ATPBy similarity

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • hydrolase activity Source: UniProtKB-KW
  • magnesium ion binding Source: UniProtKB
  • manganese ion binding Source: UniProtKB
  • RNA binding Source: UniProtKB-KW

GO - Biological processi

  • mRNA processing Source: UniProtKB-KW
  • post-embryonic development Source: UniProtKB
  • primary shoot apical meristem specification Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

mRNA processing

Keywords - Ligandi

ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

ReactomeiR-ATH-430039. mRNA decay by 5' to 3' exoribonuclease.
R-ATH-450604. KSRP (KHSRP) binds and destabilizes mRNA.

Names & Taxonomyi

Protein namesi
Recommended name:
mRNA-decapping enzyme subunit 2 (EC:3.6.1.62)
Short name:
AtDCP2
Short name:
Protein DECAPPING 2
Alternative name(s):
M(7)GpppN-mRNA hydrolase DCP2
Protein TRIDENT
Gene namesi
Name:DCP2
Synonyms:TDT
Ordered Locus Names:At5g13570
ORF Names:MSH12.3
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G13570.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

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.2 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi154 – 1541E → Q: Loss of mRNA decaping activity. 1 Publication
Mutagenesisi158 – 1581E → Q: Loss of mRNA decaping activity. 2 Publications
Mutagenesisi222 – 23211Missing : Loss of mRNA decaping activity. 1 PublicationAdd
BLAST
Mutagenesisi226 – 2261G → A: Reduced mRNA decaping activity. 1 Publication
Mutagenesisi231 – 2311K → A: Reduced mRNA decaping activity. 1 Publication
Mutagenesisi243 – 2431K → A: Reduced mRNA decaping activity. 1 Publication
Mutagenesisi248 – 2481K → A: Reduced mRNA decaping activity. 1 Publication
Mutagenesisi372 – 3732SA → PD: Enhanced stability due do reduced proteolysis. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 373373mRNA-decapping enzyme subunit 2PRO_0000418336Add
BLAST

Proteomic databases

PaxDbiQ8GW31.
PRIDEiQ8GW31.

Expressioni

Tissue specificityi

Expressed in seedlings, mostly in root tips, root hairs, and the vascular system. Also present in roots, leaves, stems, and flowers.1 Publication

Developmental stagei

Gradually accumulates upon germination.1 Publication

Gene expression databases

GenevisibleiQ8GW31. AT.

Interactioni

Subunit structurei

Homodimer. Catalytic component of the decapping complex. Interacts with DCP1, DCP5 and VCS.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
At1g08370Q9SJF32EBI-4425465,EBI-7786643

Protein-protein interaction databases

BioGridi16479. 4 interactions.
IntActiQ8GW31. 3 interactions.
MINTiMINT-8393471.
STRINGi3702.AT5G13570.2.

Structurei

3D structure databases

ProteinModelPortaliQ8GW31.
SMRiQ8GW31. Positions 22-248.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini106 – 234129Nudix hydrolasePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni233 – 25018RNA bindingAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi139 – 16022Nudix boxAdd
BLAST
Motifi370 – 3734PDZ-binding

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi7 – 115Poly-Ser

Sequence similaritiesi

Belongs to the Nudix hydrolase family. DCP2 subfamily.Curated
Contains 1 nudix hydrolase domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG2937. Eukaryota.
COG0494. LUCA.
HOGENOMiHOG000005974.
InParanoidiQ8GW31.
KOiK12613.
OMAiESHNTKP.
PhylomeDBiQ8GW31.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR007722. DCP2_BoxA.
IPR020084. NUDIX_hydrolase_CS.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PfamiPF05026. DCP2. 1 hit.
PF00293. NUDIX. 1 hit.
[Graphical view]
SMARTiSM01125. DCP2. 1 hit.
[Graphical view]
SUPFAMiSSF140586. SSF140586. 1 hit.
SSF55811. SSF55811. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
PS00893. NUDIX_BOX. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8GW31-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSGLHRSSSS SKNIGNCLPS KELLDDLCSR FVLNVPEEDQ QSFERILFLV
60 70 80 90 100
EYAYWYYEDN AVENDPKLKS LSLKEFTSLL FNSCDVLRPY VTHIDDIFKD
110 120 130 140 150
FTSYKCRVPV TGAIILDETY ERCLLVKGWK GSSWSFPRGK KSKDEEDHAC
160 170 180 190 200
AIREVLEETG FDVSKLLKRE EYIEFVFRQQ RVRLYIVAGV TEDTVFAPLT
210 220 230 240 250
KKEISEITWH RLDHLQPASN EVITHGVSGL KLYMVAPFLS SLKSWILKHP
260 270 280 290 300
SPVARRPNKP LKALCVWNAR TSVGGNGTAT VESQNRKSEL RTTTMESNSR
310 320 330 340 350
KPELKRTTME SHSTKPELRK GTMESHNTTA TVESHNTKPV VDHSQDIKPG
360 370
GSFINFKFNQ SVILQALESG NSA
Length:373
Mass (Da):42,387
Last modified:March 1, 2003 - v1
Checksum:i7BB6FB5727D0085F
GO
Isoform 2 (identifier: Q8GW31-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     154-154: E → ELSSAILLVNVAFQ

Note: Derived from EST data. No experimental confirmation available.
Show »
Length:386
Mass (Da):43,744
Checksum:iC28478505E86A884
GO

Sequence cautioni

The sequence BAB08683.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei154 – 1541E → ELSSAILLVNVAFQ in isoform 2. CuratedVSP_044026

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB006704 Genomic DNA. Translation: BAB08683.1. Sequence problems.
CP002688 Genomic DNA. Translation: AED91912.1.
CP002688 Genomic DNA. Translation: AED91913.1.
AK119112 mRNA. Translation: BAC43684.1.
BT005332 mRNA. Translation: AAO63396.1.
RefSeqiNP_001190304.1. NM_001203375.1. [Q8GW31-2]
NP_196861.2. NM_121360.3. [Q8GW31-1]
UniGeneiAt.32052.

Genome annotation databases

EnsemblPlantsiAT5G13570.1; AT5G13570.1; AT5G13570. [Q8GW31-1]
GeneIDi831201.
KEGGiath:AT5G13570.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB006704 Genomic DNA. Translation: BAB08683.1. Sequence problems.
CP002688 Genomic DNA. Translation: AED91912.1.
CP002688 Genomic DNA. Translation: AED91913.1.
AK119112 mRNA. Translation: BAC43684.1.
BT005332 mRNA. Translation: AAO63396.1.
RefSeqiNP_001190304.1. NM_001203375.1. [Q8GW31-2]
NP_196861.2. NM_121360.3. [Q8GW31-1]
UniGeneiAt.32052.

3D structure databases

ProteinModelPortaliQ8GW31.
SMRiQ8GW31. Positions 22-248.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi16479. 4 interactions.
IntActiQ8GW31. 3 interactions.
MINTiMINT-8393471.
STRINGi3702.AT5G13570.2.

Proteomic databases

PaxDbiQ8GW31.
PRIDEiQ8GW31.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G13570.1; AT5G13570.1; AT5G13570. [Q8GW31-1]
GeneIDi831201.
KEGGiath:AT5G13570.

Organism-specific databases

TAIRiAT5G13570.

Phylogenomic databases

eggNOGiKOG2937. Eukaryota.
COG0494. LUCA.
HOGENOMiHOG000005974.
InParanoidiQ8GW31.
KOiK12613.
OMAiESHNTKP.
PhylomeDBiQ8GW31.

Enzyme and pathway databases

ReactomeiR-ATH-430039. mRNA decay by 5' to 3' exoribonuclease.
R-ATH-450604. KSRP (KHSRP) binds and destabilizes mRNA.

Miscellaneous databases

PROiQ8GW31.

Gene expression databases

GenevisibleiQ8GW31. AT.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR007722. DCP2_BoxA.
IPR020084. NUDIX_hydrolase_CS.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PfamiPF05026. DCP2. 1 hit.
PF00293. NUDIX. 1 hit.
[Graphical view]
SMARTiSM01125. DCP2. 1 hit.
[Graphical view]
SUPFAMiSSF140586. SSF140586. 1 hit.
SSF55811. SSF55811. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
PS00893. NUDIX_BOX. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "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."
    Kotani H., Nakamura Y., Sato S., Kaneko T., Asamizu E., Miyajima N., Tabata S.
    DNA Res. 4:291-300(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  2. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    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.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Strain: cv. Columbia.
  5. "Arabidopsis DCP2, DCP1, and VARICOSE form a decapping complex required for postembryonic development."
    Xu J., Yang J.-Y., Niu Q.-W., Chua N.-H.
    Plant Cell 18:3386-3398(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH DCP1 AND VCS, TISSUE SPECIFICITY, DISRUPTION PHENOTYPE, MUTAGENESIS OF GLU-158.
  6. "Characterization of Arabidopsis decapping proteins AtDCP1 and AtDCP2, which are essential for post-embryonic development."
    Iwasaki S., Takeda A., Motose H., Watanabe Y.
    FEBS Lett. 581:2455-2459(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
    Strain: cv. Columbia.
  7. "Components of the Arabidopsis mRNA decapping complex are required for early seedling development."
    Goeres D.C., Van Norman J.M., Zhang W., Fauver N.A., Spencer M.L., Sieburth L.E.
    Plant Cell 19:1549-1564(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE, INTERACTION WITH VCS, HOMODIMER.
    Strain: cv. Columbia.
  8. "Identification of functional domains in Arabidopsis thaliana mRNA decapping enzyme (AtDcp2)."
    Gunawardana D., Cheng H.-C., Gayler K.R.
    Nucleic Acids Res. 36:203-216(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: CATALYTIC ACTIVITY, FUNCTION, COFACTOR, ENZYME REGULATION, MUTAGENESIS OF GLU-154; GLU-158; 222-VAL--LEU-232; GLY-226; LYS-231; LYS-243; LYS-248 AND 372-SER-ALA-373, PDZ DOMAIN-BINDING.
    Strain: cv. Columbia.
  9. "Arabidopsis decapping 5 is required for mRNA decapping, P-body formation, and translational repression during postembryonic development."
    Xu J., Chua N.-H.
    Plant Cell 21:3270-3279(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH DCP5, DEVELOPMENTAL STAGE.

Entry informationi

Entry nameiDCP2_ARATH
AccessioniPrimary (citable) accession number: Q8GW31
Secondary accession number(s): F4K3Z9, Q9FNB6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 11, 2012
Last sequence update: March 1, 2003
Last modified: May 11, 2016
This is version 105 of the entry and version 1 of the sequence. [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
  2. SIMILARITY comments
    Index of protein domains and families

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.