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Protein

Enhancer of mRNA-decapping protein 3

Gene

EDC3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Stimulates decapping of both stable and unstable mRNA during mRNA decay. Does not affect nonsense-mediated mRNA decay. Required for normal P-body assembly.2 Publications

GO - Molecular functioni

  • mRNA binding Source: SGD

GO - Biological processi

  • cytoplasmic mRNA processing body assembly Source: SGD
  • deadenylation-independent decapping of nuclear-transcribed mRNA Source: SGD
  • positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Source: SGD
Complete GO annotation...

Enzyme and pathway databases

BioCyciYEAST:G3O-30140-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Enhancer of mRNA-decapping protein 3
Gene namesi
Name:EDC3
Synonyms:LSM16
Ordered Locus Names:YEL015W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome V

Organism-specific databases

EuPathDBiFungiDB:YEL015W.
SGDiS000000741. EDC3.

Subcellular locationi

  • CytoplasmP-body 1 Publication

  • Note: Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bodies) which represent sites of mRNA decapping and 5' to 3' exonucleotidic decay.

GO - Cellular componenti

  • cytoplasm Source: SGD
  • cytoplasmic mRNA processing body Source: SGD
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi360 – 3612RH → AA: Abolishes homodimerization. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 551551Enhancer of mRNA-decapping protein 3PRO_0000202613Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei257 – 2571PhosphoserineCombined sources
Modified residuei261 – 2611PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP39998.
PeptideAtlasiP39998.

PTM databases

iPTMnetiP39998.

Interactioni

Subunit structurei

Homodimer. Interacts with DCP2.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
DCP1Q125175EBI-22300,EBI-38519
DCP2P535507EBI-22300,EBI-270
DHH1P395173EBI-22300,EBI-158
RPS28BP0C0X03EBI-22300,EBI-16112

Protein-protein interaction databases

BioGridi36716. 70 interactions.
DIPiDIP-842N.
IntActiP39998. 23 interactions.
MINTiMINT-385078.

Structurei

Secondary structure

1
551
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi91 – 944Combined sources
Turni97 – 993Combined sources
Helixi107 – 1104Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4BRUX-ray3.24B77-116[»]
ProteinModelPortaliP39998.
SMRiP39998. Positions 88-116.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini93 – 12937DFDFPROSITE-ProRule annotationAdd
BLAST
Domaini288 – 527240YjeF N-terminalPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the EDC3 family.Curated
Contains 1 DFDF domain.PROSITE-ProRule annotation
Contains 1 YjeF N-terminal domain.PROSITE-ProRule annotation

Phylogenomic databases

HOGENOMiHOG000246503.
InParanoidiP39998.
KOiK12615.
OMAiGYDDHLE.
OrthoDBiEOG78WM2C.

Family and domain databases

Gene3Di3.40.50.10260. 1 hit.
InterProiIPR025762. DFDF.
IPR019050. FDF_dom.
IPR004443. YjeF_N_dom.
[Graphical view]
PfamiPF09532. FDF. 1 hit.
PF03853. YjeF_N. 1 hit.
[Graphical view]
SMARTiSM01199. FDF. 1 hit.
[Graphical view]
SUPFAMiSSF64153. SSF64153. 1 hit.
PROSITEiPS51512. DFDF. 1 hit.
PS51385. YJEF_N. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P39998-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSQFVGFGVQ VELKDGKLIQ GKIAKATSKG LTLNDVQFGD GGKSQAFKVR
60 70 80 90 100
ASRLKDLKVL TVASQSGKRK QQRQQQQQND YNQNRGEHID WQDDDVSKIK
110 120 130 140 150
QQEDFDFQRN LGMFNKKDVF AQLKQNDDIL PENRLQGHNR KQTQLQQNNY
160 170 180 190 200
QNDELVIPDA KKDSWNKISS RNEQSTHQSQ PQQDAQDDLV LEDDEHEYDV
210 220 230 240 250
DDIDDPKYLP ITQSLNITHL IHSATNSPSI NDKTKGTVIN DKDQVLAKLG
260 270 280 290 300
QMIISQSRSN STSLPAANKQ TTIRSKNTKQ NIPMATPVQL LEMESITSEF
310 320 330 340 350
FSINSAGLLE NFAVNASFFL KQKLGGRARL RLQNSNPEPL VVILASDSNR
360 370 380 390 400
SGAKALALGR HLCQTGHIRV ITLFTCSQNE LQDSMVKKQT DIYKKCGGKI
410 420 430 440 450
VNSVSSLESA METLNSPVEI VIDAMQGYDC TLSDLAGTSE VIESRIKSMI
460 470 480 490 500
SWCNKQRGST KVWSLDIPNG FDAGSGMPDI FFSDRIEATG IICSGWPLIA
510 520 530 540 550
INNLIANLPS LEDAVLIDIG IPQGAYSQRT SLRKFQNCDL FVTDGSLLLD

L
Length:551
Mass (Da):61,340
Last modified:February 1, 1995 - v1
Checksum:iBF28AE67F9303A73
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18530 Genomic DNA. Translation: AAB64492.1.
BK006939 Genomic DNA. Translation: DAA07639.1.
PIRiS50444.
RefSeqiNP_010901.1. NM_001178830.1.

Genome annotation databases

EnsemblFungiiYEL015W; YEL015W; YEL015W.
GeneIDi856700.
KEGGisce:YEL015W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18530 Genomic DNA. Translation: AAB64492.1.
BK006939 Genomic DNA. Translation: DAA07639.1.
PIRiS50444.
RefSeqiNP_010901.1. NM_001178830.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4BRUX-ray3.24B77-116[»]
ProteinModelPortaliP39998.
SMRiP39998. Positions 88-116.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36716. 70 interactions.
DIPiDIP-842N.
IntActiP39998. 23 interactions.
MINTiMINT-385078.

PTM databases

iPTMnetiP39998.

Proteomic databases

MaxQBiP39998.
PeptideAtlasiP39998.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYEL015W; YEL015W; YEL015W.
GeneIDi856700.
KEGGisce:YEL015W.

Organism-specific databases

EuPathDBiFungiDB:YEL015W.
SGDiS000000741. EDC3.

Phylogenomic databases

HOGENOMiHOG000246503.
InParanoidiP39998.
KOiK12615.
OMAiGYDDHLE.
OrthoDBiEOG78WM2C.

Enzyme and pathway databases

BioCyciYEAST:G3O-30140-MONOMER.

Miscellaneous databases

NextBioi982763.
PROiP39998.

Family and domain databases

Gene3Di3.40.50.10260. 1 hit.
InterProiIPR025762. DFDF.
IPR019050. FDF_dom.
IPR004443. YjeF_N_dom.
[Graphical view]
PfamiPF09532. FDF. 1 hit.
PF03853. YjeF_N. 1 hit.
[Graphical view]
SMARTiSM01199. FDF. 1 hit.
[Graphical view]
SUPFAMiSSF64153. SSF64153. 1 hit.
PROSITEiPS51512. DFDF. 1 hit.
PS51385. YJEF_N. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
    Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
    J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-257, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  3. "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
    Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
    Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-257, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  4. "Crystal structure of human Edc3 and its functional implications."
    Ling S.H., Decker C.J., Walsh M.A., She M., Parker R., Song H.
    Mol. Cell. Biol. 28:5965-5976(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH DCP2, MUTAGENESIS OF 360-ARG-HIS-361.
  5. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  6. "Identification of Edc3p as an enhancer of mRNA decapping in Saccharomyces cerevisiae."
    Kshirsagar M., Parker R.
    Genetics 166:729-739(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  7. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  8. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-257 AND SER-261, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiEDC3_YEAST
AccessioniPrimary (citable) accession number: P39998
Secondary accession number(s): D3DLN5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: May 11, 2016
This is version 124 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 2340 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome V
    Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

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.