EDC3_YEAST
ID EDC3_YEAST Reviewed; 551 AA.
AC P39998; D3DLN5;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 161.
DE RecName: Full=Enhancer of mRNA-decapping protein 3;
GN Name=EDC3; Synonyms=LSM16; OrderedLocusNames=YEL015W;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169868;
RA Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
RA Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
RA Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S.,
RA Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D.,
RA Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y.,
RA Botstein D., Davis R.W.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";
RL Nature 387:78-81(1997).
RN [2]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-257, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [3]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-257, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=17287358; DOI=10.1073/pnas.0607084104;
RA Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
RA Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
RT "Analysis of phosphorylation sites on proteins from Saccharomyces
RT cerevisiae by electron transfer dissociation (ETD) mass spectrometry.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
RN [4]
RP FUNCTION, INTERACTION WITH DCP2, AND MUTAGENESIS OF 360-ARG-HIS-361.
RX PubMed=18678652; DOI=10.1128/mcb.00761-08;
RA Ling S.H., Decker C.J., Walsh M.A., She M., Parker R., Song H.;
RT "Crystal structure of human Edc3 and its functional implications.";
RL Mol. Cell. Biol. 28:5965-5976(2008).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [6]
RP FUNCTION, AND SUBCELLULAR LOCATION.
RX PubMed=15020463; DOI=10.1534/genetics.166.2.729;
RA Kshirsagar M., Parker R.;
RT "Identification of Edc3p as an enhancer of mRNA decapping in Saccharomyces
RT cerevisiae.";
RL Genetics 166:729-739(2004).
RN [7]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-257 AND SER-261, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
CC -!- FUNCTION: Stimulates decapping of both stable and unstable mRNA during
CC mRNA decay. Does not affect nonsense-mediated mRNA decay. Required for
CC normal P-body assembly. {ECO:0000269|PubMed:15020463,
CC ECO:0000269|PubMed:18678652}.
CC -!- SUBUNIT: Homodimer. Interacts with DCP2. {ECO:0000269|PubMed:18678652}.
CC -!- INTERACTION:
CC P39998; Q12517: DCP1; NbExp=4; IntAct=EBI-22300, EBI-38519;
CC P39998; P53550: DCP2; NbExp=6; IntAct=EBI-22300, EBI-270;
CC P39998; P39517: DHH1; NbExp=3; IntAct=EBI-22300, EBI-158;
CC -!- SUBCELLULAR LOCATION: Cytoplasm, P-body {ECO:0000269|PubMed:15020463}.
CC Note=Is concentrated in several cytoplasmic foci called P bodies (or
CC cytoplasmic processing bodies) which represent sites of mRNA decapping
CC and 5' to 3' exonucleotidic decay.
CC -!- MISCELLANEOUS: Present with 2340 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the EDC3 family. {ECO:0000305}.
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DR EMBL; U18530; AAB64492.1; -; Genomic_DNA.
DR EMBL; BK006939; DAA07639.1; -; Genomic_DNA.
DR PIR; S50444; S50444.
DR RefSeq; NP_010901.1; NM_001178830.1.
DR PDB; 4BRU; X-ray; 3.24 A; B=77-116.
DR PDB; 6Y3Z; X-ray; 3.49 A; C=1-66.
DR PDBsum; 4BRU; -.
DR PDBsum; 6Y3Z; -.
DR AlphaFoldDB; P39998; -.
DR SMR; P39998; -.
DR BioGRID; 36716; 94.
DR DIP; DIP-842N; -.
DR IntAct; P39998; 24.
DR MINT; P39998; -.
DR STRING; 4932.YEL015W; -.
DR iPTMnet; P39998; -.
DR MaxQB; P39998; -.
DR PaxDb; P39998; -.
DR PRIDE; P39998; -.
DR EnsemblFungi; YEL015W_mRNA; YEL015W; YEL015W.
DR GeneID; 856700; -.
DR KEGG; sce:YEL015W; -.
DR SGD; S000000741; EDC3.
DR VEuPathDB; FungiDB:YEL015W; -.
DR eggNOG; KOG2585; Eukaryota.
DR GeneTree; ENSGT00390000016435; -.
DR HOGENOM; CLU_037134_0_0_1; -.
DR InParanoid; P39998; -.
DR OMA; NLAMFDK; -.
DR BioCyc; YEAST:G3O-30140-MON; -.
DR Reactome; R-SCE-430039; mRNA decay by 5' to 3' exoribonuclease.
DR PRO; PR:P39998; -.
DR Proteomes; UP000002311; Chromosome V.
DR RNAct; P39998; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0000932; C:P-body; IDA:SGD.
DR GO; GO:0003729; F:mRNA binding; IDA:SGD.
DR GO; GO:0031087; P:deadenylation-independent decapping of nuclear-transcribed mRNA; IMP:SGD.
DR GO; GO:0033962; P:P-body assembly; IMP:SGD.
DR GO; GO:1900153; P:positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay; IMP:SGD.
DR Gene3D; 3.40.50.10260; -; 1.
DR InterPro; IPR025762; DFDF.
DR InterPro; IPR019050; FDF_dom.
DR InterPro; IPR004443; YjeF_N_dom.
DR InterPro; IPR036652; YjeF_N_dom_sf.
DR Pfam; PF09532; FDF; 1.
DR Pfam; PF03853; YjeF_N; 1.
DR SMART; SM01199; FDF; 1.
DR SUPFAM; SSF64153; SSF64153; 1.
DR PROSITE; PS51512; DFDF; 1.
DR PROSITE; PS51385; YJEF_N; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Phosphoprotein; Reference proteome.
FT CHAIN 1..551
FT /note="Enhancer of mRNA-decapping protein 3"
FT /id="PRO_0000202613"
FT DOMAIN 93..129
FT /note="DFDF"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00845"
FT DOMAIN 288..527
FT /note="YjeF N-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00719"
FT REGION 64..92
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 64..85
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 257
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17287358,
FT ECO:0007744|PubMed:17330950, ECO:0007744|PubMed:19779198"
FT MOD_RES 261
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MUTAGEN 360..361
FT /note="RH->AA: Abolishes homodimerization."
FT /evidence="ECO:0000269|PubMed:18678652"
FT STRAND 8..12
FT /evidence="ECO:0007829|PDB:6Y3Z"
FT STRAND 22..26
FT /evidence="ECO:0007829|PDB:6Y3Z"
FT STRAND 28..38
FT /evidence="ECO:0007829|PDB:6Y3Z"
FT STRAND 43..50
FT /evidence="ECO:0007829|PDB:6Y3Z"
FT HELIX 51..53
FT /evidence="ECO:0007829|PDB:6Y3Z"
FT STRAND 56..61
FT /evidence="ECO:0007829|PDB:6Y3Z"
FT HELIX 91..94
FT /evidence="ECO:0007829|PDB:4BRU"
FT TURN 97..99
FT /evidence="ECO:0007829|PDB:4BRU"
FT HELIX 107..110
FT /evidence="ECO:0007829|PDB:4BRU"
SQ SEQUENCE 551 AA; 61340 MW; BF28AE67F9303A73 CRC64;
MSQFVGFGVQ VELKDGKLIQ GKIAKATSKG LTLNDVQFGD GGKSQAFKVR ASRLKDLKVL
TVASQSGKRK QQRQQQQQND YNQNRGEHID WQDDDVSKIK QQEDFDFQRN LGMFNKKDVF
AQLKQNDDIL PENRLQGHNR KQTQLQQNNY QNDELVIPDA KKDSWNKISS RNEQSTHQSQ
PQQDAQDDLV LEDDEHEYDV DDIDDPKYLP ITQSLNITHL IHSATNSPSI NDKTKGTVIN
DKDQVLAKLG QMIISQSRSN STSLPAANKQ TTIRSKNTKQ NIPMATPVQL LEMESITSEF
FSINSAGLLE NFAVNASFFL KQKLGGRARL RLQNSNPEPL VVILASDSNR SGAKALALGR
HLCQTGHIRV ITLFTCSQNE LQDSMVKKQT DIYKKCGGKI VNSVSSLESA METLNSPVEI
VIDAMQGYDC TLSDLAGTSE VIESRIKSMI SWCNKQRGST KVWSLDIPNG FDAGSGMPDI
FFSDRIEATG IICSGWPLIA INNLIANLPS LEDAVLIDIG IPQGAYSQRT SLRKFQNCDL
FVTDGSLLLD L
