P39998 (EDC3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Enhancer of mRNA-decapping protein 3

Gene names

Name:	EDC3
Synonyms:	LSM16
Ordered Locus Names:	YEL015W

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	551 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Stimulates decapping of both stable and unstable mRNA during mRNA decay. Does not affect nonsense-mediated mRNA decay. Required for normal P-body assembly. Ref.2 Ref.4
Subunit structure	Homodimer. Interacts with DCP2. Ref.2
Subcellular location	Cytoplasm › P-body. 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. Ref.4
Miscellaneous	Present with 2340 molecules/cell in log phase SD medium. Ref.5
Sequence similarities	Belongs to the EDC3 family. Contains 1 DFDF domain. Contains 1 YjeF N-terminal domain.

Ontologies

Keywords
Cellular component	Cytoplasm
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	cytoplasmic mRNA processing body assembly Inferred from mutant phenotype. Source: SGD deadenylation-independent decapping of nuclear-transcribed mRNA Inferred from mutant phenotype. Source: SGD
Cellular component	cytoplasmic mRNA processing body Inferred from direct assay Ref.4. Source: SGD
Molecular function	protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
DCP1	Q12517	5	EBI-22300,EBI-38519
DCP2	P53550	6	EBI-22300,EBI-270
DHH1	P39517	3	EBI-22300,EBI-158

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 551	551	Enhancer of mRNA-decapping protein 3		PRO_0000202613
Regions
	Domain	93 – 129	37	DFDF
	Domain	288 – 527	240	YjeF N-terminal
Amino acid modifications
	Modified residue	257	1	Phosphoserine Ref.6 Ref.7 Ref.8
	Modified residue	261	1	Phosphoserine Ref.7 Ref.8
Experimental info
	Mutagenesis	360 – 361	2	RH → AA: Abolishes homodimerization. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	P39998 [UniParc]. Last modified February 1, 1995. Version 1. Checksum: BF28AE67F9303A73	FASTA	551	61,340
	10 20 30 40 50 60 MSQFVGFGVQ VELKDGKLIQ GKIAKATSKG LTLNDVQFGD GGKSQAFKVR ASRLKDLKVL 70 80 90 100 110 120 TVASQSGKRK QQRQQQQQND YNQNRGEHID WQDDDVSKIK QQEDFDFQRN LGMFNKKDVF 130 140 150 160 170 180 AQLKQNDDIL PENRLQGHNR KQTQLQQNNY QNDELVIPDA KKDSWNKISS RNEQSTHQSQ 190 200 210 220 230 240 PQQDAQDDLV LEDDEHEYDV DDIDDPKYLP ITQSLNITHL IHSATNSPSI NDKTKGTVIN 250 260 270 280 290 300 DKDQVLAKLG QMIISQSRSN STSLPAANKQ TTIRSKNTKQ NIPMATPVQL LEMESITSEF 310 320 330 340 350 360 FSINSAGLLE NFAVNASFFL KQKLGGRARL RLQNSNPEPL VVILASDSNR SGAKALALGR 370 380 390 400 410 420 HLCQTGHIRV ITLFTCSQNE LQDSMVKKQT DIYKKCGGKI VNSVSSLESA METLNSPVEI 430 440 450 460 470 480 VIDAMQGYDC TLSDLAGTSE VIESRIKSMI SWCNKQRGST KVWSLDIPNG FDAGSGMPDI 490 500 510 520 530 540 FFSDRIEATG IICSGWPLIA INNLIANLPS LEDAVLIDIG IPQGAYSQRT SLRKFQNCDL 550 FVTDGSLLLD L

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome V." Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E., Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S., Hyman R.W. , Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X., Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y., Botstein D., Davis R.W. Nature 387:78-81(1997) [PubMed: 9169868] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[2]	"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: 18678652] [Abstract] Cited for: FUNCTION, INTERACTION WITH DCP2, MUTAGENESIS OF 360-ARG-HIS-361.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"Identification of Edc3p as an enhancer of mRNA decapping in Saccharomyces cerevisiae." Kshirsagar M., Parker R. Genetics 166:729-739(2004) [PubMed: 15020463] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[5]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[6]	"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: 17330950] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-257, MASS SPECTROMETRY. Strain: ADR376.
[7]	"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: 17287358] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-257 AND SER-261, MASS SPECTROMETRY.
[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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-257 AND SER-261, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U18530 Genomic DNA. Translation: AAB64492.1. BK006939 Genomic DNA. Translation: DAA07639.1.
PIR	S50444.
RefSeq	NP_010901.1. NM_001178830.1.
3D structure databases
ProteinModelPortal	P39998.
SMR	P39998. Positions 2-67.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-842N.
IntAct	P39998. 23 interactions.
MINT	MINT-385078.
STRING	P39998.
Proteomic databases
PeptideAtlas	P39998.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YEL015W; YEL015W; YEL015W.
GeneID	856700.
KEGG	sce:YEL015W.
NMPDR	fig|4932.3.peg.1957.
Organism-specific databases
CYGD	YEL015w.
SGD	S000000741. EDC3.
Phylogenomic databases
eggNOG	fuNOG05594.
GeneTree	EFGT00050000003947.
HOGENOM	HBG396957.
OMA	LAMFDKK.
OrthoDB	EOG4350GH.
Gene expression databases
ArrayExpress	P39998.
Genevestigator	P39998.
GermOnline	YEL015W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR019050. DFDF_motif. IPR004443. YjeF_N. [Graphical view]
Gene3D	G3DSA:3.40.50.10260. G3DSA:3.40.50.10260. 1 hit.
KO	K12615.
Pfam	PF09532. DFDF. 1 hit. PF03853. YjeF_N. 1 hit. [Graphical view]
SUPFAM	SSF64153. YjeF_N. 1 hit.
PROSITE	PS51512. DFDF. 1 hit. PS51385. YJEF_N. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	982763.

Entry information

Entry name

EDC3_YEAST

Accession

Primary (citable) accession number: P39998
Secondary accession number(s): D3DLN5

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	December 14, 2011
This is version 88 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program