Q96F86 (EDC3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Enhancer of mRNA-decapping protein 3

Alternative name(s):
LSM16 homolog
YjeF N-terminal domain-containing protein 2
Short name=YjeF_N2
Short name=hYjeF_N2
YjeF domain-containing protein 1

Gene names

Name:	EDC3
Synonyms:	LSM16, YJDC, YJEFN2
ORF Names:	PP844

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	508 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Binds single-stranded RNA. In the process of mRNA degradation, may play a role in mRNA decapping. May play a role in spermiogenesis and oogenesis. Ref.5 Ref.7 Ref.14
Subunit structure	Homodimer (via YjeF N-terminal domain). Forms a complex with DCP1A, DCP2, DDX6 and EDC4/HEDLS, within this complex directly interacts with DCP1A and DDX6. Interacts with ZFP36. Ref.5 Ref.14 Ref.15
Subcellular location	Cytoplasm › P-body. Note: Processing bodies (PB). Ref.5
Tissue specificity	Expressed in theca and granulosa cells in ovary, and in spermatids of the meiotic division part II and apical membrane of Sertoli cells in testis (at protein level). Also expressed in brain and mammary gland. Ref.7
Domain	The DFDF domain is unstructured by itself. It assumes a helical fold upon interaction with DDX6. Ref.15
Sequence similarities	Belongs to the EDC3 family. Contains 1 DFDF domain. Contains 1 YjeF N-terminal domain.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	RNA-binding
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay Traceable author statement. Source: Reactome gene expression Traceable author statement. Source: Reactome
Cellular_component	cytoplasmic mRNA processing body Inferred from electronic annotation. Source: UniProtKB-SubCell cytosol Traceable author statement. Source: Reactome
Molecular_function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		2	EBI-997311,EBI-997311
DDX6	P26196	2	EBI-997311,EBI-351257
ZFP36	P26651	2	EBI-997311,EBI-374248

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 508

508

Enhancer of mRNA-decapping protein 3

PRO_0000119054

Regions

Domain

192 – 228

37

DFDF

Domain

283 – 487

205

YjeF N-terminal

Region

1 – 79

79

Required for P-body targeting and interaction with DCP1A By similarity

Region

191 – 296

106

Required for interaction with DDX6 By similarity

Amino acid modifications

Modified residue

131

1

Phosphoserine Ref.6 Ref.8

Modified residue

138

1

Phosphoserine Ref.12

Modified residue

140

1

Phosphoserine Ref.12

Modified residue

161

1

Phosphoserine Ref.9 Ref.10

Experimental info

Mutagenesis

204

1

F → A: Abolishes interaction with DDX6; when associated with A-206. Ref.15

Mutagenesis

206

1

F → A: Abolishes interaction with DDX6; when associated with A-204. Ref.15

Mutagenesis

306

1

E → A: Abolishes homodimerization and RNA binding; when associated with A-310. Ref.14

Mutagenesis

310

1

V → A: Abolishes homodimerization and RNA binding; when associated with A-306. Ref.14

Sequence conflict

74

1

Q → R in BAB15001. Ref.2

Secondary structure

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508

Helix Strand Turn

Details...

Turn

4 – 7

4

Beta strand

9 – 13

5

Turn

16 – 18

3

Beta strand

20 – 29

10

Turn

30 – 33

4

Beta strand

34 – 42

9

Beta strand

48 – 55

8

Helix

56 – 58

3

Beta strand

60 – 66

7

Helix

206 – 210

5

Helix

215 – 225

11

Beta strand

270 – 272

3

Beta strand

278 – 280

3

Helix

284 – 296

13

Helix

301 – 319

19

Beta strand

336 – 341

6

Helix

345 – 359

15

Beta strand

363 – 367

5

Helix

376 – 385

10

Beta strand

391 – 394

4

Helix

396 – 398

3

Beta strand

405 – 410

6

Helix

419 – 421

3

Helix

423 – 435

13

Beta strand

439 – 443

5

Beta strand

456 – 463

8

Helix

469 – 471

3

Beta strand

473 – 477

5

Helix

483 – 488

6

Turn

496 – 499

4

Beta strand

501 – 506

6

Sequences

	Sequence		Length	Mass (Da)
	Q96F86 [UniParc]. Last modified December 1, 2001. Version 1. Checksum: 95346F484FCFC3EA	FASTA	508	56,078
	10 20 30 40 50 60 MATDWLGSIV SINCGDSLGV YQGRVSAVDQ VSQTISLTRP FHNGVKCLVP EVTFRAGDIT 70 80 90 100 110 120 ELKILEIPGP GDNQHFGDLH QTELGPSGAG CQVGINQNGT GKFVKKPASS SSAPQNIPKR 130 140 150 160 170 180 TDVKSQDVAV SPQQQQCSKS YVDRHMESLS QSKSFRRRHN SWSSSSRHPN QATPKKSGLK 190 200 210 220 230 240 NGQMKNKDDE CFGDDIEEIP DTDFDFEGNL ALFDKAAVFE EIDTYERRSG TRSRGIPNER 250 260 270 280 290 300 PTRYRHDENI LESEPIVYRR IIVPHNVSKE FCTDSGLVVP SISYELHKKL LSVAEKHGLT 310 320 330 340 350 360 LERRLEMTGV CASQMALTLL GGPNRLNPKN VHQRPTVALL CGPHVKGAQG ISCGRHLANH 370 380 390 400 410 420 DVQVILFLPN FVKMLESITN ELSLFSKTQG QQVSSLKDLP TSPVDLVINC LDCPENVFLR 430 440 450 460 470 480 DQPWYKAAVA WANQNRAPVL SIDPPVHEVE QGIDAKWSLA LGLPLPLGEH AGRIYLCDIG 490 500 IPQQVFQEVG INYHSPFGCK FVIPLHSA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Large-scale cDNA transfection screening for genes related to cancer development and progression." Wan D., Gong Y., Qin W., Zhang P., Li J., Wei L., Zhou X., Li H., Qiu X., Zhong F., He L., Yu J., Yao G., Jiang H., Qian L., Yu Y., Shu H., Chen X. , Xu H., Guo M., Pan Z., Chen Y., Ge C., Yang S., Gu J. Proc. Natl. Acad. Sci. U.S.A. 101:15724-15729(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[2]	"Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S. Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[3]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Eye and Placenta.
[5]	"Multiple processing body factors and the ARE binding protein TTP activate mRNA decapping." Fenger-Groen M., Fillman C., Norrild B., Lykke-Andersen J. Mol. Cell 20:905-915(2005) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, INTERACTION WITH DCP1A; DCP2; DDX6; EDC4 AND ZFP36, SUBCELLULAR LOCATION, FUNCTION.
[6]	"A probability-based approach for high-throughput protein phosphorylation analysis and site localization." Beausoleil S.A., Villen J., Gerber S.A., Rush J., Gygi S.P. Nat. Biotechnol. 24:1285-1292(2006) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-131, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[7]	"ApoA-I-binding protein (AI-BP) and its homologues hYjeF_N2 and hYjeF_N3 comprise the YjeF_N domain protein family in humans with a role in spermiogenesis and oogenesis." Rudolph C., Sigruener A., Hartmann A., Orso E., Bals-Pratsch M., Gronwald W., Seifert B., Kalbitzer H.R., Verdorfer I., Luetjens C.M., Ortmann O., Bornstein S.R., Schmitz G. Horm. Metab. Res. 39:322-335(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, TISSUE SPECIFICITY.
[8]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-131, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[9]	"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-161, MASS SPECTROMETRY. Tissue: Leukemic T-cell.
[10]	"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis." Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M. Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-161, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[11]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]	"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation." Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B. Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-138 AND SER-140, MASS SPECTROMETRY.
[13]	"A divergent Sm fold in EDC3 proteins mediates DCP1 binding and P-body targeting." Tritschler F., Eulalio A., Truffault V., Hartmann M.D., Helms S., Schmidt S., Coles M., Izaurralde E., Weichenrieder O. Mol. Cell. Biol. 27:8600-8611(2007) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.31 ANGSTROMS) OF 1-82.
[14]	"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: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 250-508, FUNCTION, RNA-BINDING, SUBUNIT, CIRCULAR DICHROISM, MUTAGENESIS OF GLU-306 AND VAL-310.
[15]	"Structural basis for the mutually exclusive anchoring of P body components EDC3 and Tral to the DEAD box protein DDX6/Me31B." Tritschler F., Braun J.E., Eulalio A., Truffault V., Izaurralde E., Weichenrieder O. Mol. Cell 33:661-668(2009) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 192-228 IN COMPLEX WITH DDX6, INTERACTION WITH DDX6, MUTAGENESIS OF PHE-204 AND PHE-206, DOMAIN.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF193058 mRNA. Translation: AAG22486.1.
AK024781 mRNA. Translation: BAB15001.1.
AK056339 mRNA. Translation: BAG51682.1.
CH471136 Genomic DNA. Translation: EAW99316.1.
CH471136 Genomic DNA. Translation: EAW99317.1.
CH471136 Genomic DNA. Translation: EAW99318.1.
CH471136 Genomic DNA. Translation: EAW99319.1.
BC011534 mRNA. Translation: AAH11534.1.
BC021271 mRNA. Translation: AAH21271.1.

IPI

IPI00018009.

RefSeq

NP_001135915.1. NM_001142443.1.
NP_001135916.1. NM_001142444.1.
NP_079359.2. NM_025083.3.

UniGene

Hs.682454.
Hs.96852.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2VC8	X-ray	1.31	A	1-82	[»]
2WAX	X-ray	2.30	B/D	192-228	[»]
2WAY	X-ray	2.30	B/D	192-228	[»]
3D3J	X-ray	2.80	A	203-508	[»]
3D3K	X-ray	2.20	A/B/C/D	250-508	[»]

ProteinModelPortal

Q96F86.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-35516N.

IntAct

Q96F86. 9 interactions.

MINT

MINT-5005528.

STRING

9606.ENSP00000320503.

PTM databases

PhosphoSite

Q96F86.

Polymorphism databases

DMDM

74731669.

Proteomic databases

PaxDb

Q96F86.

PeptideAtlas

Q96F86.

PRIDE

Q96F86.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000315127; ENSP00000320503; ENSG00000179151.
ENST00000426797; ENSP00000401343; ENSG00000179151.
ENST00000568176; ENSP00000455580; ENSG00000179151.

GeneID

80153.

KEGG

hsa:80153.

UCSC

uc002aym.3. human.

Organism-specific databases

CTD

80153.

GeneCards

GC15M074922.

HGNC

HGNC:26114. EDC3.

HPA

HPA040650.
HPA044206.

MIM

609842. gene.

neXtProt

NX_Q96F86.

PharmGKB

PA142670551.

GenAtlas

Search...

Phylogenomic databases

eggNOG

NOG271303.

HOGENOM

HOG000231481.

HOVERGEN

HBG079428.

InParanoid

Q96F86.

KO

K12615.

OMA

KGFRRRH.

OrthoDB

EOG4W0XCZ.

PhylomeDB

Q96F86.

Enzyme and pathway databases

Reactome

REACT_21257. Metabolism of RNA.
REACT_71. Gene Expression.

Gene expression databases

ArrayExpress

Q96F86.

Bgee

Q96F86.

CleanEx

HS_EDC3.

Genevestigator

Q96F86.

GermOnline

ENSG00000179151. Homo sapiens.

Family and domain databases

Gene3D

3.40.50.10260. 1 hit.

InterPro

IPR025762. DFDF.
IPR019050. FDF_dom.
IPR025609. Lsm14_N.
IPR004443. YjeF_N_dom.
[Graphical view]

Pfam

PF09532. FDF. 1 hit.
PF12701. LSM14. 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

EvolutionaryTrace

Q96F86.

GenomeRNAi

80153.

NextBio

70444.

SOURCE

Search...

Entry information

Entry name

EDC3_HUMAN

Accession

Primary (citable) accession number: Q96F86
Secondary accession number(s): B3KPH0, D3DW61, Q9H797

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 22, 2005
Last sequence update:	December 1, 2001
Last modified:	May 1, 2013
This is version 101 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.