Reviewed, UniProtKB/Swiss-Prot Q96F86 (EDC3_HUMAN)

Names and origin

Protein names

Recommended name:
    Enhancer of mRNA-decapping protein 3
Alternative name(s):
    LSM16 homolog
    YjeF domain-containing protein 1
    YjeF N-terminal domain-containing protein 2
      Short name=YjeF_N2
      Short name=hYjeF_N2

Gene names

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

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	508 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	In the process of mRNA degradation, may play a role in mRNA decapping. May play a role in spermiogenesis and oogenesis. Ref.4 Ref.6
Subunit structure	Forms a complex with DCP1A, DCP2, DDX6 and EDC4/HEDLS, within this complex directly interacts with DCP1A and DDX6. Interacts with ZFP36. Ref.4
Subcellular location	Cytoplasm › P-body. Note: Processing bodies (PB). Ref.4
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.6
Sequence similarities	Belongs to the EDC3 family. Contains 1 YjeF N-terminal domain.

Ontologies

Keywords
Cellular component	Cytoplasm
PTM	Phosphoprotein
Technical term	3D-structure
Gene Ontology (GO)
Cellular component	cytoplasmic mRNA processing body Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	protein binding Ref.4 Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
DDX6	P26196	1	EBI-997311,EBI-351257
YWHAB	P31946	1	EBI-997311,EBI-359815
YWHAG	P61981	1	EBI-997311,EBI-359832
YWHAQ	P27348	1	EBI-997311,EBI-359854
YWHAZ	P63104	1	EBI-997311,EBI-347088
ZFP36	P26651	1	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

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.5 Ref.7 Ref.9

Modified residue

161

1

Phosphoserine Ref.8

Experimental info

Sequence conflict

74

1

Q → R in BAB15001. Ref.2

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

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

Sequences

	Sequence		Length	Mass (Da)
	Q96F86-1 [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: 15498874] [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: 14702039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[3]	"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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Eye and Placenta.
[4]	"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: 16364915] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, INTERACTION WITH DCP1A; DCP2; DDX6; EDC4 AND ZFP36, SUBCELLULAR LOCATION, FUNCTION.
[5]	"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: 16964243] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-131, MASS SPECTROMETRY. Tissue: Epithelium.
[6]	"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: 17533573] [Abstract] Cited for: FUNCTION, TISSUE SPECIFICITY.
[7]	"Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry." Molina H., Horn D.M., Tang N., Mathivanan S., Pandey A. Proc. Natl. Acad. Sci. U.S.A. 104:2199-2204(2007) [PubMed: 17287340] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-131, MASS SPECTROMETRY.
[8]	"Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis." Cantin G.T., Yi W., Lu B., Park S.K., Xu T., Lee J.-D., Yates J.R. III J. Proteome Res. 7:1346-1351(2008) [PubMed: 18220336] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-161, MASS SPECTROMETRY.
[9]	"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: 18669648] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-131, MASS SPECTROMETRY.
[10]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[11]	"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: 17923697] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.31 ANGSTROMS) OF 1-82.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AF193058 mRNA. Translation: AAG22486.1.
AK024781 mRNA. Translation: BAB15001.1.
BC011534 mRNA. Translation: AAH11534.1.
BC021271 mRNA. Translation: AAH21271.1.

IPI

IPI00018009.

RefSeq

NP_001135915.1.
NP_001135916.1.
NP_079359.2.

UniGene

Hs.96852

3D structure databases

PDBPDBe

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	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

Q96F86. 11 interactions.

PTM databases

PhosphoSite

Q96F86.

Proteomic databases

PeptideAtlas

Q96F86.

PRIDE

Q96F86.

Genome annotation databases

Ensembl

ENSG00000179151. Homo sapiens. [Contig view]

GeneID

80153.

KEGG

hsa:80153.

Organism-specific databases

GeneCards

GC15M072712.

H-InvDB

HIX0020864.

HGNC

HGNC:26114. EDC3.

MIM

609842. gene.

GenAtlas

Search...

Phylogenomic databases

HOGENOM

Q96F86.

HOVERGEN

Q96F86.

OMA

Q96F86. HAGRIYL.

Gene expression databases

ArrayExpress

Q96F86.

Bgee

Q96F86.

CleanEx

HS_EDC3.

GermOnline

ENSG00000179151. Homo sapiens.

Family and domain databases

InterPro

IPR019050. DFDF_motif.
IPR004443. YjeF_N.
[Graphical view]

Pfam

PF09532. DFDF. 1 hit.
PF03853. YjeF_N. 1 hit.
[Graphical view]

PROSITE

PS51385. YJEF_N. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

70444.

SOURCE

Search...

Entry information

Entry name

EDC3_HUMAN

Accession

Primary (citable) accession number: Q96F86
Secondary accession number(s): Q9H797

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 22, 2005
Last sequence update:	December 1, 2001
Last modified:	June 16, 2009
This is version 62 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)