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Protein

Enhancer of mRNA-decapping protein 3

Gene

EDC3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Binds single-stranded RNA. Involved in the process of mRNA degradation and in the positive regulation of mRNA decapping. May play a role in spermiogenesis and oogenesis.4 Publications

GO - Molecular functioni

  • identical protein binding Source: IntAct
  • mRNA binding Source: GO_Central
  • phosphodiesterase decapping endonuclease activity Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000179151-MONOMER.
ReactomeiR-HSA-430039. mRNA decay by 5' to 3' exoribonuclease.

Names & Taxonomyi

Protein namesi
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 namesi
Name:EDC3
Synonyms:LSM16, YJDC, YJEFN2
ORF Names:PP844
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 15

Organism-specific databases

HGNCiHGNC:26114. EDC3.

Subcellular locationi

  • CytoplasmP-body 1 Publication

  • Note: Processing bodies (PB).

GO - Cellular componenti

  • cytoplasmic mRNA processing body Source: GO_Central
  • cytosol Source: Reactome
  • membrane Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Involvement in diseasei

Mental retardation, autosomal recessive 50 (MRT50)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRT50 patients show mild intellectual disability and microcephaly.
See also OMIM:616460
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_07396354F → S in MRT50; does not enhance DCP2 decapping activity. 1 Publication1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi204F → A: Abolishes interaction with DDX6; when associated with A-206. 1 Publication1
Mutagenesisi206F → A: Abolishes interaction with DDX6; when associated with A-204. 1 Publication1
Mutagenesisi306E → A: Abolishes homodimerization and RNA binding; when associated with A-310. 1 Publication1
Mutagenesisi310V → A: Abolishes homodimerization and RNA binding; when associated with A-306. 1 Publication1

Keywords - Diseasei

Disease mutation, Mental retardation

Organism-specific databases

DisGeNETi80153.
MIMi616460. phenotype.
OpenTargetsiENSG00000179151.
PharmGKBiPA142670551.

Polymorphism and mutation databases

BioMutaiEDC3.
DMDMi74731669.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001190541 – 508Enhancer of mRNA-decapping protein 3Add BLAST508

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei131PhosphoserineCombined sources1
Modified residuei138PhosphoserineCombined sources1
Modified residuei140PhosphoserineCombined sources1
Modified residuei161PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ96F86.
MaxQBiQ96F86.
PaxDbiQ96F86.
PeptideAtlasiQ96F86.
PRIDEiQ96F86.

PTM databases

iPTMnetiQ96F86.
PhosphoSitePlusiQ96F86.

Expressioni

Tissue specificityi

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.1 Publication

Gene expression databases

BgeeiENSG00000179151.
CleanExiHS_EDC3.
ExpressionAtlasiQ96F86. baseline and differential.
GenevisibleiQ96F86. HS.

Organism-specific databases

HPAiHPA040650.
HPA044206.
HPA066137.

Interactioni

Subunit structurei

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 ZFP36.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself5EBI-997311,EBI-997311
ANXA10Q9UJ726EBI-997311,EBI-8648654
DCP1AQ9NPI611EBI-997311,EBI-374238
DCP1BQ8IZD46EBI-997311,EBI-521595
DDX6P261969EBI-997311,EBI-351257
EFHC2Q5JST65EBI-997311,EBI-2349927
ZFP36P266512EBI-997311,EBI-374248

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

BioGridi123144. 33 interactors.
DIPiDIP-35516N.
IntActiQ96F86. 26 interactors.
MINTiMINT-5005528.
STRINGi9606.ENSP00000320503.

Structurei

Secondary structure

1508
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni4 – 7Combined sources4
Beta strandi9 – 13Combined sources5
Turni16 – 18Combined sources3
Beta strandi20 – 29Combined sources10
Turni30 – 33Combined sources4
Beta strandi34 – 42Combined sources9
Beta strandi48 – 55Combined sources8
Helixi56 – 58Combined sources3
Beta strandi60 – 66Combined sources7
Helixi206 – 210Combined sources5
Helixi215 – 225Combined sources11
Beta strandi270 – 272Combined sources3
Beta strandi278 – 280Combined sources3
Helixi284 – 296Combined sources13
Helixi301 – 319Combined sources19
Beta strandi336 – 341Combined sources6
Helixi345 – 359Combined sources15
Beta strandi363 – 367Combined sources5
Helixi376 – 385Combined sources10
Beta strandi391 – 394Combined sources4
Helixi396 – 398Combined sources3
Beta strandi405 – 410Combined sources6
Helixi419 – 421Combined sources3
Helixi423 – 435Combined sources13
Beta strandi439 – 443Combined sources5
Beta strandi456 – 463Combined sources8
Helixi469 – 471Combined sources3
Beta strandi473 – 477Combined sources5
Helixi483 – 488Combined sources6
Turni496 – 499Combined sources4
Beta strandi501 – 506Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2VC8X-ray1.31A1-82[»]
2WAXX-ray2.30B/D192-228[»]
2WAYX-ray2.30B/D192-228[»]
3D3JX-ray2.80A203-508[»]
3D3KX-ray2.20A/B/C/D250-508[»]
ProteinModelPortaliQ96F86.
SMRiQ96F86.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ96F86.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini192 – 228DFDFPROSITE-ProRule annotationAdd BLAST37
Domaini283 – 487YjeF N-terminalPROSITE-ProRule annotationAdd BLAST205

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 79Required for P-body targeting and interaction with DCP1ABy similarityAdd BLAST79
Regioni191 – 296Required for interaction with DDX6By similarityAdd BLAST106

Domaini

The DFDF domain is unstructured by itself. It assumes a helical fold upon interaction with DDX6.1 Publication

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

eggNOGiKOG2585. Eukaryota.
COG0062. LUCA.
GeneTreeiENSGT00390000016435.
HOGENOMiHOG000231481.
HOVERGENiHBG079428.
InParanoidiQ96F86.
KOiK12615.
OMAiNQHFGDL.
OrthoDBiEOG091G09C2.
PhylomeDBiQ96F86.
TreeFamiTF324695.

Family and domain databases

Gene3Di3.40.50.10260. 1 hit.
InterProiIPR025762. DFDF.
IPR019050. FDF_dom.
IPR025609. Lsm14_N.
IPR004443. YjeF_N_dom.
[Graphical view]
PfamiPF09532. FDF. 1 hit.
PF12701. LSM14. 1 hit.
PF03853. YjeF_N. 1 hit.
[Graphical view]
SMARTiSM01199. FDF. 1 hit.
SM01271. LSM14. 1 hit.
[Graphical view]
SUPFAMiSSF64153. SSF64153. 1 hit.
PROSITEiPS51512. DFDF. 1 hit.
PS51385. YJEF_N. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q96F86-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATDWLGSIV SINCGDSLGV YQGRVSAVDQ VSQTISLTRP FHNGVKCLVP
60 70 80 90 100
EVTFRAGDIT ELKILEIPGP GDNQHFGDLH QTELGPSGAG CQVGINQNGT
110 120 130 140 150
GKFVKKPASS SSAPQNIPKR TDVKSQDVAV SPQQQQCSKS YVDRHMESLS
160 170 180 190 200
QSKSFRRRHN SWSSSSRHPN QATPKKSGLK NGQMKNKDDE CFGDDIEEIP
210 220 230 240 250
DTDFDFEGNL ALFDKAAVFE EIDTYERRSG TRSRGIPNER PTRYRHDENI
260 270 280 290 300
LESEPIVYRR IIVPHNVSKE FCTDSGLVVP SISYELHKKL LSVAEKHGLT
310 320 330 340 350
LERRLEMTGV CASQMALTLL GGPNRLNPKN VHQRPTVALL CGPHVKGAQG
360 370 380 390 400
ISCGRHLANH DVQVILFLPN FVKMLESITN ELSLFSKTQG QQVSSLKDLP
410 420 430 440 450
TSPVDLVINC LDCPENVFLR DQPWYKAAVA WANQNRAPVL SIDPPVHEVE
460 470 480 490 500
QGIDAKWSLA LGLPLPLGEH AGRIYLCDIG IPQQVFQEVG INYHSPFGCK

FVIPLHSA
Length:508
Mass (Da):56,078
Last modified:December 1, 2001 - v1
Checksum:i95346F484FCFC3EA
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti74Q → R in BAB15001 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_07396354F → S in MRT50; does not enhance DCP2 decapping activity. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS10267.1.
RefSeqiNP_001135915.1. NM_001142443.1.
NP_001135916.1. NM_001142444.1.
NP_079359.2. NM_025083.3.
UniGeneiHs.682454.
Hs.96852.

Genome annotation databases

EnsembliENST00000315127; ENSP00000320503; ENSG00000179151.
ENST00000426797; ENSP00000401343; ENSG00000179151.
ENST00000568176; ENSP00000455580; ENSG00000179151.
GeneIDi80153.
KEGGihsa:80153.
UCSCiuc002aym.4. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS10267.1.
RefSeqiNP_001135915.1. NM_001142443.1.
NP_001135916.1. NM_001142444.1.
NP_079359.2. NM_025083.3.
UniGeneiHs.682454.
Hs.96852.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2VC8X-ray1.31A1-82[»]
2WAXX-ray2.30B/D192-228[»]
2WAYX-ray2.30B/D192-228[»]
3D3JX-ray2.80A203-508[»]
3D3KX-ray2.20A/B/C/D250-508[»]
ProteinModelPortaliQ96F86.
SMRiQ96F86.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi123144. 33 interactors.
DIPiDIP-35516N.
IntActiQ96F86. 26 interactors.
MINTiMINT-5005528.
STRINGi9606.ENSP00000320503.

PTM databases

iPTMnetiQ96F86.
PhosphoSitePlusiQ96F86.

Polymorphism and mutation databases

BioMutaiEDC3.
DMDMi74731669.

Proteomic databases

EPDiQ96F86.
MaxQBiQ96F86.
PaxDbiQ96F86.
PeptideAtlasiQ96F86.
PRIDEiQ96F86.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000315127; ENSP00000320503; ENSG00000179151.
ENST00000426797; ENSP00000401343; ENSG00000179151.
ENST00000568176; ENSP00000455580; ENSG00000179151.
GeneIDi80153.
KEGGihsa:80153.
UCSCiuc002aym.4. human.

Organism-specific databases

CTDi80153.
DisGeNETi80153.
GeneCardsiEDC3.
HGNCiHGNC:26114. EDC3.
HPAiHPA040650.
HPA044206.
HPA066137.
MIMi609842. gene.
616460. phenotype.
neXtProtiNX_Q96F86.
OpenTargetsiENSG00000179151.
PharmGKBiPA142670551.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2585. Eukaryota.
COG0062. LUCA.
GeneTreeiENSGT00390000016435.
HOGENOMiHOG000231481.
HOVERGENiHBG079428.
InParanoidiQ96F86.
KOiK12615.
OMAiNQHFGDL.
OrthoDBiEOG091G09C2.
PhylomeDBiQ96F86.
TreeFamiTF324695.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000179151-MONOMER.
ReactomeiR-HSA-430039. mRNA decay by 5' to 3' exoribonuclease.

Miscellaneous databases

ChiTaRSiEDC3. human.
EvolutionaryTraceiQ96F86.
GeneWikiiEDC3.
GenomeRNAii80153.
PROiQ96F86.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000179151.
CleanExiHS_EDC3.
ExpressionAtlasiQ96F86. baseline and differential.
GenevisibleiQ96F86. HS.

Family and domain databases

Gene3Di3.40.50.10260. 1 hit.
InterProiIPR025762. DFDF.
IPR019050. FDF_dom.
IPR025609. Lsm14_N.
IPR004443. YjeF_N_dom.
[Graphical view]
PfamiPF09532. FDF. 1 hit.
PF12701. LSM14. 1 hit.
PF03853. YjeF_N. 1 hit.
[Graphical view]
SMARTiSM01199. FDF. 1 hit.
SM01271. LSM14. 1 hit.
[Graphical view]
SUPFAMiSSF64153. SSF64153. 1 hit.
PROSITEiPS51512. DFDF. 1 hit.
PS51385. YJEF_N. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiEDC3_HUMAN
AccessioniPrimary (citable) accession number: Q96F86
Secondary accession number(s): B3KPH0, D3DW61, Q9H797
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: December 1, 2001
Last modified: November 30, 2016
This is version 137 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 15
    Human chromosome 15: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

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.