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Protein

Enhancer of mRNA-decapping protein 3

Gene

EDC3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

Keywordsi

Molecular functionRNA-binding

Enzyme and pathway databases

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

EuPathDBiHostDB:ENSG00000179151.11
HGNCiHGNC:26114 EDC3
MIMi609842 gene
neXtProtiNX_Q96F86

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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 PublicationCorresponds to variant dbSNP:rs1057517676Ensembl.1

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
MalaCardsiEDC3
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
ProteomicsDBi76503

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 Expressed in 158 organ(s), highest expression level in testis
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

GO - Molecular functioni

Protein-protein interaction databases

BioGridi123144, 62 interactors
CORUMiQ96F86
DIPiDIP-35516N
IntActiQ96F86, 29 interactors
MINTiQ96F86
STRINGi9606.ENSP00000320503

Structurei

Secondary structure

1508
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

Phylogenomic databases

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

Family and domain databases

CDDicd01737 LSm16_N, 1 hit
Gene3Di3.40.50.10260, 1 hit
InterProiView protein in InterPro
IPR025762 DFDF
IPR019050 FDF_dom
IPR025609 Lsm14-like_N
IPR034107 Lsm16_N
IPR004443 YjeF_N_dom
IPR036652 YjeF_N_dom_sf
PfamiView protein in Pfam
PF09532 FDF, 1 hit
PF12701 LSM14, 1 hit
PF03853 YjeF_N, 1 hit
SMARTiView protein in SMART
SM01199 FDF, 1 hit
SM01271 LSM14, 1 hit
SUPFAMiSSF64153 SSF64153, 1 hit
PROSITEiView protein in PROSITE
PS51512 DFDF, 1 hit
PS51385 YJEF_N, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 12 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 12 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
H3BSQ0H3BSQ0_HUMAN
Enhancer of mRNA-decapping protein ...
EDC3
163Annotation score:
H3BPN4H3BPN4_HUMAN
Enhancer of mRNA-decapping protein ...
EDC3
213Annotation score:
H3BPW9H3BPW9_HUMAN
Enhancer of mRNA-decapping protein ...
EDC3
253Annotation score:
H3BU87H3BU87_HUMAN
Enhancer of mRNA-decapping protein ...
EDC3
131Annotation score:
H3BQ37H3BQ37_HUMAN
Enhancer of mRNA-decapping protein ...
EDC3
177Annotation score:
H3BNJ7H3BNJ7_HUMAN
Enhancer of mRNA-decapping protein ...
EDC3
57Annotation score:
H3BQP5H3BQP5_HUMAN
Enhancer of mRNA-decapping protein ...
EDC3
123Annotation score:
H3BTF8H3BTF8_HUMAN
Enhancer of mRNA-decapping protein ...
EDC3
54Annotation score:
H3BTH0H3BTH0_HUMAN
Enhancer of mRNA-decapping protein ...
EDC3
101Annotation score:
H3BMB8H3BMB8_HUMAN
Enhancer of mRNA-decapping protein ...
EDC3
92Annotation score:
There are more potential isoformsShow all

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 PublicationCorresponds to variant dbSNP:rs1057517676Ensembl.1

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

Similar proteinsi

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, 62 interactors
CORUMiQ96F86
DIPiDIP-35516N
IntActiQ96F86, 29 interactors
MINTiQ96F86
STRINGi9606.ENSP00000320503

PTM databases

iPTMnetiQ96F86
PhosphoSitePlusiQ96F86

Polymorphism and mutation databases

BioMutaiEDC3
DMDMi74731669

Proteomic databases

EPDiQ96F86
MaxQBiQ96F86
PaxDbiQ96F86
PeptideAtlasiQ96F86
PRIDEiQ96F86
ProteomicsDBi76503

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
EuPathDBiHostDB:ENSG00000179151.11
GeneCardsiEDC3
HGNCiHGNC:26114 EDC3
HPAiHPA040650
HPA044206
HPA066137
MalaCardsiEDC3
MIMi609842 gene
616460 phenotype
neXtProtiNX_Q96F86
OpenTargetsiENSG00000179151
PharmGKBiPA142670551
GenAtlasiSearch...

Phylogenomic databases

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

Enzyme and pathway databases

ReactomeiR-HSA-430039 mRNA decay by 5' to 3' exoribonuclease

Miscellaneous databases

ChiTaRSiEDC3 human
EvolutionaryTraceiQ96F86
GeneWikiiEDC3
GenomeRNAii80153
PROiPR:Q96F86
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000179151 Expressed in 158 organ(s), highest expression level in testis
CleanExiHS_EDC3
ExpressionAtlasiQ96F86 baseline and differential
GenevisibleiQ96F86 HS

Family and domain databases

CDDicd01737 LSm16_N, 1 hit
Gene3Di3.40.50.10260, 1 hit
InterProiView protein in InterPro
IPR025762 DFDF
IPR019050 FDF_dom
IPR025609 Lsm14-like_N
IPR034107 Lsm16_N
IPR004443 YjeF_N_dom
IPR036652 YjeF_N_dom_sf
PfamiView protein in Pfam
PF09532 FDF, 1 hit
PF12701 LSM14, 1 hit
PF03853 YjeF_N, 1 hit
SMARTiView protein in SMART
SM01199 FDF, 1 hit
SM01271 LSM14, 1 hit
SUPFAMiSSF64153 SSF64153, 1 hit
PROSITEiView protein in PROSITE
PS51512 DFDF, 1 hit
PS51385 YJEF_N, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiEDC3_HUMAN
AccessioniPrimary (citable) accession number: Q96F86
Secondary accession number(s): B3KPH0, D3DW61, Q9H797
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: December 1, 2001
Last modified: September 12, 2018
This is version 151 of the entry and version 1 of the sequence. See 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  5. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  6. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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