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Q3B8Q2 (IF4A3_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 62. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Eukaryotic initiation factor 4A-III

Short name=eIF-4A-III
Short name=eIF4A-III
EC=3.6.4.13
Alternative name(s):
ATP-dependent RNA helicase DDX48
ATP-dependent RNA helicase eIF4A-3
DEAD box protein 48
Eukaryotic translation initiation factor 4A isoform 3
Gene names
Name:Eif4a3
Synonyms:Ddx48
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus

Protein attributes

Sequence length411 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

ATP-dependent RNA helicase. Core component of the splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junctions on mRNAs. The EJC is a dynamic structure consisting of core proteins and several peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. The EJC marks the position of the exon-exon junction in the mature mRNA for the gene expression machinery and the core components remain bound to spliced mRNAs throughout all stages of mRNA metabolism thereby influencing downstream processes including nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Its RNA-dependent ATPase and RNA-helicase activities are induced by CASC3, but abolished in presence of the MAGOH-RBM8A heterodimer, thereby trapping the ATP-bound EJC core onto spliced mRNA in a stable conformation. The inhibition of ATPase activity by the MAGOH-RBM8A heterodimer increases the RNA-binding affinity of the EJC. Involved in translational enhancement of spliced mRNAs after formation of the 80S ribosome complex. Binds spliced mRNA in sequence-independent manner, 20-24 nucleotides upstream of mRNA exon-exon junctions. Shows higher affinity for single-stranded RNA in an ATP-bound core EJC complex than after the ATP is hydrolyzed. Involved in the splicing modulation of BCL2L1/Bcl-X (and probably other apoptotic genes); specifically inhibits formation of proapoptotic isoforms; the function is different from the established EJC assembly By similarity.

Catalytic activity

ATP + H2O = ADP + phosphate.

Enzyme regulation

The ATPase activity is increased some 4-fold in the presence of RNA.

Subunit structure

Part of the mRNA splicing-dependent exon junction complex (EJC) complex; the core complex contains CASC3, EIF4A3, MAGOH and RBM8A. Interacts with CASC3, MAGOH, NXF1, RBM8A and ALYREF/THOC4. Identified in the spliceosome C complex. May interact with NOM1. Interacts with POLDIP3. Interacts with CWC22 and PRPF19 in an RNA-independent manner. Direct interaction with CWC22 is mediated by the helicase C-terminal domain. Full interaction with CWC22 occurs only when EIF4A3 is not part of the EJC and prevents EIF4A3 binding to RNA By similarity.

Subcellular location

Nucleus. Nucleus speckle By similarity. Cytoplasm. Note: Nucleocytoplasmic shuttling protein. Travels to the cytoplasm as part of the exon junction complex (EJC) bound to mRNA By similarity. Detected in dendritic layer as well as the nuclear and cytoplasmic (somatic) compartments of neurons. Colocalizes with STAU1 and FMR1 in dendrites. Ref.3

Tissue specificity

Expressed in the CA1 field and dentate gyrus of the hippocampus (at protein level).

Sequence similarities

Belongs to the DEAD box helicase family. eIF4A subfamily.

Contains 1 helicase ATP-binding domain.

Contains 1 helicase C-terminal domain.

Ontologies

Keywords
   Biological processmRNA processing
mRNA splicing
mRNA transport
Nonsense-mediated mRNA decay
rRNA processing
Translation regulation
Transport
   Cellular componentCytoplasm
Nucleus
Spliceosome
   LigandATP-binding
Nucleotide-binding
RNA-binding
   Molecular functionHelicase
Hydrolase
   PTMAcetylation
Phosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processRNA splicing

Inferred from electronic annotation. Source: UniProtKB-KW

mRNA processing

Inferred from electronic annotation. Source: UniProtKB-KW

mRNA transport

Inferred from electronic annotation. Source: UniProtKB-KW

negative regulation of translation

Inferred from electronic annotation. Source: Ensembl

nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

Inferred from electronic annotation. Source: UniProtKB-KW

positive regulation of translation

Inferred from electronic annotation. Source: Ensembl

rRNA processing

Inferred from electronic annotation. Source: UniProtKB-KW

regulation of alternative mRNA splicing, via spliceosome

Inferred from sequence or structural similarity. Source: UniProtKB

   Cellular_componentcatalytic step 2 spliceosome

Inferred from electronic annotation. Source: Ensembl

cytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

exon-exon junction complex

Inferred from electronic annotation. Source: Ensembl

nuclear speck

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

ATP-dependent RNA helicase activity

Inferred from electronic annotation. Source: Ensembl

mRNA binding

Inferred from electronic annotation. Source: Ensembl

poly(A) binding

Inferred from electronic annotation. Source: Ensembl

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 411411Eukaryotic initiation factor 4A-III
PRO_0000378555
Initiator methionine11Removed; alternate By similarity
Chain2 – 411410Eukaryotic initiation factor 4A-III, N-terminally processed
PRO_0000423271

Regions

Domain69 – 239171Helicase ATP-binding
Domain250 – 411162Helicase C-terminal
Nucleotide binding85 – 906ATP By similarity
Nucleotide binding367 – 3715ATP By similarity
Motif38 – 6629Q motif
Motif187 – 1904DEAD box

Sites

Binding site601ATP; via carbonyl oxygen By similarity
Binding site651ATP By similarity
Binding site3421ATP By similarity

Amino acid modifications

Modified residue11N-acetylmethionine By similarity
Modified residue21N-acetylalanine; in Eukaryotic initiation factor 4A-III, N-terminally processed By similarity
Modified residue121Phosphoserine By similarity
Modified residue1631Phosphothreonine By similarity
Modified residue2961N6-acetyllysine By similarity
Modified residue3211N6-acetyllysine By similarity

Sequences

Sequence LengthMass (Da)Tools
Q3B8Q2 [UniParc].

Last modified November 22, 2005. Version 1.
Checksum: 987DAF10824DEC4D

FASTA41146,841
        10         20         30         40         50         60 
MAATATMATS GSARKRLLKE EDMTKVEFET SEEVDVTPTF DTMGLREDLL RGIYAYGFEK 

        70         80         90        100        110        120 
PSAIQQRAIK QIIKGRDVIA QSQSGTGKTA TFSISVLQCL DIQVRETQAL ILAPTRELAV 

       130        140        150        160        170        180 
QIQKGLLALG DYMNVQCHAC IGGTNVGEDI RKLDYGQHVV AGTPGRVFDM IRRRSLRTRA 

       190        200        210        220        230        240 
IKMLVLDEAD EMLNKGFKEQ IYDVYRYLPP ATQVVLISAT LPHEILEMTN KFMTDPIRIL 

       250        260        270        280        290        300 
VKRDELTLEG IKQFFVAVER EEWKFDTLCD LYDTLTITQA VIFCNTKRKV DWLTEKMREA 

       310        320        330        340        350        360 
NFTVSSMHGD MPQKERESIM KEFRSGASRV LISTDVWARG LDVPQVSLII NYDLPNNREL 

       370        380        390        400        410 
YIHRIGRSGR YGRKGVAINF VKNDDIRILR DIEQYYSTQI DEMPMNVADL I 

« Hide

References

« Hide 'large scale' references
[1]Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: Brown Norway.
[2]"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: Kidney.
[3]"The EJC factor eIF4AIII modulates synaptic strength and neuronal protein expression."
Giorgi C., Yeo G.W., Stone M.E., Katz D.B., Burge C., Turrigiano G., Moore M.J.
Cell 130:179-191(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
BC105875 mRNA. Translation: AAI05876.1.
CH473948 Genomic DNA. Translation: EDM06783.1.
RefSeqNP_001093628.1. NM_001100158.2.
UniGeneRn.202617.

3D structure databases

ProteinModelPortalQ3B8Q2.
SMRQ3B8Q2. Positions 21-411.
ModBaseSearch...
MobiDBSearch...

Proteomic databases

PRIDEQ3B8Q2.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSRNOT00000073140; ENSRNOP00000066302; ENSRNOG00000045791.
GeneID688288.
KEGGrno:688288.

Organism-specific databases

CTD9775.
RGD1591139. Eif4a3.

Phylogenomic databases

GeneTreeENSGT00530000062880.
KOK13025.
OMATQIQKVI.
OrthoDBEOG7XPZ5M.
PhylomeDBQ3B8Q2.

Gene expression databases

GenevestigatorQ3B8Q2.

Family and domain databases

Gene3D3.40.50.300. 2 hits.
InterProIPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000629. RNA-helicase_DEAD-box_CS.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]
PfamPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMSSF52540. SSF52540. 1 hit.
PROSITEPS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio736113.
PROQ3B8Q2.

Entry information

Entry nameIF4A3_RAT
AccessionPrimary (citable) accession number: Q3B8Q2
Entry history
Integrated into UniProtKB/Swiss-Prot: July 7, 2009
Last sequence update: November 22, 2005
Last modified: April 16, 2014
This is version 62 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Translation initiation factors

List of translation initiation factor entries