Q3B8Q2 (IF4A3_RAT) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Rattus norvegicus (Rat) [Reference proteome]

Taxonomic identifier

10116 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

Protein attributes

Sequence length	411 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	ATP-dependent RNA helicase. Component of a splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of a few core proteins and several more peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Core components of the EJC, that remains bound to spliced mRNAs throughout all stages of mRNA metabolism, functions to mark the position of the exon-exon junction in the mature mRNA and thereby influences downstream processes of gene expression including mRNA splicing, nuclear mRNA export, subcellular mRNA localization, translation efficiency and nonsense-mediated mRNA decay (NMD). Constitutes at least part of the platform anchoring other EJC proteins to spliced mRNAs. 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 By similarity.
Catalytic activity	ATP + H2O = ADP + phosphate.
Subunit structure	Part of the EJC core complex that contains CASC3, EIF4A3, MAGOH and RBM8A. Found in a mRNA splicing-dependent exon junction complex (EJC), at least composed of ACIN1, CASC3, EIF4A3, MAGOH, PNN, RBM8A, RNPS1, SAP18 and ALYREF/THOC4. Interacts with CASC3, MAGOH, NXF1, RBM8A and ALYREF/THOC4. Identified in the spliceosome C complex. May interact with NOM1 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 process	Nonsense-mediated mRNA decay Translation regulation Transport mRNA processing mRNA splicing mRNA transport rRNA processing
Cellular component	Cytoplasm Nucleus Spliceosome
Ligand	ATP-binding Nucleotide-binding RNA-binding
Molecular function	Helicase Hydrolase
PTM	Acetylation Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	RNA 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: Compara nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Inferred from electronic annotation. Source: UniProtKB-KW positive regulation of mRNA splicing, via spliceosome Inferred from electronic annotation. Source: Compara positive regulation of transcription from RNA polymerase II promoter Inferred from electronic annotation. Source: Compara positive regulation of translation Inferred from electronic annotation. Source: Compara rRNA processing Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	catalytic step 2 spliceosome Inferred from electronic annotation. Source: Compara cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell exon-exon junction complex Inferred from electronic annotation. Source: Compara nuclear speck Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent RNA helicase activity Inferred from electronic annotation. Source: Compara poly(A) RNA binding Inferred from electronic annotation. Source: Compara
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed By similarity
	Chain	2 – 411	410	Eukaryotic initiation factor 4A-III		PRO_0000378555
Regions
	Domain	69 – 239	171	Helicase ATP-binding
	Domain	250 – 411	162	Helicase C-terminal
	Nucleotide binding	85 – 90	6	ATP By similarity
	Nucleotide binding	367 – 371	5	ATP By similarity
	Motif	38 – 66	29	Q motif
	Motif	187 – 190	4	DEAD box
Sites
	Binding site	60	1	ATP; via carbonyl oxygen By similarity
	Binding site	65	1	ATP By similarity
	Binding site	342	1	ATP By similarity
Amino acid modifications
	Modified residue	2	1	N-acetylalanine By similarity
	Modified residue	12	1	Phosphoserine By similarity
	Modified residue	163	1	Phosphothreonine By similarity
	Modified residue	296	1	N6-acetyllysine By similarity
	Modified residue	321	1	N6-acetyllysine By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q3B8Q2 [UniParc]. Last modified November 22, 2005. Version 1. Checksum: 987DAF10824DEC4D	FASTA	411	46,841
	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

References

	« Hide 'large scale' referencesShow '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.
IPI	IPI00656385.
RefSeq	NP_001093628.1. NM_001100158.2.
UniGene	Rn.202617.
3D structure databases
HSSP	HSSP built from PDB template 2G9N based on UniProtKB P60842.
ProteinModelPortal	Q3B8Q2.
SMR	Q3B8Q2. Positions 21-411.
ModBase	Search...
Proteomic databases
PRIDE	Q3B8Q2.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSRNOT00000073140; ENSRNOP00000066302; ENSRNOG00000045791.
GeneID	688288.
KEGG	rno:688288.
Organism-specific databases
CTD	9775.
RGD	1591139. Eif4a3.
Phylogenomic databases
GeneTree	ENSGT00530000062880.
KO	K13025.
Gene expression databases
Genevestigator	Q3B8Q2.
Family and domain databases
InterPro	IPR011545. DNA/RNA_helicase_DEAD/DEAH_N. IPR014001. Helicase_ATP-bd. IPR001650. Helicase_C. IPR000629. RNA-helicase_DEAD-box_CS. IPR014014. RNA_helicase_DEAD_Q_motif. [Graphical view]
Pfam	PF00270. DEAD. 1 hit. PF00271. Helicase_C. 1 hit. [Graphical view]
SMART	SM00487. DEXDc. 1 hit. SM00490. HELICc. 1 hit. [Graphical view]
PROSITE	PS00039. DEAD_ATP_HELICASE. 1 hit. PS51192. HELICASE_ATP_BIND_1. 1 hit. PS51194. HELICASE_CTER. 1 hit. PS51195. Q_MOTIF. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	736113.

Entry information

Entry name

IF4A3_RAT

Accession

Primary (citable) accession number: Q3B8Q2

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 7, 2009
Last sequence update:	November 22, 2005
Last modified:	April 3, 2013
This is version 53 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program