IF4A3_RAT
ID IF4A3_RAT Reviewed; 411 AA.
AC Q3B8Q2;
DT 07-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 22-NOV-2005, sequence version 1.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Eukaryotic initiation factor 4A-III;
DE Short=eIF-4A-III;
DE Short=eIF4A-III;
DE EC=3.6.4.13 {ECO:0000250|UniProtKB:P38919};
DE AltName: Full=ATP-dependent RNA helicase DDX48;
DE AltName: Full=ATP-dependent RNA helicase eIF4A-3;
DE AltName: Full=DEAD box protein 48;
DE AltName: Full=Eukaryotic translation initiation factor 4A isoform 3;
DE Contains:
DE RecName: Full=Eukaryotic initiation factor 4A-III, N-terminally processed;
GN Name=Eif4a3; Synonyms=Ddx48;
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RA Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Kidney;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [3]
RP SUBCELLULAR LOCATION.
RX PubMed=17632064; DOI=10.1016/j.cell.2007.05.028;
RA Giorgi C., Yeo G.W., Stone M.E., Katz D.B., Burge C., Turrigiano G.,
RA Moore M.J.;
RT "The EJC factor eIF4AIII modulates synaptic strength and neuronal protein
RT expression.";
RL Cell 130:179-191(2007).
CC -!- FUNCTION: ATP-dependent RNA helicase. Involved in pre-mRNA splicing as
CC component of the spliceosome. Core component of the splicing-dependent
CC multiprotein exon junction complex (EJC) deposited at splice junctions
CC on mRNAs. The EJC is a dynamic structure consisting of core proteins
CC and several peripheral nuclear and cytoplasmic associated factors that
CC join the complex only transiently either during EJC assembly or during
CC subsequent mRNA metabolism. The EJC marks the position of the exon-exon
CC junction in the mature mRNA for the gene expression machinery and the
CC core components remain bound to spliced mRNAs throughout all stages of
CC mRNA metabolism thereby influencing downstream processes including
CC nuclear mRNA export, subcellular mRNA localization, translation
CC efficiency and nonsense-mediated mRNA decay (NMD). Its RNA-dependent
CC ATPase and RNA-helicase activities are induced by CASC3, but abolished
CC in presence of the MAGOH-RBM8A heterodimer, thereby trapping the ATP-
CC bound EJC core onto spliced mRNA in a stable conformation. The
CC inhibition of ATPase activity by the MAGOH-RBM8A heterodimer increases
CC the RNA-binding affinity of the EJC. Involved in translational
CC enhancement of spliced mRNAs after formation of the 80S ribosome
CC complex. Binds spliced mRNA in sequence-independent manner, 20-24
CC nucleotides upstream of mRNA exon-exon junctions. Shows higher affinity
CC for single-stranded RNA in an ATP-bound core EJC complex than after the
CC ATP is hydrolyzed. Involved in the splicing modulation of BCL2L1/Bcl-X
CC (and probably other apoptotic genes); specifically inhibits formation
CC of proapoptotic isoforms; the function is different from the
CC established EJC assembly. Involved in craniofacial development.
CC {ECO:0000250|UniProtKB:P38919}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
CC Evidence={ECO:0000250|UniProtKB:P38919};
CC -!- ACTIVITY REGULATION: The ATPase activity is increased some 4-fold in
CC the presence of RNA. {ECO:0000250|UniProtKB:P38919}.
CC -!- SUBUNIT: Identified in the spliceosome C complex. Core component of the
CC mRNA splicing-dependent exon junction complex (EJC); the core complex
CC contains CASC3, EIF4A3, MAGOH or MAGOHB, and RBM8A. Interacts with
CC CASC3, MAGOH, NXF1, RBM8A and ALYREF/THOC4. May interact with NOM1.
CC Interacts with POLDIP3. Interacts with CWC22 and PRPF19 in an RNA-
CC independent manner. Direct interaction with CWC22 is mediated by the
CC helicase C-terminal domain. Full interaction with CWC22 occurs only
CC when EIF4A3 is not part of the EJC and prevents EIF4A3 binding to RNA.
CC Identified in a complex composed of the EJC core, UPF3B and UPF2. The
CC EJC core can also interact with UPF3A (in vitro). Interacts with NCBP3
CC (By similarity). Interacts with NRDE2 (By similarity). Interacts with
CC DHX34; the interaction is RNA-independent (By similarity).
CC {ECO:0000250|UniProtKB:P38919}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:17632064}. Nucleus
CC speckle {ECO:0000250|UniProtKB:P38919}. Cytoplasm
CC {ECO:0000269|PubMed:17632064}. Note=Nucleocytoplasmic shuttling
CC protein. Travels to the cytoplasm as part of the exon junction complex
CC (EJC) bound to mRNA. Detected in dendritic layer as well as the nuclear
CC and cytoplasmic (somatic) compartments of neurons. Colocalizes with
CC STAU1 and FMR1 in dendrites. {ECO:0000269|PubMed:17632064}.
CC -!- TISSUE SPECIFICITY: Expressed in the CA1 field and dentate gyrus of the
CC hippocampus (at protein level).
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. eIF4A subfamily.
CC {ECO:0000305}.
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DR EMBL; BC105875; AAI05876.1; -; mRNA.
DR EMBL; CH473948; EDM06783.1; -; Genomic_DNA.
DR RefSeq; NP_001093628.1; NM_001100158.2.
DR AlphaFoldDB; Q3B8Q2; -.
DR SMR; Q3B8Q2; -.
DR BioGRID; 603119; 2.
DR IntAct; Q3B8Q2; 1.
DR STRING; 10116.ENSRNOP00000066302; -.
DR iPTMnet; Q3B8Q2; -.
DR PhosphoSitePlus; Q3B8Q2; -.
DR jPOST; Q3B8Q2; -.
DR PaxDb; Q3B8Q2; -.
DR PRIDE; Q3B8Q2; -.
DR Ensembl; ENSRNOT00000073140; ENSRNOP00000066302; ENSRNOG00000045791.
DR GeneID; 688288; -.
DR KEGG; rno:688288; -.
DR CTD; 9775; -.
DR RGD; 1591139; Eif4a3.
DR eggNOG; KOG0328; Eukaryota.
DR GeneTree; ENSGT00940000155037; -.
DR HOGENOM; CLU_003041_1_0_1; -.
DR InParanoid; Q3B8Q2; -.
DR OMA; FGCQALV; -.
DR OrthoDB; 726081at2759; -.
DR PhylomeDB; Q3B8Q2; -.
DR Reactome; R-RNO-1169408; ISG15 antiviral mechanism.
DR Reactome; R-RNO-159236; Transport of Mature mRNA derived from an Intron-Containing Transcript.
DR Reactome; R-RNO-429947; Deadenylation of mRNA.
DR Reactome; R-RNO-72163; mRNA Splicing - Major Pathway.
DR Reactome; R-RNO-72187; mRNA 3'-end processing.
DR Reactome; R-RNO-73856; RNA Polymerase II Transcription Termination.
DR Reactome; R-RNO-975957; Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
DR PRO; PR:Q3B8Q2; -.
DR Proteomes; UP000002494; Chromosome 10.
DR Proteomes; UP000234681; Chromosome 10.
DR Bgee; ENSRNOG00000045791; Expressed in thymus and 20 other tissues.
DR Genevisible; Q3B8Q2; RN.
DR GO; GO:0071013; C:catalytic step 2 spliceosome; ISO:RGD.
DR GO; GO:0005737; C:cytoplasm; IDA:RGD.
DR GO; GO:0030425; C:dendrite; IDA:RGD.
DR GO; GO:0035145; C:exon-exon junction complex; ISO:RGD.
DR GO; GO:0098978; C:glutamatergic synapse; IDA:SynGO.
DR GO; GO:0043025; C:neuronal cell body; IDA:RGD.
DR GO; GO:0016607; C:nuclear speck; IEA:UniProtKB-SubCell.
DR GO; GO:0005730; C:nucleolus; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IDA:RGD.
DR GO; GO:0099524; C:postsynaptic cytosol; IDA:SynGO.
DR GO; GO:1990904; C:ribonucleoprotein complex; IDA:RGD.
DR GO; GO:0071006; C:U2-type catalytic step 1 spliceosome; ISS:UniProtKB.
DR GO; GO:0005524; F:ATP binding; ISO:RGD.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003729; F:mRNA binding; ISO:RGD.
DR GO; GO:0008143; F:poly(A) binding; ISO:RGD.
DR GO; GO:0043021; F:ribonucleoprotein complex binding; IDA:RGD.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0003724; F:RNA helicase activity; ISO:RGD.
DR GO; GO:0035613; F:RNA stem-loop binding; IDA:RGD.
DR GO; GO:0035368; F:selenocysteine insertion sequence binding; IDA:RGD.
DR GO; GO:0045182; F:translation regulator activity; IDA:SynGO.
DR GO; GO:0008306; P:associative learning; IEP:RGD.
DR GO; GO:1990416; P:cellular response to brain-derived neurotrophic factor stimulus; IEP:RGD.
DR GO; GO:0072715; P:cellular response to selenite ion; IEP:RGD.
DR GO; GO:0048701; P:embryonic cranial skeleton morphogenesis; ISS:UniProtKB.
DR GO; GO:0035640; P:exploration behavior; IEP:RGD.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; ISS:UniProtKB.
DR GO; GO:0051028; P:mRNA transport; IEA:UniProtKB-KW.
DR GO; GO:0090394; P:negative regulation of excitatory postsynaptic potential; IMP:RGD.
DR GO; GO:0010629; P:negative regulation of gene expression; IMP:RGD.
DR GO; GO:1904570; P:negative regulation of selenocysteine incorporation; IDA:RGD.
DR GO; GO:1904574; P:negative regulation of selenocysteine insertion sequence binding; IDA:RGD.
DR GO; GO:0017148; P:negative regulation of translation; ISO:RGD.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; ISO:RGD.
DR GO; GO:0048026; P:positive regulation of mRNA splicing, via spliceosome; ISO:RGD.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; ISO:RGD.
DR GO; GO:0045727; P:positive regulation of translation; ISO:RGD.
DR GO; GO:0000381; P:regulation of alternative mRNA splicing, via spliceosome; ISS:UniProtKB.
DR GO; GO:1902415; P:regulation of mRNA binding; IDA:RGD.
DR GO; GO:2000622; P:regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; ISO:RGD.
DR GO; GO:0099578; P:regulation of translation at postsynapse, modulating synaptic transmission; IDA:SynGO.
DR GO; GO:0014070; P:response to organic cyclic compound; IEP:RGD.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR000629; RNA-helicase_DEAD-box_CS.
DR InterPro; IPR014014; RNA_helicase_DEAD_Q_motif.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF00271; Helicase_C; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS00039; DEAD_ATP_HELICASE; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS51195; Q_MOTIF; 1.
PE 1: Evidence at protein level;
KW Acetylation; ATP-binding; Cytoplasm; Helicase; Hydrolase; Isopeptide bond;
KW mRNA processing; mRNA splicing; mRNA transport;
KW Nonsense-mediated mRNA decay; Nucleotide-binding; Nucleus; Phosphoprotein;
KW Reference proteome; RNA-binding; rRNA processing; Spliceosome;
KW Translation regulation; Transport; Ubl conjugation.
FT CHAIN 1..411
FT /note="Eukaryotic initiation factor 4A-III"
FT /id="PRO_0000423271"
FT INIT_MET 1
FT /note="Removed; alternate"
FT /evidence="ECO:0000250|UniProtKB:P38919"
FT CHAIN 2..411
FT /note="Eukaryotic initiation factor 4A-III, N-terminally
FT processed"
FT /id="PRO_0000378555"
FT DOMAIN 69..239
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 250..411
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT MOTIF 38..66
FT /note="Q motif"
FT MOTIF 187..190
FT /note="DEAD box"
FT /evidence="ECO:0000305"
FT BINDING 60
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P38919"
FT BINDING 65
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P38919"
FT BINDING 85..90
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT BINDING 342
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P38919"
FT BINDING 367..371
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0000250|UniProtKB:P38919"
FT MOD_RES 2
FT /note="N-acetylalanine; in Eukaryotic initiation factor 4A-
FT III, N-terminally processed"
FT /evidence="ECO:0000250|UniProtKB:P38919"
FT MOD_RES 10
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P60842"
FT MOD_RES 12
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P38919"
FT MOD_RES 124
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P60842"
FT MOD_RES 163
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:P38919"
FT MOD_RES 198
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P60843"
FT MOD_RES 296
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P38919"
FT MOD_RES 321
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P38919"
FT CROSSLNK 19
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P38919"
FT CROSSLNK 152
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P60842"
FT CROSSLNK 314
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P38919"
FT CROSSLNK 374
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P60842"
FT CROSSLNK 382
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P38919"
SQ SEQUENCE 411 AA; 46841 MW; 987DAF10824DEC4D CRC64;
MAATATMATS GSARKRLLKE EDMTKVEFET SEEVDVTPTF DTMGLREDLL RGIYAYGFEK
PSAIQQRAIK QIIKGRDVIA QSQSGTGKTA TFSISVLQCL DIQVRETQAL ILAPTRELAV
QIQKGLLALG DYMNVQCHAC IGGTNVGEDI RKLDYGQHVV AGTPGRVFDM IRRRSLRTRA
IKMLVLDEAD EMLNKGFKEQ IYDVYRYLPP ATQVVLISAT LPHEILEMTN KFMTDPIRIL
VKRDELTLEG IKQFFVAVER EEWKFDTLCD LYDTLTITQA VIFCNTKRKV DWLTEKMREA
NFTVSSMHGD MPQKERESIM KEFRSGASRV LISTDVWARG LDVPQVSLII NYDLPNNREL
YIHRIGRSGR YGRKGVAINF VKNDDIRILR DIEQYYSTQI DEMPMNVADL I
