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Q3B8Q2

- IF4A3_RAT

UniProt

Q3B8Q2 - IF4A3_RAT

Protein

Eukaryotic initiation factor 4A-III

Gene

Eif4a3

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 65 (01 Oct 2014)
      Sequence version 1 (22 Nov 2005)
      Previous versions | rss
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    Functioni

    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. Involved in craniofacial development By similarity.By similarity

    Catalytic activityi

    ATP + H2O = ADP + phosphate.

    Enzyme regulationi

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

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei60 – 601ATP; via carbonyl oxygenBy similarity
    Binding sitei65 – 651ATPBy similarity
    Binding sitei342 – 3421ATPBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi85 – 906ATPPROSITE-ProRule annotation
    Nucleotide bindingi367 – 3715ATPPROSITE-ProRule annotation

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. ATP-dependent RNA helicase activity Source: Ensembl
    3. mRNA binding Source: Ensembl
    4. poly(A) binding Source: Ensembl

    GO - Biological processi

    1. embryonic cranial skeleton morphogenesis Source: UniProtKB
    2. mRNA processing Source: UniProtKB-KW
    3. mRNA transport Source: UniProtKB-KW
    4. negative regulation of translation Source: Ensembl
    5. nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Source: UniProtKB-KW
    6. positive regulation of translation Source: Ensembl
    7. regulation of alternative mRNA splicing, via spliceosome Source: UniProtKB
    8. RNA splicing Source: UniProtKB-KW
    9. rRNA processing Source: UniProtKB-KW

    Keywords - Molecular functioni

    Helicase, Hydrolase

    Keywords - Biological processi

    mRNA processing, mRNA splicing, mRNA transport, Nonsense-mediated mRNA decay, rRNA processing, Translation regulation, Transport

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding, RNA-binding

    Enzyme and pathway databases

    ReactomeiREACT_198999. ISG15 antiviral mechanism.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Eukaryotic initiation factor 4A-III (EC:3.6.4.13)
    Short name:
    eIF-4A-III
    Short name:
    eIF4A-III
    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
    Cleaved into the following chain:
    Gene namesi
    Name:Eif4a3
    Synonyms:Ddx48
    OrganismiRattus norvegicus (Rat)
    Taxonomic identifieri10116 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
    ProteomesiUP000002494: Chromosome 10

    Organism-specific databases

    RGDi1591139. Eif4a3.

    Subcellular locationi

    Nucleus 1 Publication. Nucleus speckle By similarity. Cytoplasm 1 Publication
    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.By similarity

    GO - Cellular componenti

    1. catalytic step 2 spliceosome Source: Ensembl
    2. cytoplasm Source: UniProtKB-SubCell
    3. exon-exon junction complex Source: Ensembl
    4. nuclear speck Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm, Nucleus, Spliceosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 411411Eukaryotic initiation factor 4A-IIIPRO_0000378555Add
    BLAST
    Initiator methioninei1 – 11Removed; alternateBy similarity
    Chaini2 – 411410Eukaryotic initiation factor 4A-III, N-terminally processedPRO_0000423271Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei1 – 11N-acetylmethionineBy similarity
    Modified residuei2 – 21N-acetylalanine; in Eukaryotic initiation factor 4A-III, N-terminally processedBy similarity
    Modified residuei12 – 121PhosphoserineBy similarity
    Modified residuei163 – 1631PhosphothreonineBy similarity
    Modified residuei296 – 2961N6-acetyllysineBy similarity
    Modified residuei321 – 3211N6-acetyllysineBy similarity

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    PRIDEiQ3B8Q2.

    Expressioni

    Tissue specificityi

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

    Gene expression databases

    GenevestigatoriQ3B8Q2.

    Interactioni

    Subunit structurei

    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.By similarity

    Structurei

    3D structure databases

    ProteinModelPortaliQ3B8Q2.
    SMRiQ3B8Q2. Positions 21-411.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini69 – 239171Helicase ATP-bindingPROSITE-ProRule annotationAdd
    BLAST
    Domaini250 – 411162Helicase C-terminalPROSITE-ProRule annotationAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi38 – 6629Q motifAdd
    BLAST
    Motifi187 – 1904DEAD box

    Sequence similaritiesi

    Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
    Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

    Phylogenomic databases

    GeneTreeiENSGT00530000062880.
    KOiK13025.
    OMAiHANIQAH.
    OrthoDBiEOG7XPZ5M.
    PhylomeDBiQ3B8Q2.

    Family and domain databases

    Gene3Di3.40.50.300. 2 hits.
    InterProiIPR011545. 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]
    PfamiPF00270. DEAD. 1 hit.
    PF00271. Helicase_C. 1 hit.
    [Graphical view]
    SMARTiSM00487. DEXDc. 1 hit.
    SM00490. HELICc. 1 hit.
    [Graphical view]
    SUPFAMiSSF52540. SSF52540. 1 hit.
    PROSITEiPS00039. DEAD_ATP_HELICASE. 1 hit.
    PS51192. HELICASE_ATP_BIND_1. 1 hit.
    PS51194. HELICASE_CTER. 1 hit.
    PS51195. Q_MOTIF. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q3B8Q2-1 [UniParc]FASTAAdd to Basket

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    MAATATMATS GSARKRLLKE EDMTKVEFET SEEVDVTPTF DTMGLREDLL    50
    RGIYAYGFEK PSAIQQRAIK QIIKGRDVIA QSQSGTGKTA TFSISVLQCL 100
    DIQVRETQAL ILAPTRELAV QIQKGLLALG DYMNVQCHAC IGGTNVGEDI 150
    RKLDYGQHVV AGTPGRVFDM IRRRSLRTRA IKMLVLDEAD EMLNKGFKEQ 200
    IYDVYRYLPP ATQVVLISAT LPHEILEMTN KFMTDPIRIL VKRDELTLEG 250
    IKQFFVAVER EEWKFDTLCD LYDTLTITQA VIFCNTKRKV DWLTEKMREA 300
    NFTVSSMHGD MPQKERESIM KEFRSGASRV LISTDVWARG LDVPQVSLII 350
    NYDLPNNREL YIHRIGRSGR YGRKGVAINF VKNDDIRILR DIEQYYSTQI 400
    DEMPMNVADL I 411
    Length:411
    Mass (Da):46,841
    Last modified:November 22, 2005 - v1
    Checksum:i987DAF10824DEC4D
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BC105875 mRNA. Translation: AAI05876.1.
    CH473948 Genomic DNA. Translation: EDM06783.1.
    RefSeqiNP_001093628.1. NM_001100158.2.
    UniGeneiRn.202617.

    Genome annotation databases

    EnsembliENSRNOT00000073140; ENSRNOP00000066302; ENSRNOG00000045791.
    GeneIDi688288.
    KEGGirno:688288.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BC105875 mRNA. Translation: AAI05876.1 .
    CH473948 Genomic DNA. Translation: EDM06783.1 .
    RefSeqi NP_001093628.1. NM_001100158.2.
    UniGenei Rn.202617.

    3D structure databases

    ProteinModelPortali Q3B8Q2.
    SMRi Q3B8Q2. Positions 21-411.
    ModBasei Search...
    MobiDBi Search...

    Proteomic databases

    PRIDEi Q3B8Q2.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSRNOT00000073140 ; ENSRNOP00000066302 ; ENSRNOG00000045791 .
    GeneIDi 688288.
    KEGGi rno:688288.

    Organism-specific databases

    CTDi 9775.
    RGDi 1591139. Eif4a3.

    Phylogenomic databases

    GeneTreei ENSGT00530000062880.
    KOi K13025.
    OMAi HANIQAH.
    OrthoDBi EOG7XPZ5M.
    PhylomeDBi Q3B8Q2.

    Enzyme and pathway databases

    Reactomei REACT_198999. ISG15 antiviral mechanism.

    Miscellaneous databases

    NextBioi 736113.
    PROi Q3B8Q2.

    Gene expression databases

    Genevestigatori Q3B8Q2.

    Family and domain databases

    Gene3Di 3.40.50.300. 2 hits.
    InterProi IPR011545. 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 ]
    Pfami PF00270. DEAD. 1 hit.
    PF00271. Helicase_C. 1 hit.
    [Graphical view ]
    SMARTi SM00487. DEXDc. 1 hit.
    SM00490. HELICc. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52540. SSF52540. 1 hit.
    PROSITEi 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 ]
    ProtoNeti Search...

    Publicationsi

    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.

    Entry informationi

    Entry nameiIF4A3_RAT
    AccessioniPrimary (citable) accession number: Q3B8Q2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 7, 2009
    Last sequence update: November 22, 2005
    Last modified: October 1, 2014
    This is version 65 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Translation initiation factors
      List of translation initiation factor entries
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3