IF43B_ORYSJ
ID IF43B_ORYSJ Reviewed; 404 AA.
AC Q10I26; A0A0N7KHJ1; Q94LC7;
DT 03-APR-2007, integrated into UniProtKB/Swiss-Prot.
DT 22-AUG-2006, sequence version 1.
DT 03-AUG-2022, entry version 104.
DE RecName: Full=Eukaryotic initiation factor 4A-III homolog B {ECO:0000305};
DE Short=OseIF4AIIIb {ECO:0000303|PubMed:27071313};
DE Short=eIF-4A-III {ECO:0000305};
DE Short=eIF4A-III {ECO:0000305};
DE EC=3.6.4.13 {ECO:0000305};
DE AltName: Full=DEAD-box ATP-dependent RNA helicase 34 {ECO:0000303|PubMed:27071313};
DE Short=OsRH34 {ECO:0000303|PubMed:27071313};
GN Name=EIF4A3B {ECO:0000303|PubMed:27071313};
GN Synonyms=EIF4A3 {ECO:0000305}, RH34 {ECO:0000303|PubMed:27071313};
GN OrderedLocusNames=Os03g0566800 {ECO:0000312|EMBL:BAS84961.1},
GN LOC_Os03g36930 {ECO:0000312|EMBL:ABF97164.1};
GN ORFNames=OSJNBa0026A15.3 {ECO:0000312|EMBL:AAK50586.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [6]
RP FUNCTION, INTERACTION WITH MAGO1 AND Y14B, SUBCELLULAR LOCATION, AND TISSUE
RP SPECIFICITY.
RX PubMed=27071313; DOI=10.1186/s12870-016-0769-5;
RA Huang C.K., Sie Y.S., Chen Y.F., Huang T.S., Lu C.A.;
RT "Two highly similar DEAD box proteins, OsRH2 and OsRH34, homologous to
RT eukaryotic initiation factor 4AIII, play roles of the exon junction complex
RT in regulating growth and development in rice.";
RL BMC Plant Biol. 16:84-84(2016).
CC -!- FUNCTION: ATP-dependent RNA helicase. Core component of the splicing-
CC dependent multiprotein exon junction complex (EJC) deposited at splice
CC junctions on mRNAs. The EJC is a dynamic structure consisting of core
CC proteins and several peripheral nuclear and cytoplasmic associated
CC factors that join the complex only transiently either during EJC
CC assembly or during subsequent mRNA metabolism. The EJC marks the
CC position of the exon-exon junction in the mature mRNA for the gene
CC expression machinery and the core components remain bound to spliced
CC mRNAs throughout all stages of mRNA metabolism thereby influencing
CC downstream processes including nuclear mRNA export, subcellular mRNA
CC localization, translation efficiency and nonsense-mediated mRNA decay
CC (NMD). Its RNA-dependent ATPase and RNA-helicase activities are induced
CC by MLN51/CASC3, but abolished in presence of the MAGO-Y14 heterodimer,
CC thereby trapping the ATP-bound EJC core onto spliced mRNA in a stable
CC conformation. The inhibition of ATPase activity by the MAGO-Y14
CC heterodimer increases the RNA-binding affinity of the EJC (By
CC similarity). EJC core proteins play essential roles in rice
CC development, growth and reproduction. Regulates the splicing of UDT1
CC (UNDEVELOPED TAPETUM 1) pre-mRNA transcript. UDT1 is a key regulator in
CC stamen development (PubMed:27071313). {ECO:0000250|UniProtKB:P38919,
CC ECO:0000269|PubMed:27071313}.
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:0000305};
CC -!- SUBUNIT: Interacts with MAGO1 and Y14B. {ECO:0000269|PubMed:27071313}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:27071313}. Cytoplasm
CC {ECO:0000269|PubMed:27071313}. Note=Nucleocytoplasmic shuttling
CC protein. Travels to the cytoplasm as part of the exon junction complex
CC (EJC) bound to mRNA. {ECO:0000250|UniProtKB:P38919}.
CC -!- TISSUE SPECIFICITY: Expressed in leaves, flowers and seeds.
CC {ECO:0000269|PubMed:27071313}.
CC -!- DOMAIN: The Q motif is unique to and characteristic of the DEAD box
CC family of RNA helicases and controls ATP binding and hydrolysis.
CC {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DDX48/FAL1
CC subfamily. {ECO:0000305}.
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DR EMBL; AC084404; AAK50586.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF97164.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF12420.1; -; Genomic_DNA.
DR EMBL; AP014959; BAS84961.1; -; Genomic_DNA.
DR EMBL; AK103270; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; XP_015633220.1; XM_015777734.1.
DR AlphaFoldDB; Q10I26; -.
DR SMR; Q10I26; -.
DR STRING; 4530.OS03T0566800-01; -.
DR PaxDb; Q10I26; -.
DR EnsemblPlants; Os03t0566800-01; Os03t0566800-01; Os03g0566800.
DR GeneID; 4333273; -.
DR Gramene; Os03t0566800-01; Os03t0566800-01; Os03g0566800.
DR KEGG; osa:4333273; -.
DR eggNOG; KOG0328; Eukaryota.
DR HOGENOM; CLU_003041_1_0_1; -.
DR InParanoid; Q10I26; -.
DR OMA; FTHRNGR; -.
DR OrthoDB; 726081at2759; -.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR Genevisible; Q10I26; OS.
DR GO; GO:0071013; C:catalytic step 2 spliceosome; IBA:GO_Central.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005730; C:nucleolus; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003729; F:mRNA binding; IBA:GO_Central.
DR GO; GO:0003723; F:RNA binding; IBA:GO_Central.
DR GO; GO:0003724; F:RNA helicase activity; IBA:GO_Central.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0051028; P:mRNA transport; IEA:UniProtKB-KW.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IEA:UniProtKB-KW.
DR GO; GO:0006417; P:regulation of translation; IEA:UniProtKB-KW.
DR GO; GO:0008380; P:RNA splicing; 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; 2.
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 ATP-binding; Cytoplasm; Helicase; Hydrolase; mRNA processing;
KW mRNA splicing; mRNA transport; Nonsense-mediated mRNA decay;
KW Nucleotide-binding; Nucleus; Reference proteome; RNA-binding;
KW Translation regulation; Transport.
FT CHAIN 1..404
FT /note="Eukaryotic initiation factor 4A-III homolog B"
FT /id="PRO_0000282443"
FT DOMAIN 62..232
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 243..404
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..21
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 31..59
FT /note="Q motif"
FT MOTIF 180..183
FT /note="DEAD box"
FT BINDING 75..82
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT CONFLICT 318
FT /note="S -> C (in Ref. 5; AK103270)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 404 AA; 45629 MW; 0121C48905E4F237 CRC64;
MAAATTSRRG PGAMDDENLT FETSPGVEVI SSFDQMGIRE DLLRGIYAYG FEKPSAIQQR
AVLPIISGRD VIAQAQSGTG KTSMISLSVC QIVDTAVREV QALILSPTRE LAAQTERVML
AIGDYINIQV HACIGGKSIG EDIRKLEHGV HVVSGTPGRV CDMIKRRTLR TRAIKLLILD
EADEMLGRGF KDQIYDVYRY LPPELQVCLI SATLPHEILE MTSKFMTDPV RILVKRDELT
LEGIKQFFVA VEKEEWKFDT LCDLYDTLTI TQAVIFCNTK RKVDWLTERM RSNNFTVSAM
HGDMPQKERD AIMGEFRSGA TRVLITTDVW ARGLDVQQVS LVINYDLPNN RELYIHRIGR
SGRFGRKGVA INFVKKEDIR ILRDIEQYYS TQIDEMPMNV ADLI
