ILF3A_XENLA
ID ILF3A_XENLA Reviewed; 897 AA.
AC Q91550; Q9DEU4;
DT 02-MAR-2010, integrated into UniProtKB/Swiss-Prot.
DT 02-MAR-2010, sequence version 2.
DT 03-AUG-2022, entry version 96.
DE RecName: Full=Interleukin enhancer-binding factor 3-A;
DE AltName: Full=CCAAT box transcription factor subunit {ECO:0000303|PubMed:9710639};
DE AltName: Full=Double-stranded RNA-binding protein 4F.1 {ECO:0000303|PubMed:7922339};
DE Short=DsRNA-binding protein 4F.1 {ECO:0000312|EMBL:AAA19960.1};
GN Name=ilf3-a; Synonyms=ilf3, ubp3 {ECO:0000303|PubMed:8631310};
OS Xenopus laevis (African clawed frog).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Xenopus.
OX NCBI_TaxID=8355;
RN [1] {ECO:0000305, ECO:0000312|EMBL:AAA19960.1}
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), RNA-BINDING, AND DEVELOPMENTAL
RP STAGE.
RC TISSUE=Ovary {ECO:0000312|EMBL:AAA19960.1};
RX PubMed=7922339; DOI=10.1016/s0960-9822(00)00069-5;
RA Bass B.L., Hurst S.R., Singer J.D.;
RT "Binding properties of newly identified Xenopus proteins containing dsRNA-
RT binding motifs.";
RL Curr. Biol. 4:301-314(1994).
RN [2] {ECO:0000305, ECO:0000312|EMBL:AAG22859.1}
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, RNA-BINDING, SUBCELLULAR
RP LOCATION, IDENTIFICATION IN A RIBONUCLEOPROTEIN COMPLEX WITH YBX2,
RP DEVELOPMENTAL STAGE, AND MUTAGENESIS OF PHE-433 AND PHE-552.
RX PubMed=10899122; DOI=10.1093/emboj/19.14.3683;
RA Brzostowski J., Robinson C., Orford R., Elgar S., Scarlett G., Peterkin T.,
RA Malartre M., Kneale G., Wormington M., Guille M.;
RT "RNA-dependent cytoplasmic anchoring of a transcription factor subunit
RT during Xenopus development.";
RL EMBO J. 19:3683-3693(2000).
RN [3] {ECO:0000305}
RP IDENTIFICATION OF THE MRNA IN A RIBONUCLEOPROTEIN COMPLEX.
RX PubMed=8631310; DOI=10.1002/j.1460-2075.1996.tb00424.x;
RA Wormington M., Searfoss A.M., Hurney C.A.;
RT "Overexpression of poly(A) binding protein prevents maturation-specific
RT deadenylation and translational inactivation in Xenopus oocytes.";
RL EMBO J. 15:900-909(1996).
RN [4] {ECO:0000305}
RP FUNCTION, IDENTIFICATION IN THE CBTF COMPLEX, SUBCELLULAR LOCATION, AND
RP TISSUE SPECIFICITY.
RX PubMed=9710639; DOI=10.1128/mcb.18.9.5557;
RA Orford R.L., Robinson C., Haydon J.M., Patient R.K., Guille M.J.;
RT "The maternal CCAAT box transcription factor which controls GATA-2
RT expression is novel and developmentally regulated and contains a double-
RT stranded-RNA-binding subunit.";
RL Mol. Cell. Biol. 18:5557-5566(1998).
RN [5] {ECO:0000305}
RP PHOSPHORYLATION.
RA Elgar S.J.;
RL Thesis (2001), University of Portsmouth, United Kingdom.
RN [6] {ECO:0000305}
RP FUNCTION, RNA-BINDING, DNA-BINDING, AND MUTAGENESIS OF PHE-433 AND PHE-552.
RX PubMed=15452137; DOI=10.1074/jbc.m406107200;
RA Scarlett G.P., Elgar S.J., Cary P.D., Noble A.M., Orford R.L., Kneale G.G.,
RA Guille M.J.;
RT "Intact RNA-binding domains are necessary for structure-specific DNA
RT binding and transcription control by CBTF122 during Xenopus development.";
RL J. Biol. Chem. 279:52447-52455(2004).
RN [7] {ECO:0000305}
RP PHOSPHORYLATION.
RA Cazanove O.M.P.;
RL Thesis (2006), University of Portsmouth, United Kingdom.
RN [8] {ECO:0000305}
RP FUNCTION, DNA-BINDING, AND METHYLATION.
RX PubMed=18636753; DOI=10.1021/bi7008486;
RA Cazanove O., Batut J., Scarlett G., Mumford K., Elgar S., Thresh S.,
RA Neant I., Moreau M., Guille M.;
RT "Methylation of Xilf3 by Xprmt1b alters its DNA, but not RNA, binding
RT activity.";
RL Biochemistry 47:8350-8357(2008).
RN [9] {ECO:0000305}
RP FUNCTION.
RX PubMed=19665599; DOI=10.1016/j.bbagrm.2009.07.007;
RA Llewellyn K.J., Cary P.D., McClellan J.A., Guille M.J., Scarlett G.P.;
RT "A-form DNA structure is a determinant of transcript levels from the
RT Xenopus gata2 promoter in embryos.";
RL Biochim. Biophys. Acta 1789:675-680(2009).
CC -!- FUNCTION: RNA-binding protein that plays an essential role in the
CC biogenesis of circular RNAs (circRNAs) which are produced by back-
CC splicing circularization of pre-mRNAs. Within the nucleus, promotes
CC circRNAs processing by stabilizing the regulatory elements residing in
CC the flanking introns of the circularized exons (By similarity). Plays
CC thereby a role in the back-splicing of a subset of circRNAs (By
CC similarity). As a consequence, participates in a wide range of
CC transcriptional and post-transcriptional processes (By similarity).
CC Binds to poly-U elements and AU-rich elements (AREs) in the 3'-UTR of
CC target mRNAs (By similarity). Upon viral infection, ILF3 accumulates in
CC the cytoplasm and participates in the innate antiviral response (By
CC similarity). Mechanistically, ILF3 becomes phosphorylated and activated
CC by the double-stranded RNA-activated protein kinase/PKR which releases
CC ILF3 from cellular mature circRNAs. In turn, unbound ILF3 molecules are
CC able to interact with and thus inhibit viral mRNAs (By similarity). Has
CC a cytoplasmic role early in development as part of a ribonucleoprotein
CC (mRNP) complex which may regulate mRNA transport and/or translation.
CC Following nuclear localization at the mid-blastula transition, acts as
CC a transcription factor and binds the 5'-CCAAT-3' promoter sequence to
CC regulate transcription of the gata2 gene as a subunit of the CCAAT box
CC transcription factor (CBTF). Its role as an mRNP component negatively
CC regulates its activity as a transcription factor by precluding its
CC nuclear localization (PubMed:10899122, PubMed:15452137,
CC PubMed:18636753, PubMed:19665599, PubMed:7922339, PubMed:9710639).
CC {ECO:0000250|UniProtKB:Q12906, ECO:0000269|PubMed:10899122,
CC ECO:0000269|PubMed:15452137, ECO:0000269|PubMed:18636753,
CC ECO:0000269|PubMed:19665599, ECO:0000269|PubMed:7922339,
CC ECO:0000269|PubMed:9710639}.
CC -!- SUBUNIT: A component of a ybx2/frgy2-containing mRNA-ribonucleoprotein
CC (mRNP) complex. Also a component of the CCAAT box transcription factor
CC (CBTF) complex. {ECO:0000269|PubMed:10899122,
CC ECO:0000269|PubMed:8631310, ECO:0000269|PubMed:9710639}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:10899122,
CC ECO:0000269|PubMed:9710639}. Cytoplasm {ECO:0000269|PubMed:10899122,
CC ECO:0000269|PubMed:9710639}. Note=Cytoplasmic in fertilized eggs, then
CC translocates to the nucleus prior to gastrulation. RNA-binding is
CC required for cytoplasmic retention during early development, and
CC nuclear translocation at the mid-blastula transition (MBT) is probably
CC coupled to the degradation of maternal mRNA that occurs at that stage.
CC {ECO:0000269|PubMed:10899122, ECO:0000269|PubMed:9710639}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1 {ECO:0000269|PubMed:10899122}; Synonyms=CBTF122
CC {ECO:0000269|PubMed:10899122}, p122 {ECO:0000269|PubMed:9710639};
CC IsoId=Q91550-1; Sequence=Displayed;
CC Name=2 {ECO:0000269|PubMed:7922339}; Synonyms=CBTF98
CC {ECO:0000269|PubMed:10899122};
CC IsoId=Q91550-2; Sequence=VSP_053194, VSP_053195;
CC -!- TISSUE SPECIFICITY: Expressed mainly in the ectoderm (at protein
CC level). {ECO:0000269|PubMed:9710639}.
CC -!- DEVELOPMENTAL STAGE: Expressed both maternally and zygotically
CC throughout early development (at protein level). Isoform 1 accumulates
CC throughout oogenesis but isoform 2 is translationally masked until
CC oocyte maturation. {ECO:0000269|PubMed:10899122,
CC ECO:0000269|PubMed:7922339}.
CC -!- PTM: Phosphorylated. Phosphorylation affects nuclear translocation.
CC {ECO:0000269|Ref.5, ECO:0000269|Ref.7}.
CC -!- PTM: Methylated by protein arginine N-methyltransferase 1 (prmt1b) in
CC the RGG-rich domain. Methylation decreases DNA-binding and thereby
CC decreases transcription of the gata2 gene, but does not regulate dsRNA
CC binding or subcellular localization. {ECO:0000269|PubMed:18636753}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAG22859.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; U07155; AAA19960.1; -; mRNA.
DR EMBL; AY008299; AAG22859.1; ALT_FRAME; mRNA.
DR PIR; I51652; I51652.
DR RefSeq; XP_018094990.1; XM_018239501.1. [Q91550-2]
DR RefSeq; XP_018094991.1; XM_018239502.1. [Q91550-2]
DR AlphaFoldDB; Q91550; -.
DR SMR; Q91550; -.
DR IntAct; Q91550; 1.
DR DNASU; 399197; -.
DR GeneID; 399197; -.
DR CTD; 399197; -.
DR Xenbase; XB-GENE-494371; ilf3.S.
DR Proteomes; UP000186698; Chromosome 3S.
DR Bgee; 399197; Expressed in egg cell and 19 other tissues.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:1990904; C:ribonucleoprotein complex; IDA:UniProtKB.
DR GO; GO:0003725; F:double-stranded RNA binding; IDA:UniProtKB.
DR GO; GO:0035925; F:mRNA 3'-UTR AU-rich region binding; ISS:UniProtKB.
DR GO; GO:0048027; F:mRNA 5'-UTR binding; IDA:UniProtKB.
DR GO; GO:0043565; F:sequence-specific DNA binding; IDA:UniProtKB.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IDA:UniProtKB.
DR GO; GO:0051607; P:defense response to virus; IEA:UniProtKB-KW.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IDA:UniProtKB.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IMP:UniProtKB.
DR Gene3D; 3.30.460.10; -; 2.
DR InterPro; IPR014720; dsRBD_dom.
DR InterPro; IPR006561; DZF_dom.
DR InterPro; IPR033099; ILF3/NF90.
DR InterPro; IPR043519; NT_sf.
DR PANTHER; PTHR45762:SF4; PTHR45762:SF4; 3.
DR Pfam; PF00035; dsrm; 2.
DR Pfam; PF07528; DZF; 1.
DR SMART; SM00358; DSRM; 2.
DR SMART; SM00572; DZF; 1.
DR PROSITE; PS50137; DS_RBD; 2.
DR PROSITE; PS51703; DZF; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Antiviral defense; Cytoplasm; Developmental protein;
KW DNA-binding; Methylation; Nucleus; Phosphoprotein; Reference proteome;
KW Repeat; RNA-binding; Transcription; Transcription regulation.
FT CHAIN 1..897
FT /note="Interleukin enhancer-binding factor 3-A"
FT /id="PRO_0000391689"
FT DOMAIN 5..379
FT /note="DZF"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01040"
FT DOMAIN 399..468
FT /note="DRBM 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00266"
FT DOMAIN 521..587
FT /note="DRBM 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00266"
FT REGION 52..85
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 364..403
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 466..502
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 627..650
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 708..797
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 372..390
FT /note="Bipartite nuclear localization signal"
FT /evidence="ECO:0000255"
FT COMPBIAS 68..83
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 373..400
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 718..744
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 745..797
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 681..695
FT /note="QFYSNGGASGNAGGG -> DFFTDCYGYHDFASA (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:7922339"
FT /id="VSP_053194"
FT VAR_SEQ 696..897
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:7922339"
FT /id="VSP_053195"
FT MUTAGEN 433
FT /note="F->A: Abolishes mRNA-binding and cytoplasmic
FT retention, localizing predominantly to the nucleus from
FT early development. Also disrupts DNA-binding; when
FT associated with A-552."
FT /evidence="ECO:0000269|PubMed:10899122,
FT ECO:0000269|PubMed:15452137"
FT MUTAGEN 552
FT /note="F->A: Abolishes mRNA-binding and cytoplasmic
FT retention, localizing predominantly to the nucleus from
FT early development. Also disrupts DNA-binding; when
FT associated with A-433."
FT /evidence="ECO:0000269|PubMed:10899122,
FT ECO:0000269|PubMed:15452137"
FT CONFLICT 157
FT /note="V -> I (in Ref. 2; AAG22859)"
FT /evidence="ECO:0000305"
FT CONFLICT 540
FT /note="L -> M (in Ref. 1; AAA19960)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 897 AA; 98121 MW; 1AD98A9488345C85 CRC64;
MRPMRIFLND DRHVMAKHSV VYPTQEELEA VQNMVSHTER ALKAVSDWID QQEKDCSGEQ
EQPMAEETET TEEGKDSEMK TGENPTRTLR GVMRVGLVAK GLLLKGDLDL ELVLLCRDKP
TISLLKRVAD NLVLQFETVS EDKYEVIQNI REALIVVKST KEPPLTLNIR LTSPLVREEM
EKLSAGETLT VSDPPDVLDR HKCLAALASL RHAKWFQARA NGLKSCVIVI RVLRDLCTRV
PTWEPLRGWP LELLCEKAIG TANRPMGAGE ALRRVLECLS SGILMPDGSG LYDPCEKDAS
DALEHLERQQ REDITQSAQH ALRLAAFGQL HKVLGMDPLP SKMPKKTKVE TPVIDYTVQI
PPSTTYAMPP LKRPIEEDGD DKSPSKKKKK IQKKDEKSEP PQVMNALMRL NQLKPGLQYK
LISQTGPVHA PVFTMSVEVD DKTFEASGPS KKTAKLHVAV KVLQDMGLPT GMEEKEEGTD
ESEQKPVVQT PAQPDDSAEV DSAALDQAES AKQQGPILTK HGKNPVMELN EKRRGLKYEL
ISETGGSHDK RFVMEVEVDG VKFQGSGSNK KVAKAYAALS ALEKLFPDYT MYTEAPKKKR
PPMMPRGGPK FAGKHNQGFG MMYSEVPPPQ AMRGRGRGGM NRGRGRGRGG FGGGYMNSGG
YGGGYGGNYN YQTSATAGYS QFYSNGGASG NAGGGGAGTG GYSSYYQGDS YSAPTPPKPF
VNKKPPPPQQ QQQQQPPPQH ASNPPKPSYN QGYQGHQGGQ QQQQQQQQQQ TYNQNQYSNY
GPPQKQKGGY NQGAQGAGSG GSYNYSNSYT GGTAPLGTAV ERVQEGEAAA LTQRQALVTT
QAHTPAMVEP AVLRRTKVTR SLITIKVPPD RTTVALQIIT SSLREELGVT AGIQNTT
