DX39B_RAT
ID DX39B_RAT Reviewed; 428 AA.
AC Q63413; Q811A6; Q8R2G9;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 15-MAR-2005, sequence version 3.
DT 03-AUG-2022, entry version 160.
DE RecName: Full=Spliceosome RNA helicase Ddx39b;
DE EC=3.6.4.13;
DE AltName: Full=56 kDa U2AF65-associated protein;
DE AltName: Full=ATP-dependent RNA helicase p47;
DE AltName: Full=DEAD box protein Uap56;
GN Name=Ddx39b; Synonyms=Bat1, Bat1a, Uap56;
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 [MRNA].
RX PubMed=1618789; DOI=10.1016/s0021-9258(18)42363-0;
RA Nair S., Dey R., Sanford J.P., Doyle D.;
RT "Molecular cloning and analysis of an eIF-4A-related rat liver nuclear
RT protein.";
RL J. Biol. Chem. 267:12928-12935(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=Lewis;
RX PubMed=11904681; DOI=10.1007/s00251-001-0428-2;
RA Lambracht-Washington D., Fischer Lindahl K.;
RT "Does the rat have an H2-D orthologue next to Bat1?";
RL Immunogenetics 53:1039-1046(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=Brown Norway;
RA Walter L.;
RT "Sequence analysis of the rat MHC class I region.";
RL Submitted (JUN-2001) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Lung;
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).
CC -!- FUNCTION: Involved in nuclear export of spliced and unspliced mRNA.
CC Assembling component of the TREX complex which is thought to couple
CC mRNA transcription, processing and nuclear export, and specifically
CC associates with spliced mRNA and not with unspliced pre-mRNA. TREX is
CC recruited to spliced mRNAs by a transcription-independent mechanism,
CC binds to mRNA upstream of the exon-junction complex (EJC) and is
CC recruited in a splicing- and cap-dependent manner to a region near the
CC 5' end of the mRNA where it functions in mRNA export to the cytoplasm
CC via the TAP/NFX1 pathway. May undergo several rounds of ATP hydrolysis
CC during assembly of TREX to drive subsequent loading of components such
CC as ALYREF/THOC and CHTOP onto mRNA. Also associates with pre-mRNA
CC independent of ALYREF/THOC4 and the THO complex. Involved in the
CC nuclear export of intronless mRNA; the ATP-bound form is proposed to
CC recruit export adapter ALYREF/THOC4 to intronless mRNA; its ATPase
CC activity is cooperatively stimulated by RNA and ALYREF/THOC4 and ATP
CC hydrolysis is thought to trigger the dissociation from RNA to allow the
CC association of ALYREF/THOC4 and the NXF1-NXT1 heterodimer. Involved in
CC transcription elongation and genome stability.
CC {ECO:0000250|UniProtKB:Q13838}.
CC -!- FUNCTION: Splice factor that is required for the first ATP-dependent
CC step in spliceosome assembly and for the interaction of U2 snRNP with
CC the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis
CC activity and ATP-dependent RNA unwinding activity. Even with the
CC stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP
CC but not other NTPs. The RNA stimulation of ATPase activity does not
CC have a strong preference for the sequence and length of the RNA.
CC However, ssRNA stimulates the ATPase activity much more strongly than
CC dsRNA. Can unwind 5' or 3' overhangs or blunt end RNA duplexes in
CC vitro. The ATPase and helicase activities are not influenced by U2AF2;
CC the effect of ALYREF/THOC4 is reported conflictingly with [] reporting
CC a stimulatory effect. {ECO:0000250|UniProtKB:Q13838}.
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:Q13838};
CC -!- SUBUNIT: Homodimer, and heterodimer with DDX39A. Component of the
CC transcription/export (TREX) complex at least composed of ALYREF/THOC4,
CC DDX39B, SARNP/CIP29, CHTOP and the THO subcomplex; TREX seems to have
CC dynamic structure involving ATP-dependent remodeling; in the complex
CC bridges ALYREF/THOC4 and the THO complex, and, in a ATP-dependent
CC manner, ALYREF/THOC4 and SARNP/CIP29. Component of the spliceosome.
CC Interacts directly with U2AF2. Interacts with RBM8A, RNPS1 and SRRM1,
CC FYTTD1/UIF, THOC1, MX1 and POLDIP3. Interacts with LUZP4.
CC {ECO:0000250|UniProtKB:Q13838}.
CC -!- SUBCELLULAR LOCATION: Nucleus. Nucleus speckle {ECO:0000250}. Cytoplasm
CC {ECO:0000250}. Note=Can translocate to the cytoplasm in the presence of
CC MX1. {ECO:0000250}.
CC -!- TISSUE SPECIFICITY: Highly expressed in liver.
CC -!- DOMAIN: The helicase C-terminal domain mediates interaction with
CC ALYREF/THOC4. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DECD subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA41787.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; M75168; AAA41787.1; ALT_FRAME; mRNA.
DR EMBL; AF387339; AAL98920.1; -; Genomic_DNA.
DR EMBL; AJ314857; CAC85694.1; -; Genomic_DNA.
DR EMBL; BC080243; AAH80243.1; -; mRNA.
DR PIR; A42811; A42811.
DR RefSeq; NP_579834.2; NM_133300.3.
DR AlphaFoldDB; Q63413; -.
DR SMR; Q63413; -.
DR BioGRID; 250392; 1.
DR IntAct; Q63413; 1.
DR STRING; 10116.ENSRNOP00000001115; -.
DR iPTMnet; Q63413; -.
DR PhosphoSitePlus; Q63413; -.
DR World-2DPAGE; 0004:Q63413; -.
DR jPOST; Q63413; -.
DR PaxDb; Q63413; -.
DR PRIDE; Q63413; -.
DR Ensembl; ENSRNOT00000001115; ENSRNOP00000001115; ENSRNOG00000000841.
DR GeneID; 114612; -.
DR KEGG; rno:114612; -.
DR UCSC; RGD:70923; rat.
DR CTD; 7919; -.
DR RGD; 70923; Ddx39b.
DR eggNOG; KOG0329; Eukaryota.
DR GeneTree; ENSGT00940000160110; -.
DR HOGENOM; CLU_003041_1_0_1; -.
DR InParanoid; Q63413; -.
DR OMA; IKPICRK; -.
DR OrthoDB; 779000at2759; -.
DR PhylomeDB; Q63413; -.
DR TreeFam; TF300442; -.
DR Reactome; R-RNO-159236; Transport of Mature mRNA derived from an Intron-Containing Transcript.
DR Reactome; R-RNO-72187; mRNA 3'-end processing.
DR Reactome; R-RNO-73856; RNA Polymerase II Transcription Termination.
DR Reactome; R-RNO-9013418; RHOBTB2 GTPase cycle.
DR PRO; PR:Q63413; -.
DR Proteomes; UP000002494; Chromosome 20.
DR Bgee; ENSRNOG00000000841; Expressed in thymus and 20 other tissues.
DR ExpressionAtlas; Q63413; baseline and differential.
DR Genevisible; Q63413; RN.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0016363; C:nuclear matrix; IDA:RGD.
DR GO; GO:0016607; C:nuclear speck; ISO:RGD.
DR GO; GO:0005634; C:nucleus; ISO:RGD.
DR GO; GO:0032991; C:protein-containing complex; IDA:RGD.
DR GO; GO:0005681; C:spliceosomal complex; ISO:RGD.
DR GO; GO:0000346; C:transcription export complex; ISO:RGD.
DR GO; GO:0005687; C:U4 snRNP; ISO:RGD.
DR GO; GO:0005688; C:U6 snRNP; ISO:RGD.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; ISO:RGD.
DR GO; GO:0008186; F:ATP-dependent activity, acting on RNA; ISO:RGD.
DR GO; GO:0043008; F:ATP-dependent protein binding; ISO:RGD.
DR GO; GO:0042802; F:identical protein binding; ISO:RGD.
DR GO; GO:0044877; F:protein-containing 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:0030621; F:U4 snRNA binding; ISO:RGD.
DR GO; GO:0017070; F:U6 snRNA binding; ISO:RGD.
DR GO; GO:0001889; P:liver development; IEP:RGD.
DR GO; GO:0006406; P:mRNA export from nucleus; ISO:RGD.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; ISO:RGD.
DR GO; GO:2000002; P:negative regulation of DNA damage checkpoint; ISS:UniProtKB.
DR GO; GO:0061051; P:positive regulation of cell growth involved in cardiac muscle cell development; IMP:RGD.
DR GO; GO:2000573; P:positive regulation of DNA biosynthetic process; IMP:RGD.
DR GO; GO:0032786; P:positive regulation of DNA-templated transcription, elongation; ISS:UniProtKB.
DR GO; GO:0045727; P:positive regulation of translation; IMP:RGD.
DR GO; GO:1904707; P:positive regulation of vascular associated smooth muscle cell proliferation; IMP:RGD.
DR GO; GO:0010501; P:RNA secondary structure unwinding; ISO:RGD.
DR GO; GO:0008380; P:RNA splicing; ISO:RGD.
DR GO; GO:0000245; P:spliceosomal complex assembly; ISO:RGD.
DR GO; GO:0046784; P:viral mRNA export from host cell nucleus; ISO:RGD.
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; 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; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
DR PROSITE; PS51195; Q_MOTIF; 1.
PE 2: Evidence at transcript level;
KW Acetylation; ATP-binding; Cytoplasm; Helicase; Hydrolase; Isopeptide bond;
KW mRNA processing; mRNA splicing; mRNA transport; Nucleotide-binding;
KW Nucleus; Phosphoprotein; Reference proteome; RNA-binding; Spliceosome;
KW Transport; Ubl conjugation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250|UniProtKB:Q13838"
FT CHAIN 2..428
FT /note="Spliceosome RNA helicase Ddx39b"
FT /id="PRO_0000055077"
FT DOMAIN 76..249
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT DOMAIN 261..422
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542"
FT REGION 1..31
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 45..73
FT /note="Q motif"
FT MOTIF 196..199
FT /note="DECD box"
FT COMPBIAS 1..22
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 89..96
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541"
FT MOD_RES 2
FT /note="N-acetylalanine"
FT /evidence="ECO:0000250|UniProtKB:Q13838"
FT MOD_RES 36
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q13838"
FT MOD_RES 38
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q13838"
FT MOD_RES 41
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q13838"
FT MOD_RES 172
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:Q13838"
FT CROSSLNK 36
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2); alternate"
FT /evidence="ECO:0000250|UniProtKB:Q13838"
FT CONFLICT 236
FT /note="R -> P (in Ref. 2; AAL98920)"
FT /evidence="ECO:0000305"
FT CONFLICT 286
FT /note="E -> Q (in Ref. 2; AAL98920)"
FT /evidence="ECO:0000305"
FT CONFLICT 312
FT /note="F -> L (in Ref. 1; AAA41787)"
FT /evidence="ECO:0000305"
FT CONFLICT 354
FT /note="E -> V (in Ref. 1; AAA41787)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 428 AA; 49035 MW; D5AA6B3905FDC968 CRC64;
MAENDVDNEL LDYEDDEVET AAGADGTEAP AKKDVKGSYV SIHSSGFRDF LLKPELLRAI
VDCGFEHPSE VQHECIPQAI LGMDVLCQAK SGMGKTAVFV LATLQQLEPV TGQVSVLVMC
HTRELAFQIS KEYERFSKYM PNVKVAVFFG GLSIKKDEEV LKKNCPHIVV GTPGRILALA
RNKSLNLKHI KHFILDECDK MLEQLDMRRD VQEIFRMTPH EKQVMMFSAT LSKEIRPVCR
KFMQDPMEIF VDDETKLTLH GLQQYYVKLK DNEKNRKLFD LLDVLEFNQV VIFVKSVQRC
IALAQLLVEQ NFPAIAIHRG MPQEERLSRY QQFKDFQRRI LVATNLFGRG MDIERVNIAF
NYDMPEDSDT YLHRVARAGR FGTKGLAITF VSDENDAKIL NDVQDRFEVN ISELPDEIDI
SSYIEQTR
