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Database: UniProt
Entry: Q63413
LinkDB: Q63413
Original site: Q63413 
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   16-OCT-2019, entry version 147.
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;
OC   Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
OC   Muroidea; Muridae; Murinae; Rattus.
OX   NCBI_TaxID=10116;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RX   PubMed=1618789;
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
RT   project: the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
CC   -!- FUNCTION: Involved in nuclear export of spliced and unspliced
CC       mRNA. Assembling component of the TREX complex which is thought to
CC       couple mRNA transcription, processing and nuclear export, and
CC       specifically associates with spliced mRNA and not with unspliced
CC       pre-mRNA. TREX is recruited to spliced mRNAs by a transcription-
CC       independent mechanism, binds to mRNA upstream of the exon-junction
CC       complex (EJC) and is recruited in a splicing- and cap-dependent
CC       manner to a region near the 5' end of the mRNA where it functions
CC       in mRNA export to the cytoplasm via the TAP/NFX1 pathway. May
CC       undergo several rounds of ATP hydrolysis during assembly of TREX
CC       to drive subsequent loading of components such as ALYREF/THOC and
CC       CHTOP onto mRNA. Also associates with pre-mRNA independent of
CC       ALYREF/THOC4 and the THO complex. Involved in the nuclear export
CC       of intronless mRNA; the ATP-bound form is proposed to recruit
CC       export adapter ALYREF/THOC4 to intronless mRNA; its ATPase
CC       activity is cooperatively stimulated by RNA and ALYREF/THOC4 and
CC       ATP hydrolysis is thought to trigger the dissociation from RNA to
CC       allow the association of ALYREF/THOC4 and the NXF1-NXT1
CC       heterodimer. Involved in transcription elongation and genome
CC       stability (By similarity). {ECO:0000250}.
CC   -!- FUNCTION: Splice factor that is required for the first ATP-
CC       dependent step in spliceosome assembly and for the interaction of
CC       U2 snRNP with the branchpoint. Has both RNA-stimulated ATP
CC       binding/hydrolysis activity and ATP-dependent RNA unwinding
CC       activity. Even with the stimulation of RNA, the ATPase activity is
CC       weak. Can only hydrolyze ATP but not other NTPs. The RNA
CC       stimulation of ATPase activity does not have a strong preference
CC       for the sequence and length of the RNA. However, ssRNA stimulates
CC       the ATPase activity much more strongly than dsRNA. Can unwind 5'
CC       or 3' overhangs or blunt end RNA duplexes in vitro. The ATPase and
CC       helicase activities are not influenced by U2AF2; the effect of
CC       ALYREF/THOC4 is reported conflictingly (By similarity).
CC       {ECO:0000250}.
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   -!- SUBUNIT: Homodimer, and heterodimer with DDX39A. Component of the
CC       transcription/export (TREX) complex at least composed of
CC       ALYREF/THOC4, DDX39B, SARNP/CIP29, CHTOP and the THO subcomplex;
CC       TREX seems to have dynamic structure involving ATP-dependent
CC       remodeling; in the complex bridges ALYREF/THOC4 and the THO
CC       complex, and, in a ATP-dependent manner, ALYREF/THOC4 and
CC       SARNP/CIP29. Component of the spliceosome. Interacts directly with
CC       U2AF2. Interacts with RBM8A, RNPS1 and SRRM1, FYTTD1/UIF, THOC1,
CC       MX1 and POLDIP3. Interacts with LUZP4 (By similarity).
CC       {ECO:0000250|UniProtKB:Q13838}.
CC   -!- SUBCELLULAR LOCATION: Nucleus. Nucleus speckle {ECO:0000250}.
CC       Cytoplasm {ECO:0000250}. Note=Can translocate to the cytoplasm in
CC       the presence of 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
CC       subfamily. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAA41787.1; Type=Frameshift; Evidence={ECO:0000305};
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   SMR; Q63413; -.
DR   BioGrid; 250392; 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   eggNOG; COG0513; LUCA.
DR   GeneTree; ENSGT00940000160110; -.
DR   InParanoid; Q63413; -.
DR   KO; K12812; -.
DR   OMA; VCADEAP; -.
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   PRO; PR:Q63413; -.
DR   Proteomes; UP000002494; Chromosome 20.
DR   Bgee; ENSRNOG00000000841; Expressed in 10 organ(s), highest expression level in spleen.
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; IEA:UniProtKB-SubCell.
DR   GO; GO:0032991; C:protein-containing complex; IDA:RGD.
DR   GO; GO:0005681; C:spliceosomal complex; IEA:UniProtKB-KW.
DR   GO; GO:0000346; C:transcription export complex; IBA:GO_Central.
DR   GO; GO:0005687; C:U4 snRNP; IEA:Ensembl.
DR   GO; GO:0005688; C:U6 snRNP; IEA:Ensembl.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0043008; F:ATP-dependent protein binding; IEA:Ensembl.
DR   GO; GO:0042802; F:identical protein binding; IEA:Ensembl.
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; IEA:UniProtKB-EC.
DR   GO; GO:0008186; F:RNA-dependent ATPase activity; IEA:Ensembl.
DR   GO; GO:0030621; F:U4 snRNA binding; IEA:Ensembl.
DR   GO; GO:0017070; F:U6 snRNA binding; IEA:Ensembl.
DR   GO; GO:0001889; P:liver development; IEP:RGD.
DR   GO; GO:0006406; P:mRNA export from nucleus; IEA:Ensembl.
DR   GO; GO:0000398; P:mRNA splicing, via spliceosome; IBA:GO_Central.
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 smooth muscle cell proliferation; IMP:RGD.
DR   GO; GO:0010501; P:RNA secondary structure unwinding; IEA:Ensembl.
DR   GO; GO:0000245; P:spliceosomal complex assembly; IEA:Ensembl.
DR   GO; GO:0046784; P:viral mRNA export from host cell nucleus; IEA:Ensembl.
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; Complete proteome; Cytoplasm; Helicase;
KW   Hydrolase; Isopeptide bond; mRNA processing; mRNA splicing;
KW   mRNA transport; Nucleotide-binding; Nucleus; Phosphoprotein;
KW   Reference proteome; RNA-binding; Spliceosome; Transport;
KW   Ubl conjugation.
FT   INIT_MET      1      1       Removed. {ECO:0000250|UniProtKB:Q13838}.
FT   CHAIN         2    428       Spliceosome RNA helicase Ddx39b.
FT                                /FTId=PRO_0000055077.
FT   DOMAIN       76    249       Helicase ATP-binding.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00541}.
FT   DOMAIN      261    422       Helicase C-terminal.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00542}.
FT   NP_BIND      89     96       ATP. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00541}.
FT   MOTIF        45     73       Q motif.
FT   MOTIF       196    199       DECD box.
FT   MOD_RES       2      2       N-acetylalanine.
FT                                {ECO:0000250|UniProtKB:Q13838}.
FT   MOD_RES      36     36       N6-acetyllysine; alternate.
FT                                {ECO:0000250|UniProtKB:Q13838}.
FT   MOD_RES      38     38       Phosphoserine.
FT                                {ECO:0000250|UniProtKB:Q13838}.
FT   MOD_RES      41     41       Phosphoserine.
FT                                {ECO:0000250|UniProtKB:Q13838}.
FT   MOD_RES     172    172       Phosphothreonine.
FT                                {ECO:0000250|UniProtKB:Q13838}.
FT   CROSSLNK     36     36       Glycyl lysine isopeptide (Lys-Gly)
FT                                (interchain with G-Cter in SUMO2);
FT                                alternate.
FT                                {ECO:0000250|UniProtKB:Q13838}.
FT   CONFLICT    236    236       R -> P (in Ref. 2; AAL98920).
FT                                {ECO:0000305}.
FT   CONFLICT    286    286       E -> Q (in Ref. 2; AAL98920).
FT                                {ECO:0000305}.
FT   CONFLICT    312    312       F -> L (in Ref. 1; AAA41787).
FT                                {ECO:0000305}.
FT   CONFLICT    354    354       E -> V (in Ref. 1; AAA41787).
FT                                {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
//
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