Full text data of DDX39B
DDX39B
(BAT1, UAP56)
[Confidence: low (only semi-automatic identification from reviews)]
Spliceosome RNA helicase DDX39B; 3.6.4.13 (56 kDa U2AF65-associated protein; ATP-dependent RNA helicase p47; DEAD box protein UAP56; HLA-B-associated transcript 1 protein)
Note: presumably soluble (membrane word is not in UniProt keywords or features)
Spliceosome RNA helicase DDX39B; 3.6.4.13 (56 kDa U2AF65-associated protein; ATP-dependent RNA helicase p47; DEAD box protein UAP56; HLA-B-associated transcript 1 protein)
Note: presumably soluble (membrane word is not in UniProt keywords or features)
UniProt
Q13838
ID DX39B_HUMAN Reviewed; 428 AA.
AC Q13838; B0S8C0; O43496; Q0EFA1; Q2L6F9; Q53GL9; Q5RJ64; Q5RJ66;
read moreAC Q5ST94; Q5STB4; Q5STB5; Q5STB7; Q5STB8; Q5STU4; Q5STU5; Q5STU6;
AC Q5STU8; Q71V76;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 22-JAN-2014, entry version 143.
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;
DE AltName: Full=HLA-B-associated transcript 1 protein;
GN Name=DDX39B; Synonyms=BAT1, UAP56;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), AND SUBCELLULAR LOCATION.
RX PubMed=7601445; DOI=10.1016/0888-7543(95)80203-X;
RA Peelman L., Chardon P., Nunes M., Renard C., Geffrotin C., Vaiman M.,
RA van Zeveren A., Coppieters W., van de Weghe A., Bouquet Y., Choy W.,
RA Strominger J., Spies T.;
RT "The BAT1 gene in the MHC encodes an evolutionarily conserved putative
RT nuclear RNA helicase of the DEAD family.";
RL Genomics 26:210-218(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RA Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S.,
RA Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y.,
RA Phelan M., Farmer A.;
RT "Cloning of human full-length CDSs in BD Creator(TM) system donor
RT vector.";
RL Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Kidney epithelium;
RA Suzuki Y., Sugano S., Totoki Y., Toyoda A., Takeda T., Sakaki Y.,
RA Tanaka A., Yokoyama S.;
RL Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16702430; DOI=10.1534/genetics.106.057034;
RA Shiina T., Ota M., Shimizu S., Katsuyama Y., Hashimoto N., Takasu M.,
RA Anzai T., Kulski J.K., Kikkawa E., Naruse T., Kimura N., Yanagiya K.,
RA Watanabe A., Hosomichi K., Kohara S., Iwamoto C., Umehara Y.,
RA Meyer A., Wanner V., Sano K., Macquin C., Ikeo K., Tokunaga K.,
RA Gojobori T., Inoko H., Bahram S.;
RT "Rapid evolution of major histocompatibility complex class I genes in
RT primates generates new disease alleles in humans via hitchhiking
RT diversity.";
RL Genetics 173:1555-1570(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=14574404; DOI=10.1038/nature02055;
RA Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L.,
RA Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E.,
RA Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R.,
RA Almeida J.P., Ambrose K.D., Andrews T.D., Ashwell R.I.S.,
RA Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J.,
RA Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P.,
RA Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y.,
RA Burford D.C., Burrill W., Burton J., Carder C., Carter N.P.,
RA Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V.,
RA Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J.,
RA Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E.,
RA Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A.,
RA Frankland J., French L., Garner P., Garnett J., Ghori M.J.,
RA Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M.,
RA Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S.,
RA Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R.,
RA Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E.,
RA Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A.,
RA Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C.,
RA Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M.,
RA Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M.,
RA Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K.,
RA McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T.,
RA Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R.,
RA Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W.,
RA Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M.,
RA Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L.,
RA Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J.,
RA Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B.,
RA Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L.,
RA Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W.,
RA Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A.,
RA Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.;
RT "The DNA sequence and analysis of human chromosome 6.";
RL Nature 425:805-811(2003).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L.,
RA Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R.,
RA Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V.,
RA Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R.,
RA Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H.,
RA Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G.,
RA Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W.,
RA Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Muscle;
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).
RN [8]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 145-428.
RA Allcock R.J.N., Price P., Gaudieri S., Leelayuwat C., Witt C.S.,
RA Dawkins R.L.;
RT "Homo sapiens BAT1 (BAT1) gene, partial cds; and PERB18 pseudogene,
RT complete sequence.";
RL Submitted (OCT-1997) to the EMBL/GenBank/DDBJ databases.
RN [9]
RP FUNCTION, INTERACTION WITH U2AF2 AND THE SPLICEOSOME, AND SUBCELLULAR
RP LOCATION.
RX PubMed=9242493;
RA Fleckner J., Zhang M., Valcarcel J., Green M.R.;
RT "U2AF65 recruits a novel human DEAD box protein required for the U2
RT snRNP-branchpoint interaction.";
RL Genes Dev. 11:1864-1872(1997).
RN [10]
RP FUNCTION, INTERACTION WITH ALYREF/THOC4 AND THE SPLICEOSOME, AND
RP SUBCELLULAR LOCATION.
RX PubMed=11675789; DOI=10.1038/35098106;
RA Luo M.-J., Zhou Z., Magni K., Christoforides C., Rappsilber J.,
RA Mann M., Reed R.;
RT "Pre-mRNA splicing and mRNA export linked by direct interactions
RT between UAP56 and Aly.";
RL Nature 413:644-647(2001).
RN [11]
RP INTERACTION WITH RBM8A; RNPS1; SRRM1 AND ALYREF/THOC4.
RX PubMed=12944400; DOI=10.1074/jbc.M306856200;
RA McCracken S., Longman D., Johnstone I.L., Caceres J.F., Blencowe B.J.;
RT "An evolutionarily conserved role for SRm160 in 3'-end processing that
RT functions independently of exon junction complex formation.";
RL J. Biol. Chem. 278:44153-44160(2003).
RN [12]
RP HOMODIMERIZATION, AND INTERACTION WITH ALYREF/THOC4 AND DDX39A.
RX PubMed=14667819; DOI=10.1016/S0888-7543(03)00235-0;
RA Lehner B., Semple J.I., Brown S.E., Counsell D., Campbell R.D.,
RA Sanderson C.M.;
RT "Analysis of a high-throughput yeast two-hybrid system and its use to
RT predict the function of intracellular proteins encoded within the
RT human MHC class III region.";
RL Genomics 83:153-167(2004).
RN [13]
RP IDENTIFICATION IN THE TREX COMPLEX, FUNCTION OF THE TREX COMPLEX, AND
RP MASS SPECTROMETRY.
RX PubMed=15833825; DOI=10.1158/0008-5472.CAN-04-3624;
RA Guo S., Hakimi M.A., Baillat D., Chen X., Farber M.J.,
RA Klein-Szanto A.J., Cooch N.S., Godwin A.K., Shiekhattar R.;
RT "Linking transcriptional elongation and messenger RNA export to
RT metastatic breast cancers.";
RL Cancer Res. 65:3011-3016(2005).
RN [14]
RP IDENTIFICATION IN THE TREX COMPLEX, FUNCTION OF THE TREX COMPLEX, MASS
RP SPECTROMETRY, INTERACTION WITH ALYREF/THOC4, AND DOMAIN.
RX PubMed=15998806; DOI=10.1101/gad.1302205;
RA Masuda S., Das R., Cheng H., Hurt E., Dorman N., Reed R.;
RT "Recruitment of the human TREX complex to mRNA during splicing.";
RL Genes Dev. 19:1512-1517(2005).
RN [15]
RP INTERACTION WITH THOC1, AND SUBCELLULAR LOCATION.
RX PubMed=15870275; DOI=10.1128/MCB.25.10.4023-4033.2005;
RA Li Y., Wang X., Zhang X., Goodrich D.W.;
RT "Human hHpr1/p84/Thoc1 regulates transcriptional elongation and
RT physically links RNA polymerase II and RNA processing factors.";
RL Mol. Cell. Biol. 25:4023-4033(2005).
RN [16]
RP FUNCTION OF THE TREX COMPLEX.
RX PubMed=17190602; DOI=10.1016/j.cell.2006.10.044;
RA Cheng H., Dufu K., Lee C.-S., Hsu J.L., Dias A., Reed R.;
RT "Human mRNA export machinery recruited to the 5' end of mRNA.";
RL Cell 127:1389-1400(2006).
RN [17]
RP INTERACTION WITH HHV-5 PROTEIN UL69.
RX PubMed=16478985; DOI=10.1128/MCB.26.5.1631-1643.2006;
RA Lischka P., Toth Z., Thomas M., Mueller R., Stamminger T.;
RT "The UL69 transactivator protein of human cytomegalovirus interacts
RT with DEXD/H-Box RNA helicase UAP56 to promote cytoplasmic accumulation
RT of unspliced RNA.";
RL Mol. Cell. Biol. 26:1631-1643(2006).
RN [18]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF
RP 94-GLY--THR-96; LYS-95; GLU-197; ASP-199 AND 228-SER--THR-230.
RX PubMed=17562711; DOI=10.1074/jbc.M702304200;
RA Shen J., Zhang L., Zhao R.;
RT "Biochemical characterization of the ATPase and helicase activity of
RT UAP56, an essential pre-mRNA splicing and mRNA export factor.";
RL J. Biol. Chem. 282:22544-22550(2007).
RN [19]
RP FUNCTION, INTERACTION WITH ALYREF, CATALYTIC ACTIVITY, AND MUTAGENESIS
RP OF LYS-95.
RX PubMed=17984224; DOI=10.1128/MCB.01341-07;
RA Taniguchi I., Ohno M.;
RT "ATP-dependent recruitment of export factor Aly/REF onto intronless
RT mRNAs by RNA helicase UAP56.";
RL Mol. Cell. Biol. 28:601-608(2008).
RN [20]
RP FUNCTION OF THE TREX COMPLEX.
RX PubMed=18974867; DOI=10.1371/journal.ppat.1000194;
RA Boyne J.R., Colgan K.J., Whitehouse A.;
RT "Recruitment of the complete hTREX complex is required for Kaposi's
RT sarcoma-associated herpesvirus intronless mRNA nuclear export and
RT virus replication.";
RL PLoS Pathog. 4:E1000194-E1000194(2008).
RN [21]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=18669648; DOI=10.1073/pnas.0805139105;
RA Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
RA Elledge S.J., Gygi S.P.;
RT "A quantitative atlas of mitotic phosphorylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
RN [22]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, MASS SPECTROMETRY, AND
RP CLEAVAGE OF INITIATOR METHIONINE.
RX PubMed=19413330; DOI=10.1021/ac9004309;
RA Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J.,
RA Mohammed S.;
RT "Lys-N and trypsin cover complementary parts of the phosphoproteome in
RT a refined SCX-based approach.";
RL Anal. Chem. 81:4493-4501(2009).
RN [23]
RP INTERACTION WITH FYTTD1.
RX PubMed=19836239; DOI=10.1016/j.cub.2009.09.041;
RA Hautbergue G.M., Hung M.L., Walsh M.J., Snijders A.P., Chang C.T.,
RA Jones R., Ponting C.P., Dickman M.J., Wilson S.A.;
RT "UIF, a new mRNA export adaptor that works together with REF/ALY,
RT requires FACT for recruitment to mRNA.";
RL Curr. Biol. 19:1918-1924(2009).
RN [24]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-36, AND MASS SPECTROMETRY.
RX PubMed=19608861; DOI=10.1126/science.1175371;
RA Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M.,
RA Walther T.C., Olsen J.V., Mann M.;
RT "Lysine acetylation targets protein complexes and co-regulates major
RT cellular functions.";
RL Science 325:834-840(2009).
RN [25]
RP FUNCTION, AND INTERACTON WITH ALYREF AND SARNP.
RX PubMed=20844015; DOI=10.1101/gad.1898610;
RA Dufu K., Livingstone M.J., Seebacher J., Gygi S.P., Wilson S.A.,
RA Reed R.;
RT "ATP is required for interactions between UAP56 and two conserved mRNA
RT export proteins, Aly and CIP29, to assemble the TREX complex.";
RL Genes Dev. 24:2043-2053(2010).
RN [26]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-38 AND THR-172, AND MASS
RP SPECTROMETRY.
RC TISSUE=Cervix carcinoma;
RX PubMed=20068231; DOI=10.1126/scisignal.2000475;
RA Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
RA Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S.,
RA Mann M.;
RT "Quantitative phosphoproteomics reveals widespread full
RT phosphorylation site occupancy during mitosis.";
RL Sci. Signal. 3:RA3-RA3(2010).
RN [27]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
RA Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [28]
RP SUBCELLULAR LOCATION, AND INTERACTION WITH MX1.
RX PubMed=21859714; DOI=10.1074/jbc.M111.251843;
RA Wisskirchen C., Ludersdorfer T.H., Mueller D.A., Moritz E.,
RA Pavlovic J.;
RT "Interferon-induced antiviral protein MxA interacts with the cellular
RT RNA helicases UAP56 and URH49.";
RL J. Biol. Chem. 286:34743-34751(2011).
RN [29]
RP FUNCTION.
RX PubMed=22144908; DOI=10.1371/journal.pgen.1002386;
RA Dominguez-Sanchez M.S., Barroso S., Gomez-Gonzalez B., Luna R.,
RA Aguilera A.;
RT "Genome instability and transcription elongation impairment in human
RT cells depleted of THO/TREX.";
RL PLoS Genet. 7:E1002386-E1002386(2011).
RN [30]
RP INTERACTION WITH POLDIP3.
RX PubMed=22928037; DOI=10.1371/journal.pone.0043804;
RA Folco E.G., Lee C.S., Dufu K., Yamazaki T., Reed R.;
RT "The proteins PDIP3 and ZC11A associate with the human TREX complex in
RT an ATP-dependent manner and function in mRNA export.";
RL PLoS ONE 7:E43804-E43804(2012).
RN [31]
RP FUNCTION, AND INTERACTION WITH CHTOP.
RX PubMed=23299939; DOI=10.1038/emboj.2012.342;
RA Chang C.T., Hautbergue G.M., Walsh M.J., Viphakone N., van Dijk T.B.,
RA Philipsen S., Wilson S.A.;
RT "Chtop is a component of the dynamic TREX mRNA export complex.";
RL EMBO J. 32:473-486(2013).
RN [32]
RP FUNCTION.
RX PubMed=23222130; DOI=10.1093/nar/gks1188;
RA Chi B., Wang Q., Wu G., Tan M., Wang L., Shi M., Chang X., Cheng H.;
RT "Aly and THO are required for assembly of the human TREX complex and
RT association of TREX components with the spliced mRNA.";
RL Nucleic Acids Res. 41:1294-1306(2013).
RN [33]
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 44-428 IN COMPLEX WITH ADP,
RP FUNCTION, AND MUTAGENESIS OF CYS-198.
RX PubMed=15585580; DOI=10.1073/pnas.0408172101;
RA Shi H., Cordin O., Minder C.M., Linder P., Xu R.-M.;
RT "Crystal structure of the human ATP-dependent splicing and export
RT factor UAP56.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:17628-17633(2004).
RN [34]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 34-428, AND DIMERIZATION.
RX PubMed=15296731; DOI=10.1016/j.str.2004.06.006;
RA Zhao R., Shen J., Green M.R., MacMorris M., Blumenthal T.;
RT "Crystal structure of UAP56, a DExD/H-box protein involved in pre-mRNA
RT splicing and mRNA export.";
RL Structure 12:1373-1381(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. The TREX complex is essential for the export of
CC Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs
CC and infectious virus production. 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
CC to recruit export adapter ALYREF/THOC4 to intronless mRNA; its
CC ATPase activity is cooperatively stimulated by RNA and
CC ALYREF/THOC4 and ATP hydrolysis is thought to trigger the
CC dissociation from RNA to allow the association of ALYREF/THOC4 and
CC the NXF1-NXT1 heterodimer. Involved in transcription elongation
CC and genome stability.
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 with [PubMed:23299939]
CC reporting a stimulatory effect.
CC -!- CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=3.3 uM for ATP;
CC Vmax=0.126 uM/min/mg enzyme with ATP as substrate;
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 human cytomegalovirus/HHV-5
CC protein UL69.
CC -!- SUBCELLULAR LOCATION: Nucleus. Nucleus speckle. Cytoplasm.
CC Note=Can translocate to the cytoplasm in the presence of MX1. TREX
CC complex assembly seems to occur in regions surrounding nuclear
CC speckles known as perispeckles.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q13838-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q13838-2; Sequence=VSP_026347;
CC Note=No experimental confirmation available;
CC -!- DOMAIN: The helicase C-terminal domain mediates interaction with
CC ALYREF/THOC4.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DECD
CC subfamily.
CC -!- SIMILARITY: Contains 1 helicase ATP-binding domain.
CC -!- SIMILARITY: Contains 1 helicase C-terminal domain.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAI17665.2; Type=Erroneous gene model prediction;
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DR EMBL; Z37166; CAA85523.1; -; mRNA.
DR EMBL; BT009909; AAP88911.1; -; mRNA.
DR EMBL; AK222912; BAD96632.1; -; mRNA.
DR EMBL; AB088115; BAC54953.1; -; Genomic_DNA.
DR EMBL; AB103621; BAF31287.1; -; Genomic_DNA.
DR EMBL; AB202112; BAE78637.1; -; Genomic_DNA.
DR EMBL; BA000025; BAB63306.1; -; Genomic_DNA.
DR EMBL; AL662847; CAI17664.2; -; Genomic_DNA.
DR EMBL; AL662847; CAI17665.2; ALT_SEQ; Genomic_DNA.
DR EMBL; AL662801; CAI18279.2; -; Genomic_DNA.
DR EMBL; AL662801; CAI18280.1; -; Genomic_DNA.
DR EMBL; AL662801; CAI18281.2; -; Genomic_DNA.
DR EMBL; AL662801; CAI18282.2; -; Genomic_DNA.
DR EMBL; AL662801; CAI18283.2; -; Genomic_DNA.
DR EMBL; BX001040; CAI18634.1; -; Genomic_DNA.
DR EMBL; BX248516; CAI41922.1; -; Genomic_DNA.
DR EMBL; BX927320; CAQ09974.1; -; Genomic_DNA.
DR EMBL; CR753820; CAQ07176.1; -; Genomic_DNA.
DR EMBL; CR753864; CAQ10634.1; -; Genomic_DNA.
DR EMBL; CH471081; EAX03404.1; -; Genomic_DNA.
DR EMBL; BC000361; AAH00361.1; -; mRNA.
DR EMBL; BC013006; AAH13006.1; -; mRNA.
DR EMBL; AF029061; AAB94615.1; -; Genomic_DNA.
DR EMBL; AF029062; AAC63046.1; -; Genomic_DNA.
DR PIR; I37201; I37201.
DR RefSeq; NP_004631.1; NM_004640.6.
DR RefSeq; NP_542165.1; NM_080598.5.
DR UniGene; Hs.254042; -.
DR UniGene; Hs.730849; -.
DR PDB; 1T5I; X-ray; 1.90 A; A=259-428.
DR PDB; 1T6N; X-ray; 1.94 A; A/B=34-251.
DR PDB; 1XTI; X-ray; 1.95 A; A=44-428.
DR PDB; 1XTJ; X-ray; 2.70 A; A=44-423.
DR PDB; 1XTK; X-ray; 2.40 A; A=45-428.
DR PDBsum; 1T5I; -.
DR PDBsum; 1T6N; -.
DR PDBsum; 1XTI; -.
DR PDBsum; 1XTJ; -.
DR PDBsum; 1XTK; -.
DR ProteinModelPortal; Q13838; -.
DR SMR; Q13838; 46-426.
DR IntAct; Q13838; 33.
DR MINT; MINT-1032422; -.
DR TCDB; 3.A.18.1.1; the nuclear mrna exporter (mrna-e) family.
DR PhosphoSite; Q13838; -.
DR DMDM; 2500529; -.
DR PaxDb; Q13838; -.
DR PRIDE; Q13838; -.
DR DNASU; 7919; -.
DR Ensembl; ENST00000383508; ENSP00000373000; ENSG00000215425.
DR Ensembl; ENST00000396172; ENSP00000379475; ENSG00000198563.
DR Ensembl; ENST00000400295; ENSP00000383151; ENSG00000215425.
DR Ensembl; ENST00000400296; ENSP00000383152; ENSG00000215425.
DR Ensembl; ENST00000412106; ENSP00000393712; ENSG00000225073.
DR Ensembl; ENST00000412330; ENSP00000398775; ENSG00000225859.
DR Ensembl; ENST00000413678; ENSP00000391463; ENSG00000229496.
DR Ensembl; ENST00000414440; ENSP00000411853; ENSG00000229496.
DR Ensembl; ENST00000415689; ENSP00000390999; ENSG00000225073.
DR Ensembl; ENST00000416863; ENSP00000407419; ENSG00000229496.
DR Ensembl; ENST00000430784; ENSP00000399030; ENSG00000235439.
DR Ensembl; ENST00000431360; ENSP00000404695; ENSG00000235439.
DR Ensembl; ENST00000441425; ENSP00000388880; ENSG00000230624.
DR Ensembl; ENST00000445218; ENSP00000411136; ENSG00000225859.
DR Ensembl; ENST00000448296; ENSP00000405560; ENSG00000225859.
DR Ensembl; ENST00000453138; ENSP00000387994; ENSG00000230624.
DR Ensembl; ENST00000456476; ENSP00000400326; ENSG00000225073.
DR Ensembl; ENST00000456666; ENSP00000394160; ENSG00000230624.
DR Ensembl; ENST00000458640; ENSP00000416269; ENSG00000198563.
DR GeneID; 7919; -.
DR KEGG; hsa:7919; -.
DR UCSC; uc003ntt.3; human.
DR CTD; 7919; -.
DR GeneCards; GC06M031500; -.
DR GeneCards; GC06Mj31485; -.
DR GeneCards; GC06Mk31480; -.
DR GeneCards; GC06Ml31538; -.
DR GeneCards; GC06Mm31574; -.
DR GeneCards; GC06Mn31488; -.
DR GeneCards; GC06Mo31487; -.
DR HGNC; HGNC:13917; DDX39B.
DR HPA; CAB034012; -.
DR MIM; 142560; gene.
DR neXtProt; NX_Q13838; -.
DR PharmGKB; PA25262; -.
DR eggNOG; COG0513; -.
DR HOVERGEN; HBG107334; -.
DR InParanoid; Q13838; -.
DR KO; K12812; -.
DR PhylomeDB; Q13838; -.
DR ChiTaRS; DDX39B; human.
DR EvolutionaryTrace; Q13838; -.
DR GeneWiki; BAT1; -.
DR GenomeRNAi; 7919; -.
DR NextBio; 30405; -.
DR PRO; PR:Q13838; -.
DR ArrayExpress; Q13838; -.
DR Bgee; Q13838; -.
DR CleanEx; HS_BAT1; -.
DR Genevestigator; Q13838; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0016607; C:nuclear speck; IEA:UniProtKB-SubCell.
DR GO; GO:0005681; C:spliceosomal complex; IDA:BHF-UCL.
DR GO; GO:0000346; C:transcription export complex; IDA:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0043008; F:ATP-dependent protein binding; IDA:BHF-UCL.
DR GO; GO:0004004; F:ATP-dependent RNA helicase activity; IDA:UniProtKB.
DR GO; GO:0030621; F:U4 snRNA binding; IDA:BHF-UCL.
DR GO; GO:0017070; F:U6 snRNA binding; IDA:BHF-UCL.
DR GO; GO:2000002; P:negative regulation of DNA damage checkpoint; IMP:UniProtKB.
DR GO; GO:0032786; P:positive regulation of DNA-dependent transcription, elongation; IMP:UniProtKB.
DR GO; GO:0010501; P:RNA secondary structure unwinding; IDA:BHF-UCL.
DR GO; GO:0000245; P:spliceosomal complex assembly; IDA:BHF-UCL.
DR GO; GO:0046784; P:viral mRNA export from host cell nucleus; IDA:UniProtKB.
DR InterPro; IPR011545; DNA/RNA_helicase_DEAD/DEAH_N.
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 1: Evidence at protein level;
KW 3D-structure; Acetylation; Alternative splicing; ATP-binding;
KW Complete proteome; Cytoplasm; Helicase; Hydrolase; mRNA processing;
KW mRNA splicing; mRNA transport; Nucleotide-binding; Nucleus;
KW Phosphoprotein; Reference proteome; RNA-binding; Spliceosome;
KW Transport.
FT INIT_MET 1 1 Removed.
FT CHAIN 2 428 Spliceosome RNA helicase DDX39B.
FT /FTId=PRO_0000055071.
FT DOMAIN 76 249 Helicase ATP-binding.
FT DOMAIN 261 422 Helicase C-terminal.
FT NP_BIND 89 96 ATP.
FT MOTIF 45 73 Q motif.
FT MOTIF 196 199 DECD box.
FT MOD_RES 2 2 N-acetylalanine.
FT MOD_RES 36 36 N6-acetyllysine.
FT MOD_RES 38 38 Phosphoserine.
FT MOD_RES 172 172 Phosphothreonine.
FT VAR_SEQ 114 114 V -> VYLGRVLGRGFWLGLV (in isoform 2).
FT /FTId=VSP_026347.
FT MUTAGEN 94 96 GKT->AAA: Loss of ATPase and helicase
FT activity.
FT MUTAGEN 95 95 K->A: Loss of ATPase and helicase
FT activity.
FT MUTAGEN 197 197 E->A: Loss of ATPase and helicase
FT activity.
FT MUTAGEN 198 198 C->A: No effect on ATPase activity.
FT MUTAGEN 199 199 D->A: Increased ATPase activity and loss
FT of helicase activity.
FT MUTAGEN 228 230 SAT->AAA: Decreased ATPase activity and
FT loss of helicase activity.
FT CONFLICT 289 289 Q -> R (in Ref. 3; BAD96632).
FT HELIX 47 50
FT HELIX 54 62
FT HELIX 70 80
FT STRAND 85 88
FT HELIX 95 106
FT STRAND 116 119
FT HELIX 123 136
FT TURN 137 139
FT STRAND 145 149
FT HELIX 154 163
FT STRAND 167 171
FT HELIX 173 181
FT STRAND 183 185
FT STRAND 192 197
FT HELIX 198 202
FT HELIX 205 216
FT STRAND 220 229
FT TURN 233 235
FT HELIX 236 240
FT STRAND 247 250
FT STRAND 263 268
FT HELIX 271 273
FT HELIX 274 284
FT STRAND 288 293
FT HELIX 297 309
FT STRAND 314 317
FT STRAND 319 321
FT HELIX 323 334
FT STRAND 335 337
FT STRAND 339 345
FT HELIX 353 355
FT STRAND 357 363
FT HELIX 368 378
FT HELIX 380 382
FT STRAND 386 391
FT HELIX 394 407
FT STRAND 411 413
FT STRAND 417 419
FT HELIX 420 422
SQ SEQUENCE 428 AA; 48991 MW; 7A55167BF576FB6F CRC64;
MAENDVDNEL LDYEDDEVET AAGGDGAEAP 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
//
ID DX39B_HUMAN Reviewed; 428 AA.
AC Q13838; B0S8C0; O43496; Q0EFA1; Q2L6F9; Q53GL9; Q5RJ64; Q5RJ66;
read moreAC Q5ST94; Q5STB4; Q5STB5; Q5STB7; Q5STB8; Q5STU4; Q5STU5; Q5STU6;
AC Q5STU8; Q71V76;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 22-JAN-2014, entry version 143.
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;
DE AltName: Full=HLA-B-associated transcript 1 protein;
GN Name=DDX39B; Synonyms=BAT1, UAP56;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), AND SUBCELLULAR LOCATION.
RX PubMed=7601445; DOI=10.1016/0888-7543(95)80203-X;
RA Peelman L., Chardon P., Nunes M., Renard C., Geffrotin C., Vaiman M.,
RA van Zeveren A., Coppieters W., van de Weghe A., Bouquet Y., Choy W.,
RA Strominger J., Spies T.;
RT "The BAT1 gene in the MHC encodes an evolutionarily conserved putative
RT nuclear RNA helicase of the DEAD family.";
RL Genomics 26:210-218(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RA Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S.,
RA Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y.,
RA Phelan M., Farmer A.;
RT "Cloning of human full-length CDSs in BD Creator(TM) system donor
RT vector.";
RL Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Kidney epithelium;
RA Suzuki Y., Sugano S., Totoki Y., Toyoda A., Takeda T., Sakaki Y.,
RA Tanaka A., Yokoyama S.;
RL Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16702430; DOI=10.1534/genetics.106.057034;
RA Shiina T., Ota M., Shimizu S., Katsuyama Y., Hashimoto N., Takasu M.,
RA Anzai T., Kulski J.K., Kikkawa E., Naruse T., Kimura N., Yanagiya K.,
RA Watanabe A., Hosomichi K., Kohara S., Iwamoto C., Umehara Y.,
RA Meyer A., Wanner V., Sano K., Macquin C., Ikeo K., Tokunaga K.,
RA Gojobori T., Inoko H., Bahram S.;
RT "Rapid evolution of major histocompatibility complex class I genes in
RT primates generates new disease alleles in humans via hitchhiking
RT diversity.";
RL Genetics 173:1555-1570(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=14574404; DOI=10.1038/nature02055;
RA Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L.,
RA Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E.,
RA Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R.,
RA Almeida J.P., Ambrose K.D., Andrews T.D., Ashwell R.I.S.,
RA Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J.,
RA Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P.,
RA Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y.,
RA Burford D.C., Burrill W., Burton J., Carder C., Carter N.P.,
RA Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V.,
RA Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J.,
RA Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E.,
RA Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A.,
RA Frankland J., French L., Garner P., Garnett J., Ghori M.J.,
RA Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M.,
RA Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S.,
RA Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R.,
RA Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E.,
RA Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A.,
RA Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C.,
RA Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M.,
RA Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M.,
RA Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K.,
RA McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T.,
RA Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R.,
RA Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W.,
RA Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M.,
RA Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L.,
RA Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J.,
RA Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B.,
RA Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L.,
RA Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W.,
RA Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A.,
RA Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.;
RT "The DNA sequence and analysis of human chromosome 6.";
RL Nature 425:805-811(2003).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L.,
RA Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R.,
RA Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V.,
RA Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R.,
RA Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H.,
RA Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G.,
RA Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W.,
RA Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Muscle;
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).
RN [8]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 145-428.
RA Allcock R.J.N., Price P., Gaudieri S., Leelayuwat C., Witt C.S.,
RA Dawkins R.L.;
RT "Homo sapiens BAT1 (BAT1) gene, partial cds; and PERB18 pseudogene,
RT complete sequence.";
RL Submitted (OCT-1997) to the EMBL/GenBank/DDBJ databases.
RN [9]
RP FUNCTION, INTERACTION WITH U2AF2 AND THE SPLICEOSOME, AND SUBCELLULAR
RP LOCATION.
RX PubMed=9242493;
RA Fleckner J., Zhang M., Valcarcel J., Green M.R.;
RT "U2AF65 recruits a novel human DEAD box protein required for the U2
RT snRNP-branchpoint interaction.";
RL Genes Dev. 11:1864-1872(1997).
RN [10]
RP FUNCTION, INTERACTION WITH ALYREF/THOC4 AND THE SPLICEOSOME, AND
RP SUBCELLULAR LOCATION.
RX PubMed=11675789; DOI=10.1038/35098106;
RA Luo M.-J., Zhou Z., Magni K., Christoforides C., Rappsilber J.,
RA Mann M., Reed R.;
RT "Pre-mRNA splicing and mRNA export linked by direct interactions
RT between UAP56 and Aly.";
RL Nature 413:644-647(2001).
RN [11]
RP INTERACTION WITH RBM8A; RNPS1; SRRM1 AND ALYREF/THOC4.
RX PubMed=12944400; DOI=10.1074/jbc.M306856200;
RA McCracken S., Longman D., Johnstone I.L., Caceres J.F., Blencowe B.J.;
RT "An evolutionarily conserved role for SRm160 in 3'-end processing that
RT functions independently of exon junction complex formation.";
RL J. Biol. Chem. 278:44153-44160(2003).
RN [12]
RP HOMODIMERIZATION, AND INTERACTION WITH ALYREF/THOC4 AND DDX39A.
RX PubMed=14667819; DOI=10.1016/S0888-7543(03)00235-0;
RA Lehner B., Semple J.I., Brown S.E., Counsell D., Campbell R.D.,
RA Sanderson C.M.;
RT "Analysis of a high-throughput yeast two-hybrid system and its use to
RT predict the function of intracellular proteins encoded within the
RT human MHC class III region.";
RL Genomics 83:153-167(2004).
RN [13]
RP IDENTIFICATION IN THE TREX COMPLEX, FUNCTION OF THE TREX COMPLEX, AND
RP MASS SPECTROMETRY.
RX PubMed=15833825; DOI=10.1158/0008-5472.CAN-04-3624;
RA Guo S., Hakimi M.A., Baillat D., Chen X., Farber M.J.,
RA Klein-Szanto A.J., Cooch N.S., Godwin A.K., Shiekhattar R.;
RT "Linking transcriptional elongation and messenger RNA export to
RT metastatic breast cancers.";
RL Cancer Res. 65:3011-3016(2005).
RN [14]
RP IDENTIFICATION IN THE TREX COMPLEX, FUNCTION OF THE TREX COMPLEX, MASS
RP SPECTROMETRY, INTERACTION WITH ALYREF/THOC4, AND DOMAIN.
RX PubMed=15998806; DOI=10.1101/gad.1302205;
RA Masuda S., Das R., Cheng H., Hurt E., Dorman N., Reed R.;
RT "Recruitment of the human TREX complex to mRNA during splicing.";
RL Genes Dev. 19:1512-1517(2005).
RN [15]
RP INTERACTION WITH THOC1, AND SUBCELLULAR LOCATION.
RX PubMed=15870275; DOI=10.1128/MCB.25.10.4023-4033.2005;
RA Li Y., Wang X., Zhang X., Goodrich D.W.;
RT "Human hHpr1/p84/Thoc1 regulates transcriptional elongation and
RT physically links RNA polymerase II and RNA processing factors.";
RL Mol. Cell. Biol. 25:4023-4033(2005).
RN [16]
RP FUNCTION OF THE TREX COMPLEX.
RX PubMed=17190602; DOI=10.1016/j.cell.2006.10.044;
RA Cheng H., Dufu K., Lee C.-S., Hsu J.L., Dias A., Reed R.;
RT "Human mRNA export machinery recruited to the 5' end of mRNA.";
RL Cell 127:1389-1400(2006).
RN [17]
RP INTERACTION WITH HHV-5 PROTEIN UL69.
RX PubMed=16478985; DOI=10.1128/MCB.26.5.1631-1643.2006;
RA Lischka P., Toth Z., Thomas M., Mueller R., Stamminger T.;
RT "The UL69 transactivator protein of human cytomegalovirus interacts
RT with DEXD/H-Box RNA helicase UAP56 to promote cytoplasmic accumulation
RT of unspliced RNA.";
RL Mol. Cell. Biol. 26:1631-1643(2006).
RN [18]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF
RP 94-GLY--THR-96; LYS-95; GLU-197; ASP-199 AND 228-SER--THR-230.
RX PubMed=17562711; DOI=10.1074/jbc.M702304200;
RA Shen J., Zhang L., Zhao R.;
RT "Biochemical characterization of the ATPase and helicase activity of
RT UAP56, an essential pre-mRNA splicing and mRNA export factor.";
RL J. Biol. Chem. 282:22544-22550(2007).
RN [19]
RP FUNCTION, INTERACTION WITH ALYREF, CATALYTIC ACTIVITY, AND MUTAGENESIS
RP OF LYS-95.
RX PubMed=17984224; DOI=10.1128/MCB.01341-07;
RA Taniguchi I., Ohno M.;
RT "ATP-dependent recruitment of export factor Aly/REF onto intronless
RT mRNAs by RNA helicase UAP56.";
RL Mol. Cell. Biol. 28:601-608(2008).
RN [20]
RP FUNCTION OF THE TREX COMPLEX.
RX PubMed=18974867; DOI=10.1371/journal.ppat.1000194;
RA Boyne J.R., Colgan K.J., Whitehouse A.;
RT "Recruitment of the complete hTREX complex is required for Kaposi's
RT sarcoma-associated herpesvirus intronless mRNA nuclear export and
RT virus replication.";
RL PLoS Pathog. 4:E1000194-E1000194(2008).
RN [21]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=18669648; DOI=10.1073/pnas.0805139105;
RA Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
RA Elledge S.J., Gygi S.P.;
RT "A quantitative atlas of mitotic phosphorylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
RN [22]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, MASS SPECTROMETRY, AND
RP CLEAVAGE OF INITIATOR METHIONINE.
RX PubMed=19413330; DOI=10.1021/ac9004309;
RA Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J.,
RA Mohammed S.;
RT "Lys-N and trypsin cover complementary parts of the phosphoproteome in
RT a refined SCX-based approach.";
RL Anal. Chem. 81:4493-4501(2009).
RN [23]
RP INTERACTION WITH FYTTD1.
RX PubMed=19836239; DOI=10.1016/j.cub.2009.09.041;
RA Hautbergue G.M., Hung M.L., Walsh M.J., Snijders A.P., Chang C.T.,
RA Jones R., Ponting C.P., Dickman M.J., Wilson S.A.;
RT "UIF, a new mRNA export adaptor that works together with REF/ALY,
RT requires FACT for recruitment to mRNA.";
RL Curr. Biol. 19:1918-1924(2009).
RN [24]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-36, AND MASS SPECTROMETRY.
RX PubMed=19608861; DOI=10.1126/science.1175371;
RA Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M.,
RA Walther T.C., Olsen J.V., Mann M.;
RT "Lysine acetylation targets protein complexes and co-regulates major
RT cellular functions.";
RL Science 325:834-840(2009).
RN [25]
RP FUNCTION, AND INTERACTON WITH ALYREF AND SARNP.
RX PubMed=20844015; DOI=10.1101/gad.1898610;
RA Dufu K., Livingstone M.J., Seebacher J., Gygi S.P., Wilson S.A.,
RA Reed R.;
RT "ATP is required for interactions between UAP56 and two conserved mRNA
RT export proteins, Aly and CIP29, to assemble the TREX complex.";
RL Genes Dev. 24:2043-2053(2010).
RN [26]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-38 AND THR-172, AND MASS
RP SPECTROMETRY.
RC TISSUE=Cervix carcinoma;
RX PubMed=20068231; DOI=10.1126/scisignal.2000475;
RA Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
RA Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S.,
RA Mann M.;
RT "Quantitative phosphoproteomics reveals widespread full
RT phosphorylation site occupancy during mitosis.";
RL Sci. Signal. 3:RA3-RA3(2010).
RN [27]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
RA Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [28]
RP SUBCELLULAR LOCATION, AND INTERACTION WITH MX1.
RX PubMed=21859714; DOI=10.1074/jbc.M111.251843;
RA Wisskirchen C., Ludersdorfer T.H., Mueller D.A., Moritz E.,
RA Pavlovic J.;
RT "Interferon-induced antiviral protein MxA interacts with the cellular
RT RNA helicases UAP56 and URH49.";
RL J. Biol. Chem. 286:34743-34751(2011).
RN [29]
RP FUNCTION.
RX PubMed=22144908; DOI=10.1371/journal.pgen.1002386;
RA Dominguez-Sanchez M.S., Barroso S., Gomez-Gonzalez B., Luna R.,
RA Aguilera A.;
RT "Genome instability and transcription elongation impairment in human
RT cells depleted of THO/TREX.";
RL PLoS Genet. 7:E1002386-E1002386(2011).
RN [30]
RP INTERACTION WITH POLDIP3.
RX PubMed=22928037; DOI=10.1371/journal.pone.0043804;
RA Folco E.G., Lee C.S., Dufu K., Yamazaki T., Reed R.;
RT "The proteins PDIP3 and ZC11A associate with the human TREX complex in
RT an ATP-dependent manner and function in mRNA export.";
RL PLoS ONE 7:E43804-E43804(2012).
RN [31]
RP FUNCTION, AND INTERACTION WITH CHTOP.
RX PubMed=23299939; DOI=10.1038/emboj.2012.342;
RA Chang C.T., Hautbergue G.M., Walsh M.J., Viphakone N., van Dijk T.B.,
RA Philipsen S., Wilson S.A.;
RT "Chtop is a component of the dynamic TREX mRNA export complex.";
RL EMBO J. 32:473-486(2013).
RN [32]
RP FUNCTION.
RX PubMed=23222130; DOI=10.1093/nar/gks1188;
RA Chi B., Wang Q., Wu G., Tan M., Wang L., Shi M., Chang X., Cheng H.;
RT "Aly and THO are required for assembly of the human TREX complex and
RT association of TREX components with the spliced mRNA.";
RL Nucleic Acids Res. 41:1294-1306(2013).
RN [33]
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 44-428 IN COMPLEX WITH ADP,
RP FUNCTION, AND MUTAGENESIS OF CYS-198.
RX PubMed=15585580; DOI=10.1073/pnas.0408172101;
RA Shi H., Cordin O., Minder C.M., Linder P., Xu R.-M.;
RT "Crystal structure of the human ATP-dependent splicing and export
RT factor UAP56.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:17628-17633(2004).
RN [34]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 34-428, AND DIMERIZATION.
RX PubMed=15296731; DOI=10.1016/j.str.2004.06.006;
RA Zhao R., Shen J., Green M.R., MacMorris M., Blumenthal T.;
RT "Crystal structure of UAP56, a DExD/H-box protein involved in pre-mRNA
RT splicing and mRNA export.";
RL Structure 12:1373-1381(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. The TREX complex is essential for the export of
CC Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs
CC and infectious virus production. 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
CC to recruit export adapter ALYREF/THOC4 to intronless mRNA; its
CC ATPase activity is cooperatively stimulated by RNA and
CC ALYREF/THOC4 and ATP hydrolysis is thought to trigger the
CC dissociation from RNA to allow the association of ALYREF/THOC4 and
CC the NXF1-NXT1 heterodimer. Involved in transcription elongation
CC and genome stability.
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 with [PubMed:23299939]
CC reporting a stimulatory effect.
CC -!- CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=3.3 uM for ATP;
CC Vmax=0.126 uM/min/mg enzyme with ATP as substrate;
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 human cytomegalovirus/HHV-5
CC protein UL69.
CC -!- SUBCELLULAR LOCATION: Nucleus. Nucleus speckle. Cytoplasm.
CC Note=Can translocate to the cytoplasm in the presence of MX1. TREX
CC complex assembly seems to occur in regions surrounding nuclear
CC speckles known as perispeckles.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q13838-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q13838-2; Sequence=VSP_026347;
CC Note=No experimental confirmation available;
CC -!- DOMAIN: The helicase C-terminal domain mediates interaction with
CC ALYREF/THOC4.
CC -!- SIMILARITY: Belongs to the DEAD box helicase family. DECD
CC subfamily.
CC -!- SIMILARITY: Contains 1 helicase ATP-binding domain.
CC -!- SIMILARITY: Contains 1 helicase C-terminal domain.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAI17665.2; Type=Erroneous gene model prediction;
CC -----------------------------------------------------------------------
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DR EMBL; Z37166; CAA85523.1; -; mRNA.
DR EMBL; BT009909; AAP88911.1; -; mRNA.
DR EMBL; AK222912; BAD96632.1; -; mRNA.
DR EMBL; AB088115; BAC54953.1; -; Genomic_DNA.
DR EMBL; AB103621; BAF31287.1; -; Genomic_DNA.
DR EMBL; AB202112; BAE78637.1; -; Genomic_DNA.
DR EMBL; BA000025; BAB63306.1; -; Genomic_DNA.
DR EMBL; AL662847; CAI17664.2; -; Genomic_DNA.
DR EMBL; AL662847; CAI17665.2; ALT_SEQ; Genomic_DNA.
DR EMBL; AL662801; CAI18279.2; -; Genomic_DNA.
DR EMBL; AL662801; CAI18280.1; -; Genomic_DNA.
DR EMBL; AL662801; CAI18281.2; -; Genomic_DNA.
DR EMBL; AL662801; CAI18282.2; -; Genomic_DNA.
DR EMBL; AL662801; CAI18283.2; -; Genomic_DNA.
DR EMBL; BX001040; CAI18634.1; -; Genomic_DNA.
DR EMBL; BX248516; CAI41922.1; -; Genomic_DNA.
DR EMBL; BX927320; CAQ09974.1; -; Genomic_DNA.
DR EMBL; CR753820; CAQ07176.1; -; Genomic_DNA.
DR EMBL; CR753864; CAQ10634.1; -; Genomic_DNA.
DR EMBL; CH471081; EAX03404.1; -; Genomic_DNA.
DR EMBL; BC000361; AAH00361.1; -; mRNA.
DR EMBL; BC013006; AAH13006.1; -; mRNA.
DR EMBL; AF029061; AAB94615.1; -; Genomic_DNA.
DR EMBL; AF029062; AAC63046.1; -; Genomic_DNA.
DR PIR; I37201; I37201.
DR RefSeq; NP_004631.1; NM_004640.6.
DR RefSeq; NP_542165.1; NM_080598.5.
DR UniGene; Hs.254042; -.
DR UniGene; Hs.730849; -.
DR PDB; 1T5I; X-ray; 1.90 A; A=259-428.
DR PDB; 1T6N; X-ray; 1.94 A; A/B=34-251.
DR PDB; 1XTI; X-ray; 1.95 A; A=44-428.
DR PDB; 1XTJ; X-ray; 2.70 A; A=44-423.
DR PDB; 1XTK; X-ray; 2.40 A; A=45-428.
DR PDBsum; 1T5I; -.
DR PDBsum; 1T6N; -.
DR PDBsum; 1XTI; -.
DR PDBsum; 1XTJ; -.
DR PDBsum; 1XTK; -.
DR ProteinModelPortal; Q13838; -.
DR SMR; Q13838; 46-426.
DR IntAct; Q13838; 33.
DR MINT; MINT-1032422; -.
DR TCDB; 3.A.18.1.1; the nuclear mrna exporter (mrna-e) family.
DR PhosphoSite; Q13838; -.
DR DMDM; 2500529; -.
DR PaxDb; Q13838; -.
DR PRIDE; Q13838; -.
DR DNASU; 7919; -.
DR Ensembl; ENST00000383508; ENSP00000373000; ENSG00000215425.
DR Ensembl; ENST00000396172; ENSP00000379475; ENSG00000198563.
DR Ensembl; ENST00000400295; ENSP00000383151; ENSG00000215425.
DR Ensembl; ENST00000400296; ENSP00000383152; ENSG00000215425.
DR Ensembl; ENST00000412106; ENSP00000393712; ENSG00000225073.
DR Ensembl; ENST00000412330; ENSP00000398775; ENSG00000225859.
DR Ensembl; ENST00000413678; ENSP00000391463; ENSG00000229496.
DR Ensembl; ENST00000414440; ENSP00000411853; ENSG00000229496.
DR Ensembl; ENST00000415689; ENSP00000390999; ENSG00000225073.
DR Ensembl; ENST00000416863; ENSP00000407419; ENSG00000229496.
DR Ensembl; ENST00000430784; ENSP00000399030; ENSG00000235439.
DR Ensembl; ENST00000431360; ENSP00000404695; ENSG00000235439.
DR Ensembl; ENST00000441425; ENSP00000388880; ENSG00000230624.
DR Ensembl; ENST00000445218; ENSP00000411136; ENSG00000225859.
DR Ensembl; ENST00000448296; ENSP00000405560; ENSG00000225859.
DR Ensembl; ENST00000453138; ENSP00000387994; ENSG00000230624.
DR Ensembl; ENST00000456476; ENSP00000400326; ENSG00000225073.
DR Ensembl; ENST00000456666; ENSP00000394160; ENSG00000230624.
DR Ensembl; ENST00000458640; ENSP00000416269; ENSG00000198563.
DR GeneID; 7919; -.
DR KEGG; hsa:7919; -.
DR UCSC; uc003ntt.3; human.
DR CTD; 7919; -.
DR GeneCards; GC06M031500; -.
DR GeneCards; GC06Mj31485; -.
DR GeneCards; GC06Mk31480; -.
DR GeneCards; GC06Ml31538; -.
DR GeneCards; GC06Mm31574; -.
DR GeneCards; GC06Mn31488; -.
DR GeneCards; GC06Mo31487; -.
DR HGNC; HGNC:13917; DDX39B.
DR HPA; CAB034012; -.
DR MIM; 142560; gene.
DR neXtProt; NX_Q13838; -.
DR PharmGKB; PA25262; -.
DR eggNOG; COG0513; -.
DR HOVERGEN; HBG107334; -.
DR InParanoid; Q13838; -.
DR KO; K12812; -.
DR PhylomeDB; Q13838; -.
DR ChiTaRS; DDX39B; human.
DR EvolutionaryTrace; Q13838; -.
DR GeneWiki; BAT1; -.
DR GenomeRNAi; 7919; -.
DR NextBio; 30405; -.
DR PRO; PR:Q13838; -.
DR ArrayExpress; Q13838; -.
DR Bgee; Q13838; -.
DR CleanEx; HS_BAT1; -.
DR Genevestigator; Q13838; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0016607; C:nuclear speck; IEA:UniProtKB-SubCell.
DR GO; GO:0005681; C:spliceosomal complex; IDA:BHF-UCL.
DR GO; GO:0000346; C:transcription export complex; IDA:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0043008; F:ATP-dependent protein binding; IDA:BHF-UCL.
DR GO; GO:0004004; F:ATP-dependent RNA helicase activity; IDA:UniProtKB.
DR GO; GO:0030621; F:U4 snRNA binding; IDA:BHF-UCL.
DR GO; GO:0017070; F:U6 snRNA binding; IDA:BHF-UCL.
DR GO; GO:2000002; P:negative regulation of DNA damage checkpoint; IMP:UniProtKB.
DR GO; GO:0032786; P:positive regulation of DNA-dependent transcription, elongation; IMP:UniProtKB.
DR GO; GO:0010501; P:RNA secondary structure unwinding; IDA:BHF-UCL.
DR GO; GO:0000245; P:spliceosomal complex assembly; IDA:BHF-UCL.
DR GO; GO:0046784; P:viral mRNA export from host cell nucleus; IDA:UniProtKB.
DR InterPro; IPR011545; DNA/RNA_helicase_DEAD/DEAH_N.
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 1: Evidence at protein level;
KW 3D-structure; Acetylation; Alternative splicing; ATP-binding;
KW Complete proteome; Cytoplasm; Helicase; Hydrolase; mRNA processing;
KW mRNA splicing; mRNA transport; Nucleotide-binding; Nucleus;
KW Phosphoprotein; Reference proteome; RNA-binding; Spliceosome;
KW Transport.
FT INIT_MET 1 1 Removed.
FT CHAIN 2 428 Spliceosome RNA helicase DDX39B.
FT /FTId=PRO_0000055071.
FT DOMAIN 76 249 Helicase ATP-binding.
FT DOMAIN 261 422 Helicase C-terminal.
FT NP_BIND 89 96 ATP.
FT MOTIF 45 73 Q motif.
FT MOTIF 196 199 DECD box.
FT MOD_RES 2 2 N-acetylalanine.
FT MOD_RES 36 36 N6-acetyllysine.
FT MOD_RES 38 38 Phosphoserine.
FT MOD_RES 172 172 Phosphothreonine.
FT VAR_SEQ 114 114 V -> VYLGRVLGRGFWLGLV (in isoform 2).
FT /FTId=VSP_026347.
FT MUTAGEN 94 96 GKT->AAA: Loss of ATPase and helicase
FT activity.
FT MUTAGEN 95 95 K->A: Loss of ATPase and helicase
FT activity.
FT MUTAGEN 197 197 E->A: Loss of ATPase and helicase
FT activity.
FT MUTAGEN 198 198 C->A: No effect on ATPase activity.
FT MUTAGEN 199 199 D->A: Increased ATPase activity and loss
FT of helicase activity.
FT MUTAGEN 228 230 SAT->AAA: Decreased ATPase activity and
FT loss of helicase activity.
FT CONFLICT 289 289 Q -> R (in Ref. 3; BAD96632).
FT HELIX 47 50
FT HELIX 54 62
FT HELIX 70 80
FT STRAND 85 88
FT HELIX 95 106
FT STRAND 116 119
FT HELIX 123 136
FT TURN 137 139
FT STRAND 145 149
FT HELIX 154 163
FT STRAND 167 171
FT HELIX 173 181
FT STRAND 183 185
FT STRAND 192 197
FT HELIX 198 202
FT HELIX 205 216
FT STRAND 220 229
FT TURN 233 235
FT HELIX 236 240
FT STRAND 247 250
FT STRAND 263 268
FT HELIX 271 273
FT HELIX 274 284
FT STRAND 288 293
FT HELIX 297 309
FT STRAND 314 317
FT STRAND 319 321
FT HELIX 323 334
FT STRAND 335 337
FT STRAND 339 345
FT HELIX 353 355
FT STRAND 357 363
FT HELIX 368 378
FT HELIX 380 382
FT STRAND 386 391
FT HELIX 394 407
FT STRAND 411 413
FT STRAND 417 419
FT HELIX 420 422
SQ SEQUENCE 428 AA; 48991 MW; 7A55167BF576FB6F CRC64;
MAENDVDNEL LDYEDDEVET AAGGDGAEAP 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
//
MIM
142560
*RECORD*
*FIELD* NO
142560
*FIELD* TI
*142560 DEAD BOX POLYPEPTIDE 39B; DDX39B
;;HLA-B-ASSOCIATED TRANSCRIPT 1; BAT1;;
U2AF65-ASSOCIATED PROTEIN, 56-KD; UAP56;;
read moreD6S81E
*FIELD* TX
DESCRIPTION
UAP56 (BAT1) is an essential splicing factor that is recruited to the
pre-mRNA dependent on U2AF65 (191318) and is required for the U2
snRNP-branchpoint interaction. UAP56 is a member of the DEAD box family
of RNA-dependent ATPases, which mediate ATP hydrolysis during several
steps of pre-mRNA splicing (Fleckner et al., 1997).
CLONING
By chromosome walking with overlapping cosmids, Spies et al. (1989)
isolated a 435-kb DNA segment that was centromeric to HLA-B (142830) in
the human major histocompatibility complex. The presence of additional
genes was suggested by a large cluster of CpG islands. With cosmid
probes, 5 distinct transcripts were detected in RNA samples from a
variety of cell lines, and the corresponding cDNA clones were isolated
and designated 'HLA-B-associated transcripts' (BAT1 through BAT5,
142620).
Peelman et al. (1995) sequenced both human and pig BAT1 and showed that
the genes are members of the DEAD-box family of ATP-dependent RNA
helicases, which are involved in a number of cellular functions
including initiation of translation, RNA splicing, and ribosome
assembly. Proteins of this family have 9 conserved amino acid motifs but
differ at their amino and carboxyl ends. From studies of other family
members, the first block is involved in ATP binding, the fifth block may
be an ATPase, the sixth block is needed for RNA helicase activity, and
the ninth block is involved with ATP hydrolysis-independent RNA
interactions during unwinding. The gene contains 10 exons spanning about
10 kb of genomic DNA and encodes a 428-amino acid protein. Peelman et
al. (1995) detected 3 different length mRNAs (4.1, 17, and 0.9 kb) in
all tissues analyzed, although at different relative levels. The protein
is highly conserved, with 98% identity to the p47 rat liver nuclear
protein and 99% identity to the pig BAT1 homolog. Peelman et al. (1995)
showed that a recombinant epitope-tagged BAT1 construct was expressed in
COS cells and showed localization of the protein to the nucleus.
Fleckner et al. (1997) cloned a human 56-kD U2AF65-associated protein
that they termed UAP56. Using a yeast 2-hybrid assay, Fleckner et al.
(1997) identified UAP56 as the splicing factor that interacts with
U2AF65 amino acids 138 to 183. UAP56 encodes a protein of 428 amino
acids containing the 7 consensus motifs characteristic of DEAD box RNA
helicases.
GENE FUNCTION
Spies et al. (1989) raised the question of whether variation at one of
the BAT genes, rather than at HLA-B itself, determines susceptibility to
ankylosing spondylitis (106300).
Allcock et al. (2001) used antisense DNA corresponding to exons 2
through 5 of the BAT1 gene and showed that after antigenic stimulation,
monocytic and T-cell lines produced higher levels of the acute phase
cytokines TNF, interleukin-1 (IL1; see 147760), and IL6 (147620) than
cells containing the transfecting vector alone. These results suggested
that BAT1 is a negative regulator of inflammation.
Fleckner et al. (1997) demonstrated that UAP56 is an essential splicing
factor that is required for U2 snRNP-branchpoint interaction. It is a
component of the spliceosome. Luo et al. (2001) demonstrated that UAP56
interacts directly and highly specifically with ALY (THOC4; 604171).
Moreover, UAP56 is present together with ALY in a spliced mRNA-protein
complex (mRNP). Excess UAP56 is a potent dominant-negative inhibitor of
mRNA export. Excess UAP56 also inhibits the recruitment of ALY to the
spliced mRNP. Furthermore, mutation in ALY that blocks its interaction
with UAP56 prevents recruitment of ALY to the spliced mRNP. Luo et al.
(2001) concluded that the splicing factor UAP56 functions in coupling
the splicing and export machineries by recruiting ALY to the spliced
mRNP.
Strasser et al. (2002) showed that UAP56 is part of the RNase-resistant
TREX (transcription/export) complex, which includes TEX1 (THOC3;
606929), HPR1 (THOC1; 606930), THO2 (THOC2; 300395), and ALY and is
conserved from yeast to humans. Functional studies in yeast led them to
conclude that the TREX complex is specifically recruited to the
transcribing gene and travels with the polymerase during transcriptional
elongation. Strasser et al. (2002) suggested that it physically links
proteins that function in mRNA export or transcription.
Using immunoprecipitation and mass spectrometric analysis of HeLa cell
nuclear extracts, Masuda et al. (2005) found that the human TREX complex
contained THO2, FSAP79 (THOC5; 612733), HPR1, UAP56, TEX1, FSAP35
(THOC6; 615403), ALY, and FSAP24 (THOC7; 611965). Immunodepletion and
gel-filtration analyses revealed that THO2, HPR1, FSAP79, FSAP35, and
FSAP24 were tightly associated in the THO complex, whereas UAP56, ALY,
and TEX1 were more loosely associated. Immunoprecipitation of any TREX
component efficiently immunoprecipitated spliced mRNA and cDNA
transcripts, but not unspliced pre-mRNAs. Immunodepletion of any
component had no effect on spliceosome assembly, splicing, or RNA
stability. The TREX complex assembled on every mRNA examined. Mutation
analysis showed that the C terminus of ALY was required for binding of
both UAP56 and the THO complex. The C terminus of UAP56 was sufficient
for ALY binding. The N terminus of UAP56 interacted weakly with the THO
complex and TEX1, suggesting that other regions of UAP56 are required
for maximal binding. Masuda et al. (2005) concluded that recruitment of
the human TREX complex is not directly coupled to transcription, as in
yeast.
GENE STRUCTURE
Peelman et al. (1995) demonstrated that the BAT1 gene contains 10 exons
spanning about 10 kb of genomic DNA.
MAPPING
By chromosome walking with overlapping cosmids, Spies et al. (1989)
isolated a 435-kb DNA segment that is centromeric to HLA-B in the human
major histocompatibility complex on chromosome 6p21. Within the cloned
region, the genes for the tumor necrosis factors (TNFA, 191160; TNFB,
153440) and HLA-B (142830) were 210 kb apart. The human homolog of the
mouse gene B144 (LST1; 109170) is located near TNFA. The presence of
additional genes was suggested by a large cluster of CpG islands. With
cosmid probes, 5 distinct transcripts were detected in RNA samples from
a variety of cell lines and the corresponding cDNA clones were isolated.
These 'HLA-B-associated transcripts' (BAT1-BAT5) mapped to different
locations within a 160-kb region that included the TNFA and TNFB genes.
In the pig, BAT1 was shown to be about 30 kb upstream of TNF (Nunes et
al., 1994). The location of BAT1 at the telomeric end of the class III
region is conserved in both humans and pig (Peelman et al., 1995).
*FIELD* RF
1. Allcock, R. J. N.; Williams, J. H.; Price, P.: The central MHC
gene, BAT1, may encode a protein that down-regulates cytokine production. Genes
Cells 6: 487-494, 2001.
2. Fleckner, J.; Zhang, M.; Valcarcel, J.; Green, M. R.: U2AF(65)
recruits a novel human DEAD box protein required for the U2 snRNP-branchpoint
interaction. Genes Dev. 11: 1864-1872, 1997.
3. Luo, M.-J.; Zhou, Z.; Magni, K.; Christoforides, C.; Rappsilber,
J.; Mann, M.; Reed, R.: Pre-mRNA splicing and mRNA export linked
by direct interactions between UAP56 and Aly. Nature 413: 644-647,
2001.
4. Masuda, S.; Das, R.; Cheng, H.; Hurt, E.; Dorman, N.; Reed, R.
: Recruitment of the human TREX complex to mRNA during splicing. Genes
Dev. 19: 1512-1517, 2005.
5. Nunes, M.; Peelman, L.; Vaiman, M.; Bourgeaux, N.; Chardon, P.
: Characterization of six new loci within the swine major histocompatibility
complex class III region. Mammalian Genome 5: 616-622, 1994.
6. Peelman, L. J.; Chardon, P.; Nunes, M.; Renard, C.; Geffrotin,
C.; Vaiman, M.; Van Zeveren, A.; Coppieters, W.; van de Weghe, A.;
Bouquet, Y.; Choy, W. W.; Strominger, J. L.; Spies, T.: The BAT1
gene in the MHC encodes an evolutionarily conserved putative nuclear
RNA helicase of the DEAD family. Genomics 26: 210-218, 1995.
7. Spies, T.; Blanck, G.; Bresnahan, M.; Sands, J.; Strominger, J.
L.: A new cluster of genes within the human major histocompatibility
complex. Science 243: 214-217, 1989.
8. Strasser, K.; Masuda, S.; Mason, P.; Pfannstiel, J.; Oppizzi, M.;
Rodriguez-Navarro, S.; Rondon, A. G.; Aguilera, A.; Struhl, K.; Reed,
R.; Hurt, E.: TREX is a conserved complex coupling transcription
with messenger RNA export. Nature 417: 304-308, 2002.
*FIELD* CN
Patricia A. Hartz - updated: 11/2/2011
Alan F. Scott - updated: 10/10/1995
*FIELD* CD
Victor A. McKusick: 2/2/1989
*FIELD* ED
mgross: 09/06/2013
mgross: 11/9/2011
terry: 11/2/2011
alopez: 8/15/2011
mgross: 10/24/2007
carol: 1/17/2006
mgross: 1/25/2002
carol: 7/18/2001
terry: 2/28/2000
carol: 2/22/1999
mark: 9/8/1997
alopez: 9/5/1997
mark: 10/10/1995
terry: 10/7/1994
carol: 4/14/1992
supermim: 3/16/1992
carol: 1/25/1991
supermim: 3/20/1990
*RECORD*
*FIELD* NO
142560
*FIELD* TI
*142560 DEAD BOX POLYPEPTIDE 39B; DDX39B
;;HLA-B-ASSOCIATED TRANSCRIPT 1; BAT1;;
U2AF65-ASSOCIATED PROTEIN, 56-KD; UAP56;;
read moreD6S81E
*FIELD* TX
DESCRIPTION
UAP56 (BAT1) is an essential splicing factor that is recruited to the
pre-mRNA dependent on U2AF65 (191318) and is required for the U2
snRNP-branchpoint interaction. UAP56 is a member of the DEAD box family
of RNA-dependent ATPases, which mediate ATP hydrolysis during several
steps of pre-mRNA splicing (Fleckner et al., 1997).
CLONING
By chromosome walking with overlapping cosmids, Spies et al. (1989)
isolated a 435-kb DNA segment that was centromeric to HLA-B (142830) in
the human major histocompatibility complex. The presence of additional
genes was suggested by a large cluster of CpG islands. With cosmid
probes, 5 distinct transcripts were detected in RNA samples from a
variety of cell lines, and the corresponding cDNA clones were isolated
and designated 'HLA-B-associated transcripts' (BAT1 through BAT5,
142620).
Peelman et al. (1995) sequenced both human and pig BAT1 and showed that
the genes are members of the DEAD-box family of ATP-dependent RNA
helicases, which are involved in a number of cellular functions
including initiation of translation, RNA splicing, and ribosome
assembly. Proteins of this family have 9 conserved amino acid motifs but
differ at their amino and carboxyl ends. From studies of other family
members, the first block is involved in ATP binding, the fifth block may
be an ATPase, the sixth block is needed for RNA helicase activity, and
the ninth block is involved with ATP hydrolysis-independent RNA
interactions during unwinding. The gene contains 10 exons spanning about
10 kb of genomic DNA and encodes a 428-amino acid protein. Peelman et
al. (1995) detected 3 different length mRNAs (4.1, 17, and 0.9 kb) in
all tissues analyzed, although at different relative levels. The protein
is highly conserved, with 98% identity to the p47 rat liver nuclear
protein and 99% identity to the pig BAT1 homolog. Peelman et al. (1995)
showed that a recombinant epitope-tagged BAT1 construct was expressed in
COS cells and showed localization of the protein to the nucleus.
Fleckner et al. (1997) cloned a human 56-kD U2AF65-associated protein
that they termed UAP56. Using a yeast 2-hybrid assay, Fleckner et al.
(1997) identified UAP56 as the splicing factor that interacts with
U2AF65 amino acids 138 to 183. UAP56 encodes a protein of 428 amino
acids containing the 7 consensus motifs characteristic of DEAD box RNA
helicases.
GENE FUNCTION
Spies et al. (1989) raised the question of whether variation at one of
the BAT genes, rather than at HLA-B itself, determines susceptibility to
ankylosing spondylitis (106300).
Allcock et al. (2001) used antisense DNA corresponding to exons 2
through 5 of the BAT1 gene and showed that after antigenic stimulation,
monocytic and T-cell lines produced higher levels of the acute phase
cytokines TNF, interleukin-1 (IL1; see 147760), and IL6 (147620) than
cells containing the transfecting vector alone. These results suggested
that BAT1 is a negative regulator of inflammation.
Fleckner et al. (1997) demonstrated that UAP56 is an essential splicing
factor that is required for U2 snRNP-branchpoint interaction. It is a
component of the spliceosome. Luo et al. (2001) demonstrated that UAP56
interacts directly and highly specifically with ALY (THOC4; 604171).
Moreover, UAP56 is present together with ALY in a spliced mRNA-protein
complex (mRNP). Excess UAP56 is a potent dominant-negative inhibitor of
mRNA export. Excess UAP56 also inhibits the recruitment of ALY to the
spliced mRNP. Furthermore, mutation in ALY that blocks its interaction
with UAP56 prevents recruitment of ALY to the spliced mRNP. Luo et al.
(2001) concluded that the splicing factor UAP56 functions in coupling
the splicing and export machineries by recruiting ALY to the spliced
mRNP.
Strasser et al. (2002) showed that UAP56 is part of the RNase-resistant
TREX (transcription/export) complex, which includes TEX1 (THOC3;
606929), HPR1 (THOC1; 606930), THO2 (THOC2; 300395), and ALY and is
conserved from yeast to humans. Functional studies in yeast led them to
conclude that the TREX complex is specifically recruited to the
transcribing gene and travels with the polymerase during transcriptional
elongation. Strasser et al. (2002) suggested that it physically links
proteins that function in mRNA export or transcription.
Using immunoprecipitation and mass spectrometric analysis of HeLa cell
nuclear extracts, Masuda et al. (2005) found that the human TREX complex
contained THO2, FSAP79 (THOC5; 612733), HPR1, UAP56, TEX1, FSAP35
(THOC6; 615403), ALY, and FSAP24 (THOC7; 611965). Immunodepletion and
gel-filtration analyses revealed that THO2, HPR1, FSAP79, FSAP35, and
FSAP24 were tightly associated in the THO complex, whereas UAP56, ALY,
and TEX1 were more loosely associated. Immunoprecipitation of any TREX
component efficiently immunoprecipitated spliced mRNA and cDNA
transcripts, but not unspliced pre-mRNAs. Immunodepletion of any
component had no effect on spliceosome assembly, splicing, or RNA
stability. The TREX complex assembled on every mRNA examined. Mutation
analysis showed that the C terminus of ALY was required for binding of
both UAP56 and the THO complex. The C terminus of UAP56 was sufficient
for ALY binding. The N terminus of UAP56 interacted weakly with the THO
complex and TEX1, suggesting that other regions of UAP56 are required
for maximal binding. Masuda et al. (2005) concluded that recruitment of
the human TREX complex is not directly coupled to transcription, as in
yeast.
GENE STRUCTURE
Peelman et al. (1995) demonstrated that the BAT1 gene contains 10 exons
spanning about 10 kb of genomic DNA.
MAPPING
By chromosome walking with overlapping cosmids, Spies et al. (1989)
isolated a 435-kb DNA segment that is centromeric to HLA-B in the human
major histocompatibility complex on chromosome 6p21. Within the cloned
region, the genes for the tumor necrosis factors (TNFA, 191160; TNFB,
153440) and HLA-B (142830) were 210 kb apart. The human homolog of the
mouse gene B144 (LST1; 109170) is located near TNFA. The presence of
additional genes was suggested by a large cluster of CpG islands. With
cosmid probes, 5 distinct transcripts were detected in RNA samples from
a variety of cell lines and the corresponding cDNA clones were isolated.
These 'HLA-B-associated transcripts' (BAT1-BAT5) mapped to different
locations within a 160-kb region that included the TNFA and TNFB genes.
In the pig, BAT1 was shown to be about 30 kb upstream of TNF (Nunes et
al., 1994). The location of BAT1 at the telomeric end of the class III
region is conserved in both humans and pig (Peelman et al., 1995).
*FIELD* RF
1. Allcock, R. J. N.; Williams, J. H.; Price, P.: The central MHC
gene, BAT1, may encode a protein that down-regulates cytokine production. Genes
Cells 6: 487-494, 2001.
2. Fleckner, J.; Zhang, M.; Valcarcel, J.; Green, M. R.: U2AF(65)
recruits a novel human DEAD box protein required for the U2 snRNP-branchpoint
interaction. Genes Dev. 11: 1864-1872, 1997.
3. Luo, M.-J.; Zhou, Z.; Magni, K.; Christoforides, C.; Rappsilber,
J.; Mann, M.; Reed, R.: Pre-mRNA splicing and mRNA export linked
by direct interactions between UAP56 and Aly. Nature 413: 644-647,
2001.
4. Masuda, S.; Das, R.; Cheng, H.; Hurt, E.; Dorman, N.; Reed, R.
: Recruitment of the human TREX complex to mRNA during splicing. Genes
Dev. 19: 1512-1517, 2005.
5. Nunes, M.; Peelman, L.; Vaiman, M.; Bourgeaux, N.; Chardon, P.
: Characterization of six new loci within the swine major histocompatibility
complex class III region. Mammalian Genome 5: 616-622, 1994.
6. Peelman, L. J.; Chardon, P.; Nunes, M.; Renard, C.; Geffrotin,
C.; Vaiman, M.; Van Zeveren, A.; Coppieters, W.; van de Weghe, A.;
Bouquet, Y.; Choy, W. W.; Strominger, J. L.; Spies, T.: The BAT1
gene in the MHC encodes an evolutionarily conserved putative nuclear
RNA helicase of the DEAD family. Genomics 26: 210-218, 1995.
7. Spies, T.; Blanck, G.; Bresnahan, M.; Sands, J.; Strominger, J.
L.: A new cluster of genes within the human major histocompatibility
complex. Science 243: 214-217, 1989.
8. Strasser, K.; Masuda, S.; Mason, P.; Pfannstiel, J.; Oppizzi, M.;
Rodriguez-Navarro, S.; Rondon, A. G.; Aguilera, A.; Struhl, K.; Reed,
R.; Hurt, E.: TREX is a conserved complex coupling transcription
with messenger RNA export. Nature 417: 304-308, 2002.
*FIELD* CN
Patricia A. Hartz - updated: 11/2/2011
Alan F. Scott - updated: 10/10/1995
*FIELD* CD
Victor A. McKusick: 2/2/1989
*FIELD* ED
mgross: 09/06/2013
mgross: 11/9/2011
terry: 11/2/2011
alopez: 8/15/2011
mgross: 10/24/2007
carol: 1/17/2006
mgross: 1/25/2002
carol: 7/18/2001
terry: 2/28/2000
carol: 2/22/1999
mark: 9/8/1997
alopez: 9/5/1997
mark: 10/10/1995
terry: 10/7/1994
carol: 4/14/1992
supermim: 3/16/1992
carol: 1/25/1991
supermim: 3/20/1990