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Q9Z1N5

- DX39B_MOUSE

UniProt

Q9Z1N5 - DX39B_MOUSE

Protein

Spliceosome RNA helicase Ddx39b

Gene

Ddx39b

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 115 (01 Oct 2014)
      Sequence version 1 (01 May 1999)
      Previous versions | rss
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    Functioni

    Involved in nuclear export of spliced and unspliced mRNA. Assembling component of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and specifically associates with spliced mRNA and not with unspliced pre-mRNA. TREX is recruited to spliced mRNAs by a transcription-independent mechanism, binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export to the cytoplasm via the TAP/NFX1 pathway. May undergo several rounds of ATP hydrolysis during assembly of TREX to drive subsequent loading of components such as ALYREF/THOC and CHTOP onto mRNA. Also associates with pre-mRNA independent of ALYREF/THOC4 and the THO complex. Involved in the nuclear export of intronless mRNA; the ATP-bound form is proposed to recruit export adapter ALYREF/THOC4 to intronless mRNA; its ATPase activity is cooperatively stimulated by RNA and ALYREF/THOC4 and ATP hydrolysis is thought to trigger the dissociation from RNA to allow the association of ALYREF/THOC4 and the NXF1-NXT1 heterodimer. Involved in transcription elongation and genome stability By similarity.By similarity
    Splice factor that is required for the first ATP-dependent step in spliceosome assembly and for the interaction of U2 snRNP with the branchpoint. Has both RNA-stimulated ATP binding/hydrolysis activity and ATP-dependent RNA unwinding activity. Even with the stimulation of RNA, the ATPase activity is weak. Can only hydrolyze ATP but not other NTPs. The RNA stimulation of ATPase activity does not have a strong preference for the sequence and length of the RNA. However, ssRNA stimulates the ATPase activity much more strongly than dsRNA. Can unwind 5' or 3' overhangs or blunt end RNA duplexes in vitro. The ATPase and helicase activities are not influenced by U2AF2; the effect of ALYREF/THOC4 is reported conflictingly By similarity.By similarity

    Catalytic activityi

    ATP + H2O = ADP + phosphate.

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi89 – 968ATPPROSITE-ProRule annotation

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. ATP-dependent RNA helicase activity Source: Ensembl
    3. U4 snRNA binding Source: Ensembl
    4. U6 snRNA binding Source: Ensembl

    GO - Biological processi

    1. negative regulation of DNA damage checkpoint Source: UniProtKB
    2. positive regulation of DNA-templated transcription, elongation Source: UniProtKB
    3. RNA secondary structure unwinding Source: Ensembl
    4. spliceosomal complex assembly Source: Ensembl
    5. viral mRNA export from host cell nucleus Source: Ensembl

    Keywords - Molecular functioni

    Helicase, Hydrolase

    Keywords - Biological processi

    mRNA processing, mRNA splicing, mRNA transport, Transport

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding, RNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Spliceosome RNA helicase Ddx39b (EC:3.6.4.13)
    Alternative name(s):
    56 kDa U2AF65-associated protein
    DEAD box protein UAP56
    HLA-B-associated transcript 1 protein
    Gene namesi
    Name:Ddx39b
    Synonyms:Bat1, Bat1a, Uap56
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 17

    Organism-specific databases

    MGIiMGI:99240. Ddx39b.

    Subcellular locationi

    Nucleus By similarity. Nucleus speckle By similarity. Cytoplasm By similarity
    Note: Can translocate to the cytoplasm in the presence of MX1.By similarity

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell
    2. nuclear speck Source: UniProtKB-SubCell
    3. spliceosomal complex Source: UniProtKB-KW
    4. transcription export complex Source: Ensembl
    5. U4 snRNP Source: Ensembl
    6. U6 snRNP Source: Ensembl

    Keywords - Cellular componenti

    Cytoplasm, Nucleus, Spliceosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11RemovedBy similarity
    Chaini2 – 428427Spliceosome RNA helicase Ddx39bPRO_0000055073Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylalanineBy similarity
    Modified residuei36 – 361N6-acetyllysineBy similarity
    Modified residuei38 – 381PhosphoserineBy similarity
    Modified residuei172 – 1721PhosphothreonineBy similarity

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    MaxQBiQ9Z1N5.
    PaxDbiQ9Z1N5.
    PRIDEiQ9Z1N5.

    PTM databases

    PhosphoSiteiQ9Z1N5.

    Expressioni

    Gene expression databases

    ArrayExpressiQ9Z1N5.
    BgeeiQ9Z1N5.
    CleanExiMM_BAT1A.
    GenevestigatoriQ9Z1N5.

    Interactioni

    Subunit structurei

    Homodimer, and heterodimer with DDX39A. Component of the transcription/export (TREX) complex at least composed of ALYREF/THOC4, DDX39B, SARNP/CIP29, CHTOP and the THO subcomplex; TREX seems to have dynamic structure involving ATP-dependent remodeling; in the complex bridges ALYREF/THOC4 and the THO complex, and, in a ATP-dependent manner, ALYREF/THOC4 and SARNP/CIP29. Component of the spliceosome. Interacts directly with U2AF2. Interacts with RBM8A, RNPS1 and SRRM1, FYTTD1/UIF, THOC1, MX1 and POLDIP3 By similarity.By similarity

    Protein-protein interaction databases

    BioGridi207488. 4 interactions.
    IntActiQ9Z1N5. 3 interactions.
    MINTiMINT-1867862.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9Z1N5.
    SMRiQ9Z1N5. Positions 46-426.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini76 – 249174Helicase ATP-bindingPROSITE-ProRule annotationAdd
    BLAST
    Domaini261 – 422162Helicase C-terminalPROSITE-ProRule annotationAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi45 – 7329Q motifAdd
    BLAST
    Motifi196 – 1994DECD box

    Domaini

    The helicase C-terminal domain mediates interaction with ALYREF/THOC4.By similarity

    Sequence similaritiesi

    Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
    Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0513.
    GeneTreeiENSGT00750000117579.
    HOVERGENiHBG107334.
    InParanoidiQ9Z1N5.
    KOiK12812.
    OMAiFMNNPLE.
    OrthoDBiEOG7W154N.
    PhylomeDBiQ9Z1N5.
    TreeFamiTF300442.

    Family and domain databases

    Gene3Di3.40.50.300. 2 hits.
    InterProiIPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
    IPR014001. Helicase_ATP-bd.
    IPR001650. Helicase_C.
    IPR027417. P-loop_NTPase.
    IPR014014. RNA_helicase_DEAD_Q_motif.
    [Graphical view]
    PfamiPF00270. DEAD. 1 hit.
    PF00271. Helicase_C. 1 hit.
    [Graphical view]
    SMARTiSM00487. DEXDc. 1 hit.
    SM00490. HELICc. 1 hit.
    [Graphical view]
    SUPFAMiSSF52540. SSF52540. 1 hit.
    PROSITEiPS51192. HELICASE_ATP_BIND_1. 1 hit.
    PS51194. HELICASE_CTER. 1 hit.
    PS51195. Q_MOTIF. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q9Z1N5-1 [UniParc]FASTAAdd to Basket

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    MAENDVDNEL LDYEDDEVET AAGADGTEAP AKKDVKGSYV SIHSSGFRDF    50
    LLKPELLRAI VDCGFEHPSE VQHECIPQAI LGMDVLCQAK SGMGKTAVFV 100
    LATLQQLEPV TGQVSVLVMC HTRELAFQIS KEYERFSKYM PNVKVAVFFG 150
    GLSIKKDEEV LKKNCPHIVV GTPGRILALA RNKSLNLKHI KHFILDECDK 200
    MLEQLDMRRD VQEIFRMTPH EKQVMMFSAT LSKEIRPVCR KFMQDPMEIF 250
    VDDETKLTLH GLQQYYVKLK DNEKNRKLFD LLDVLEFNQV VIFVKSVQRC 300
    IALAQLLVEQ NFPAIAIHRG MPQEERLSRY QQFKDFQRRI LVATNLFGRG 350
    MDIERVNIAF NYDMPEDSDT YLHRVARAGR FGTKGLAITF VSDENDAKIL 400
    NDVQDRFEVN ISELPDEIDI SSYIEQTR 428
    Length:428
    Mass (Da):49,035
    Last modified:May 1, 1999 - v1
    Checksum:iD5AA6B3905FDC968
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF118128 mRNA. Translation: AAD13115.1.
    AY255786 mRNA. Translation: AAP91685.1.
    AY255787 mRNA. Translation: AAP91686.1.
    AC007080 Genomic DNA. Translation: AAD30177.1.
    AK088867 mRNA. Translation: BAC40624.1.
    AK051034 mRNA. Translation: BAC34505.1.
    BC011067 mRNA. Translation: AAH11067.1.
    BC024859 mRNA. Translation: AAH24859.1.
    CCDSiCCDS28695.1.
    RefSeqiNP_001239386.1. NM_001252457.1.
    NP_062667.1. NM_019693.3.
    UniGeneiMm.439827.

    Genome annotation databases

    EnsembliENSMUST00000068056; ENSMUSP00000070682; ENSMUSG00000019432.
    ENSMUST00000172549; ENSMUSP00000134178; ENSMUSG00000019432.
    ENSMUST00000173731; ENSMUSP00000133428; ENSMUSG00000019432.
    GeneIDi53817.
    KEGGimmu:53817.
    UCSCiuc008cha.2. mouse.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF118128 mRNA. Translation: AAD13115.1 .
    AY255786 mRNA. Translation: AAP91685.1 .
    AY255787 mRNA. Translation: AAP91686.1 .
    AC007080 Genomic DNA. Translation: AAD30177.1 .
    AK088867 mRNA. Translation: BAC40624.1 .
    AK051034 mRNA. Translation: BAC34505.1 .
    BC011067 mRNA. Translation: AAH11067.1 .
    BC024859 mRNA. Translation: AAH24859.1 .
    CCDSi CCDS28695.1.
    RefSeqi NP_001239386.1. NM_001252457.1.
    NP_062667.1. NM_019693.3.
    UniGenei Mm.439827.

    3D structure databases

    ProteinModelPortali Q9Z1N5.
    SMRi Q9Z1N5. Positions 46-426.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 207488. 4 interactions.
    IntActi Q9Z1N5. 3 interactions.
    MINTi MINT-1867862.

    PTM databases

    PhosphoSitei Q9Z1N5.

    Proteomic databases

    MaxQBi Q9Z1N5.
    PaxDbi Q9Z1N5.
    PRIDEi Q9Z1N5.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000068056 ; ENSMUSP00000070682 ; ENSMUSG00000019432 .
    ENSMUST00000172549 ; ENSMUSP00000134178 ; ENSMUSG00000019432 .
    ENSMUST00000173731 ; ENSMUSP00000133428 ; ENSMUSG00000019432 .
    GeneIDi 53817.
    KEGGi mmu:53817.
    UCSCi uc008cha.2. mouse.

    Organism-specific databases

    CTDi 7919.
    MGIi MGI:99240. Ddx39b.

    Phylogenomic databases

    eggNOGi COG0513.
    GeneTreei ENSGT00750000117579.
    HOVERGENi HBG107334.
    InParanoidi Q9Z1N5.
    KOi K12812.
    OMAi FMNNPLE.
    OrthoDBi EOG7W154N.
    PhylomeDBi Q9Z1N5.
    TreeFami TF300442.

    Miscellaneous databases

    NextBioi 310679.
    PROi Q9Z1N5.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q9Z1N5.
    Bgeei Q9Z1N5.
    CleanExi MM_BAT1A.
    Genevestigatori Q9Z1N5.

    Family and domain databases

    Gene3Di 3.40.50.300. 2 hits.
    InterProi IPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
    IPR014001. Helicase_ATP-bd.
    IPR001650. Helicase_C.
    IPR027417. P-loop_NTPase.
    IPR014014. RNA_helicase_DEAD_Q_motif.
    [Graphical view ]
    Pfami PF00270. DEAD. 1 hit.
    PF00271. Helicase_C. 1 hit.
    [Graphical view ]
    SMARTi SM00487. DEXDc. 1 hit.
    SM00490. HELICc. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52540. SSF52540. 1 hit.
    PROSITEi PS51192. HELICASE_ATP_BIND_1. 1 hit.
    PS51194. HELICASE_CTER. 1 hit.
    PS51195. Q_MOTIF. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Sequence analysis of a mouse homolog of the human BAT1 gene (nuclear RNA helicase of the DEAD box protein family)."
      Handel-Fernandez M.E., Vincek V.
      Submitted (JAN-1999) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Strain: C57BL/10.
    2. "Characterization of murine Bat1, a putative immunoregulator of Tnfa."
      Dolecki K.J., Wong A.M.L., Price P.
      Submitted (MAR-2003) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Strain: BALB/c and C57BL/10 X DBA/2.
    3. "Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse."
      Xie T., Rowen L., Aguado B., Ahearn M.E., Madan A., Qin S., Campbell R.D., Hood L.
      Genome Res. 13:2621-2636(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 129.
    4. "The transcriptional landscape of the mammalian genome."
      Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
      , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
      Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: C57BL/6J and NOD.
      Tissue: Embryo and Thymus.
    5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: FVB/N.
      Tissue: Eye and Mammary tumor.
    6. Lubec G., Kang S.U.
      Submitted (APR-2007) to UniProtKB
      Cited for: PROTEIN SEQUENCE OF 145-155, IDENTIFICATION BY MASS SPECTROMETRY.
      Strain: C57BL/6.
      Tissue: Brain.

    Entry informationi

    Entry nameiDX39B_MOUSE
    AccessioniPrimary (citable) accession number: Q9Z1N5
    Secondary accession number(s): Q8HW97
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 15, 2005
    Last sequence update: May 1, 1999
    Last modified: October 1, 2014
    This is version 115 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3