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Q9Z1N5 (DX39B_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 111. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:Ddx39b
Synonyms:Bat1, Bat1a, Uap56
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length428 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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.

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.

Catalytic activity

ATP + H2O = ADP + phosphate.

Subunit structure

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.

Subcellular location

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

Domain

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

Sequence similarities

Belongs to the DEAD box helicase family. DECD subfamily.

Contains 1 helicase ATP-binding domain.

Contains 1 helicase C-terminal domain.

Ontologies

Keywords
   Biological processmRNA processing
mRNA splicing
mRNA transport
Transport
   Cellular componentCytoplasm
Nucleus
Spliceosome
   LigandATP-binding
Nucleotide-binding
RNA-binding
   Molecular functionHelicase
Hydrolase
   PTMAcetylation
Phosphoprotein
   Technical termComplete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processRNA secondary structure unwinding

Inferred from electronic annotation. Source: Ensembl

negative regulation of DNA damage checkpoint

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of DNA-templated transcription, elongation

Inferred from sequence or structural similarity. Source: UniProtKB

spliceosomal complex assembly

Inferred from electronic annotation. Source: Ensembl

viral mRNA export from host cell nucleus

Inferred from electronic annotation. Source: Ensembl

   Cellular_componentU4 snRNP

Inferred from electronic annotation. Source: Ensembl

U6 snRNP

Inferred from electronic annotation. Source: Ensembl

cytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

nuclear speck

Inferred from electronic annotation. Source: UniProtKB-SubCell

spliceosomal complex

Inferred from electronic annotation. Source: UniProtKB-KW

transcription export complex

Inferred from electronic annotation. Source: Ensembl

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

ATP-dependent RNA helicase activity

Inferred from electronic annotation. Source: Ensembl

U4 snRNA binding

Inferred from electronic annotation. Source: Ensembl

U6 snRNA binding

Inferred from electronic annotation. Source: Ensembl

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed By similarity
Chain2 – 428427Spliceosome RNA helicase Ddx39b
PRO_0000055073

Regions

Domain76 – 249174Helicase ATP-binding
Domain261 – 422162Helicase C-terminal
Nucleotide binding89 – 968ATP By similarity
Motif45 – 7329Q motif
Motif196 – 1994DECD box

Amino acid modifications

Modified residue21N-acetylalanine By similarity
Modified residue361N6-acetyllysine By similarity
Modified residue381Phosphoserine By similarity
Modified residue1721Phosphothreonine By similarity

Sequences

Sequence LengthMass (Da)Tools
Q9Z1N5 [UniParc].

Last modified May 1, 1999. Version 1.
Checksum: D5AA6B3905FDC968

FASTA42849,035
        10         20         30         40         50         60 
MAENDVDNEL LDYEDDEVET AAGADGTEAP AKKDVKGSYV SIHSSGFRDF LLKPELLRAI 

        70         80         90        100        110        120 
VDCGFEHPSE VQHECIPQAI LGMDVLCQAK SGMGKTAVFV LATLQQLEPV TGQVSVLVMC 

       130        140        150        160        170        180 
HTRELAFQIS KEYERFSKYM PNVKVAVFFG GLSIKKDEEV LKKNCPHIVV GTPGRILALA 

       190        200        210        220        230        240 
RNKSLNLKHI KHFILDECDK MLEQLDMRRD VQEIFRMTPH EKQVMMFSAT LSKEIRPVCR 

       250        260        270        280        290        300 
KFMQDPMEIF VDDETKLTLH GLQQYYVKLK DNEKNRKLFD LLDVLEFNQV VIFVKSVQRC 

       310        320        330        340        350        360 
IALAQLLVEQ NFPAIAIHRG MPQEERLSRY QQFKDFQRRI LVATNLFGRG MDIERVNIAF 

       370        380        390        400        410        420 
NYDMPEDSDT YLHRVARAGR FGTKGLAITF VSDENDAKIL NDVQDRFEVN ISELPDEIDI 


SSYIEQTR 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_001239386.1. NM_001252457.1.
NP_062667.1. NM_019693.3.
UniGeneMm.439827.

3D structure databases

ProteinModelPortalQ9Z1N5.
SMRQ9Z1N5. Positions 46-426.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid207488. 3 interactions.
IntActQ9Z1N5. 3 interactions.
MINTMINT-1867862.

PTM databases

PhosphoSiteQ9Z1N5.

Proteomic databases

PaxDbQ9Z1N5.
PRIDEQ9Z1N5.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000068056; ENSMUSP00000070682; ENSMUSG00000019432.
ENSMUST00000172549; ENSMUSP00000134178; ENSMUSG00000019432.
ENSMUST00000173731; ENSMUSP00000133428; ENSMUSG00000019432.
GeneID53817.
KEGGmmu:53817.
UCSCuc008cha.2. mouse.

Organism-specific databases

CTD7919.
MGIMGI:99240. Ddx39b.

Phylogenomic databases

eggNOGCOG0513.
GeneTreeENSGT00750000117579.
HOVERGENHBG107334.
InParanoidQ9Z1N5.
KOK12812.
OMAMDRVARY.
OrthoDBEOG7W154N.
PhylomeDBQ9Z1N5.
TreeFamTF300442.

Gene expression databases

ArrayExpressQ9Z1N5.
BgeeQ9Z1N5.
CleanExMM_BAT1A.
GenevestigatorQ9Z1N5.

Family and domain databases

Gene3D3.40.50.300. 2 hits.
InterProIPR011545. 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]
PfamPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]
SMARTSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMSSF52540. SSF52540. 1 hit.
PROSITEPS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio310679.
PROQ9Z1N5.
SOURCESearch...

Entry information

Entry nameDX39B_MOUSE
AccessionPrimary (citable) accession number: Q9Z1N5
Secondary accession number(s): Q8HW97
Entry history
Integrated into UniProtKB/Swiss-Prot: March 15, 2005
Last sequence update: May 1, 1999
Last modified: April 16, 2014
This is version 111 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot