InnateDB: Systems Biology of the Innate Immune Response

Mus musculus Protein: Ddx39b

Summary

InnateDB Protein

IDBP-628158.3

Last Modified

2014-10-13 [Report errors or provide feedback]

Gene Symbol

Ddx39b

Protein Name

DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B

Synonyms

0610030D10Rik; AI428441; Bat-1; Bat1; Bat1a; D17H6S81E; D17H6S81E-1; D6S81Eh;

Species

Mus musculus

Ensembl Protein

ENSMUSP00000134178

InnateDB Gene

IDBG-177489 (Ddx39b)

Protein Structure

UniProt Annotation

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). {ECO:0000250}.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). {ECO:0000250}.

Subcellular Localization

Nucleus {ECO:0000250}. Nucleus speckle {ECO:0000250}. Cytoplasm {ECO:0000250}. Note=Can translocate to the cytoplasm in the presence of MX1. {ECO:0000250}.

Disease Associations

Tissue Specificity

Comments

Interactions

Number of Interactions

This gene and/or its encoded proteins are associated with 12 experimentally validated interaction(s) in this database.
They are also associated with 54 interaction(s) predicted by orthology.

Experimentally validated
Total	12 [view]
Protein-Protein	12 [view]
Protein-DNA	0
Protein-RNA	0
DNA-DNA	0
RNA-RNA	0
DNA-RNA	0

Predicted by orthology
Total	54 [view]

Gene Ontology

Molecular Function

Accession	GO Term
GO:0003676	nucleic acid binding
GO:0003677	DNA binding
GO:0004004	ATP-dependent RNA helicase activity
GO:0004386	helicase activity
GO:0005515	protein binding
GO:0005524	ATP binding
GO:0008186	RNA-dependent ATPase activity
GO:0016787	hydrolase activity
GO:0017070	U6 snRNA binding
GO:0030621	U4 snRNA binding
GO:0043008	ATP-dependent protein binding
GO:0044822	poly(A) RNA binding

Biological Process

GO:0000245	spliceosomal complex assembly
GO:0000398	mRNA splicing, via spliceosome
GO:0006200	ATP catabolic process
GO:0006406	mRNA export from nucleus
GO:0008380	RNA splicing
GO:0010501	RNA secondary structure unwinding
GO:0032786	positive regulation of DNA-templated transcription, elongation
GO:0046784	intronless viral mRNA export from host nucleus
GO:2000002	negative regulation of DNA damage checkpoint

Cellular Component

GO:0000346	transcription export complex
GO:0005634	nucleus
GO:0005681	spliceosomal complex
GO:0005687	U4 snRNP
GO:0005688	U6 snRNP
GO:0005737	cytoplasm
GO:0016607	nuclear speck

Protein Structure and Domains

PDB ID

MGI:99240

InterPro

IPR001650 Helicase, C-terminal
IPR006935 Helicase/UvrB domain
IPR011545 DNA/RNA helicase, DEAD/DEAH box type, N-terminal
IPR014001 Helicase, superfamily 1/2, ATP-binding domain
IPR014014 RNA helicase, DEAD-box type, Q motif
IPR027417 P-loop containing nucleoside triphosphate hydrolase

PFAM

PF00271
PF04851
PF00270

PRINTS

PIRSF

SMART

SM00490
SM00487

TIGRFAMs

Post-translational Modifications

Modification

Cross-References

SwissProt

Q9Z1N5