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Protein

Spliceosome RNA helicase Ddx39b

Gene

Ddx39b

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

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

GO - Biological processi

  • liver development Source: RGD
  • negative regulation of DNA damage checkpoint Source: UniProtKB
  • positive regulation of cell growth involved in cardiac muscle cell development Source: RGD
  • positive regulation of DNA biosynthetic process Source: RGD
  • positive regulation of DNA-templated transcription, elongation Source: UniProtKB
  • positive regulation of translation Source: RGD
  • positive regulation of vascular smooth muscle cell proliferation Source: RGD
  • RNA secondary structure unwinding Source: Ensembl
  • spliceosomal complex assembly Source: Ensembl
  • viral mRNA export from host cell nucleus Source: Ensembl
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

mRNA processing, mRNA splicing, mRNA transport, Transport

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

ReactomeiR-RNO-109688. Cleavage of Growing Transcript in the Termination Region.
R-RNO-159236. Transport of Mature mRNA derived from an Intron-Containing Transcript.
R-RNO-72187. mRNA 3'-end processing.

Names & Taxonomyi

Protein namesi
Recommended name:
Spliceosome RNA helicase Ddx39b (EC:3.6.4.13)
Alternative name(s):
56 kDa U2AF65-associated protein
ATP-dependent RNA helicase p47
DEAD box protein Uap56
Gene namesi
Name:Ddx39b
Synonyms:Bat1, Bat1a, Uap56
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 20

Organism-specific databases

RGDi70923. Ddx39b.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • nuclear matrix Source: RGD
  • nuclear speck Source: UniProtKB-SubCell
  • protein complex Source: RGD
  • spliceosomal complex Source: UniProtKB-KW
  • transcription export complex Source: Ensembl
  • U4 snRNP Source: Ensembl
  • U6 snRNP Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 428427Spliceosome RNA helicase Ddx39bPRO_0000055077Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineBy similarity
Modified residuei36 – 361N6-acetyllysine; alternateBy similarity
Cross-linki36 – 36Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateBy similarity
Modified residuei38 – 381PhosphoserineBy similarity
Modified residuei172 – 1721PhosphothreonineBy similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ63413.
PRIDEiQ63413.

2D gel databases

World-2DPAGE0004:Q63413.

PTM databases

iPTMnetiQ63413.

Expressioni

Tissue specificityi

Highly expressed in liver.

Gene expression databases

ExpressionAtlasiQ63413. baseline and differential.
GenevisibleiQ63413. RN.

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. Interacts with LUZP4 (By similarity).By similarity

GO - Molecular functioni

  • protein complex binding Source: RGD

Protein-protein interaction databases

BioGridi250392. 1 interaction.
STRINGi10116.ENSRNOP00000001115.

Structurei

3D structure databases

ProteinModelPortaliQ63413.
SMRiQ63413. 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

eggNOGiKOG0329. Eukaryota.
COG0513. LUCA.
GeneTreeiENSGT00830000128348.
HOVERGENiHBG107334.
InParanoidiQ63413.
KOiK12812.
OMAiFMNNPLE.
OrthoDBiEOG7W154N.
PhylomeDBiQ63413.
TreeFamiTF300442.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
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.

Q63413-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAENDVDNEL LDYEDDEVET AAGADGTEAP AKKDVKGSYV SIHSSGFRDF
60 70 80 90 100
LLKPELLRAI VDCGFEHPSE VQHECIPQAI LGMDVLCQAK SGMGKTAVFV
110 120 130 140 150
LATLQQLEPV TGQVSVLVMC HTRELAFQIS KEYERFSKYM PNVKVAVFFG
160 170 180 190 200
GLSIKKDEEV LKKNCPHIVV GTPGRILALA RNKSLNLKHI KHFILDECDK
210 220 230 240 250
MLEQLDMRRD VQEIFRMTPH EKQVMMFSAT LSKEIRPVCR KFMQDPMEIF
260 270 280 290 300
VDDETKLTLH GLQQYYVKLK DNEKNRKLFD LLDVLEFNQV VIFVKSVQRC
310 320 330 340 350
IALAQLLVEQ NFPAIAIHRG MPQEERLSRY QQFKDFQRRI LVATNLFGRG
360 370 380 390 400
MDIERVNIAF NYDMPEDSDT YLHRVARAGR FGTKGLAITF VSDENDAKIL
410 420
NDVQDRFEVN ISELPDEIDI SSYIEQTR
Length:428
Mass (Da):49,035
Last modified:March 15, 2005 - v3
Checksum:iD5AA6B3905FDC968
GO

Sequence cautioni

The sequence AAA41787.1 differs from that shown. Reason: Frameshift at position 388. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti236 – 2361R → P in AAL98920 (PubMed:11904681).Curated
Sequence conflicti286 – 2861E → Q in AAL98920 (PubMed:11904681).Curated
Sequence conflicti312 – 3121F → L in AAA41787 (PubMed:1618789).Curated
Sequence conflicti354 – 3541E → V in AAA41787 (PubMed:1618789).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M75168 mRNA. Translation: AAA41787.1. Frameshift.
AF387339 Genomic DNA. Translation: AAL98920.1.
AJ314857 Genomic DNA. Translation: CAC85694.1.
BC080243 mRNA. Translation: AAH80243.1.
PIRiA42811.
RefSeqiNP_579834.2. NM_133300.3.
UniGeneiRn.202950.

Genome annotation databases

EnsembliENSRNOT00000001115; ENSRNOP00000001115; ENSRNOG00000000841.
GeneIDi114612.
KEGGirno:114612.
UCSCiRGD:70923. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M75168 mRNA. Translation: AAA41787.1. Frameshift.
AF387339 Genomic DNA. Translation: AAL98920.1.
AJ314857 Genomic DNA. Translation: CAC85694.1.
BC080243 mRNA. Translation: AAH80243.1.
PIRiA42811.
RefSeqiNP_579834.2. NM_133300.3.
UniGeneiRn.202950.

3D structure databases

ProteinModelPortaliQ63413.
SMRiQ63413. Positions 46-426.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi250392. 1 interaction.
STRINGi10116.ENSRNOP00000001115.

PTM databases

iPTMnetiQ63413.

2D gel databases

World-2DPAGE0004:Q63413.

Proteomic databases

PaxDbiQ63413.
PRIDEiQ63413.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000001115; ENSRNOP00000001115; ENSRNOG00000000841.
GeneIDi114612.
KEGGirno:114612.
UCSCiRGD:70923. rat.

Organism-specific databases

CTDi7919.
RGDi70923. Ddx39b.

Phylogenomic databases

eggNOGiKOG0329. Eukaryota.
COG0513. LUCA.
GeneTreeiENSGT00830000128348.
HOVERGENiHBG107334.
InParanoidiQ63413.
KOiK12812.
OMAiFMNNPLE.
OrthoDBiEOG7W154N.
PhylomeDBiQ63413.
TreeFamiTF300442.

Enzyme and pathway databases

ReactomeiR-RNO-109688. Cleavage of Growing Transcript in the Termination Region.
R-RNO-159236. Transport of Mature mRNA derived from an Intron-Containing Transcript.
R-RNO-72187. mRNA 3'-end processing.

Miscellaneous databases

PROiQ63413.

Gene expression databases

ExpressionAtlasiQ63413. baseline and differential.
GenevisibleiQ63413. RN.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR011545. DEAD/DEAH_box_helicase_dom.
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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular cloning and analysis of an eIF-4A-related rat liver nuclear protein."
    Nair S., Dey R., Sanford J.P., Doyle D.
    J. Biol. Chem. 267:12928-12935(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: Lewis.
  3. "Sequence analysis of the rat MHC class I region."
    Walter L.
    Submitted (JUN-2001) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: Brown Norway.
  4. "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].
    Tissue: Lung.

Entry informationi

Entry nameiDX39B_RAT
AccessioniPrimary (citable) accession number: Q63413
Secondary accession number(s): Q811A6, Q8R2G9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: March 15, 2005
Last modified: June 8, 2016
This is version 125 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.