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UniProtKB - Q13838 (DX39B_HUMAN)

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Protein

Spliceosome RNA helicase DDX39B

Gene

DDX39B

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein 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. The TREX complex is essential for the export of Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production. 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.
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 with [PubMed:23299939] reporting a stimulatory effect.

Catalytic activityi

ATP + H2O = ADP + phosphate.1 Publication

Kineticsi

  1. KM=3.3 µM for ATP1 Publication
  1. Vmax=0.126 µM/min/mg enzyme with ATP as substrate1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi89 – 96ATP8

GO - Molecular functioni

  • ATPase activity Source: Reactome
  • ATP binding Source: UniProtKB-KW
  • ATP-dependent protein binding Source: BHF-UCL
  • ATP-dependent RNA helicase activity Source: UniProtKB
  • identical protein binding Source: IntAct
  • protein-containing complex binding Source: Ensembl
  • RNA binding Source: UniProtKB
  • RNA-dependent ATPase activity Source: UniProtKB
  • U4 snRNA binding Source: BHF-UCL
  • U6 snRNA binding Source: BHF-UCL
View the complete GO annotation on QuickGO ...

GO - Biological processi

  • liver development Source: Ensembl
  • mRNA 3'-end processing Source: Reactome
  • mRNA export from nucleus Source: UniProtKB
  • mRNA splicing, via spliceosome Source: UniProtKB
  • negative regulation of DNA damage checkpoint Source: UniProtKB
  • positive regulation of cell growth involved in cardiac muscle cell development Source: Ensembl
  • positive regulation of DNA biosynthetic process Source: Ensembl
  • positive regulation of DNA-templated transcription, elongation Source: UniProtKB
  • positive regulation of translation Source: Ensembl
  • positive regulation of vascular smooth muscle cell proliferation Source: Ensembl
  • RNA export from nucleus Source: Reactome
  • RNA secondary structure unwinding Source: BHF-UCL
  • RNA splicing Source: BHF-UCL
  • spliceosomal complex assembly Source: BHF-UCL
  • viral mRNA export from host cell nucleus Source: UniProtKB
View the complete GO annotation on QuickGO ...

Keywordsi

Molecular functionHelicase, Hydrolase, RNA-binding
Biological processmRNA processing, mRNA splicing, mRNA transport, Transport
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

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

Protein family/group databases

TCDBi3.A.18.1.1 the nuclear mrna exporter (mrna-e) family

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
HLA-B-associated transcript 1 protein
Gene namesi
Name:DDX39B
Synonyms:BAT1, UAP56
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

EuPathDBiHostDB:ENSG00000198563.13
HGNCiHGNC:13917 DDX39B
MIMi142560 gene
neXtProtiNX_Q13838

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi94 – 96GKT → AAA: Loss of ATPase and helicase activity. 1 Publication3
Mutagenesisi95K → A: Loss of ATPase and helicase activity. 2 Publications1
Mutagenesisi197E → A: Loss of ATPase and helicase activity. 1 Publication1
Mutagenesisi198C → A: No effect on ATPase activity. 1 Publication1
Mutagenesisi199D → A: Increased ATPase activity and loss of helicase activity. 1 Publication1
Mutagenesisi228 – 230SAT → AAA: Decreased ATPase activity and loss of helicase activity. 1 Publication3

Organism-specific databases

DisGeNETi7919
OpenTargetsiENSG00000198563
PharmGKBiPA25262

Chemistry databases

DrugBankiDB02325 Isopropyl Alcohol

Polymorphism and mutation databases

BioMutaiDDX39B
DMDMi2500529

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00000550712 – 428Spliceosome RNA helicase DDX39BAdd BLAST427

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineCombined sources1
Modified residuei36N6-acetyllysine; alternateCombined sources1
Cross-linki36Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Modified residuei38PhosphoserineCombined sources1
Modified residuei41PhosphoserineCombined sources1
Modified residuei172PhosphothreonineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ13838
MaxQBiQ13838
PaxDbiQ13838
PeptideAtlasiQ13838
PRIDEiQ13838
ProteomicsDBi59701
59702 [Q13838-2]

PTM databases

iPTMnetiQ13838
PhosphoSitePlusiQ13838
SwissPalmiQ13838

Expressioni

Gene expression databases

BgeeiENSG00000198563
CleanExiHS_BAT1
ExpressionAtlasiQ13838 baseline and differential
GenevisibleiQ13838 HS

Organism-specific databases

HPAiCAB034012
HPA055334
HPA058450

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 human cytomegalovirus/HHV-5 protein UL69. Interacts with LUZP4.16 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • ATP-dependent protein binding Source: BHF-UCL
  • identical protein binding Source: IntAct
View the complete GO annotation on QuickGO ...

Protein-protein interaction databases

BioGridi113649, 92 interactors
CORUMiQ13838
IntActiQ13838, 60 interactors
MINTiQ13838
STRINGi9606.ENSP00000379475

Structurei

Secondary structure

1428
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi47 – 50Combined sources4
Helixi54 – 62Combined sources9
Helixi70 – 80Combined sources11
Beta strandi85 – 88Combined sources4
Helixi95 – 106Combined sources12
Beta strandi116 – 119Combined sources4
Helixi123 – 136Combined sources14
Turni137 – 139Combined sources3
Beta strandi145 – 149Combined sources5
Helixi154 – 163Combined sources10
Beta strandi167 – 171Combined sources5
Helixi173 – 181Combined sources9
Beta strandi183 – 185Combined sources3
Beta strandi192 – 197Combined sources6
Helixi198 – 202Combined sources5
Helixi205 – 216Combined sources12
Beta strandi220 – 229Combined sources10
Turni233 – 235Combined sources3
Helixi236 – 240Combined sources5
Beta strandi247 – 250Combined sources4
Beta strandi263 – 268Combined sources6
Helixi271 – 273Combined sources3
Helixi274 – 284Combined sources11
Beta strandi288 – 293Combined sources6
Helixi297 – 309Combined sources13
Beta strandi314 – 317Combined sources4
Beta strandi319 – 321Combined sources3
Helixi323 – 334Combined sources12
Beta strandi335 – 337Combined sources3
Beta strandi339 – 345Combined sources7
Helixi353 – 355Combined sources3
Beta strandi357 – 363Combined sources7
Helixi368 – 378Combined sources11
Helixi380 – 382Combined sources3
Beta strandi386 – 391Combined sources6
Helixi394 – 407Combined sources14
Beta strandi411 – 413Combined sources3
Beta strandi417 – 419Combined sources3
Helixi420 – 422Combined sources3

3D structure databases

ProteinModelPortaliQ13838
SMRiQ13838
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ13838

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini76 – 249Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST174
Domaini261 – 422Helicase C-terminalPROSITE-ProRule annotationAdd BLAST162

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi45 – 73Q motifAdd BLAST29
Motifi196 – 199DECD box4

Domaini

The helicase C-terminal domain mediates interaction with ALYREF/THOC4.1 Publication

Sequence similaritiesi

Belongs to the DEAD box helicase family. DECD subfamily.Curated

Phylogenomic databases

eggNOGiKOG0329 Eukaryota
COG0513 LUCA
GeneTreeiENSGT00830000128348
HOVERGENiHBG107334
InParanoidiQ13838
KOiK12812
OMAiCRKFMQN
OrthoDBiEOG091G0H5W
PhylomeDBiQ13838
TreeFamiTF300442

Family and domain databases

CDDicd00079 HELICc, 1 hit
InterProiView protein in InterPro
IPR011545 DEAD/DEAH_box_helicase_dom
IPR014001 Helicase_ATP-bd
IPR001650 Helicase_C
IPR027417 P-loop_NTPase
IPR014014 RNA_helicase_DEAD_Q_motif
PfamiView protein in Pfam
PF00270 DEAD, 1 hit
PF00271 Helicase_C, 1 hit
SMARTiView protein in SMART
SM00487 DEXDc, 1 hit
SM00490 HELICc, 1 hit
SUPFAMiSSF52540 SSF52540, 1 hit
PROSITEiView protein in PROSITE
PS51192 HELICASE_ATP_BIND_1, 1 hit
PS51194 HELICASE_CTER, 1 hit
PS51195 Q_MOTIF, 1 hit

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q13838-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAENDVDNEL LDYEDDEVET AAGGDGAEAP 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):48,991
Last modified:November 1, 1996 - v1
Checksum:i7A55167BF576FB6F
GO
Isoform 2 (identifier: Q13838-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     114-114: V → VYLGRVLGRGFWLGLV

Note: No experimental confirmation available.
Show »
Length:443
Mass (Da):50,679
Checksum:i5B25C9C18CA433A4
GO

Sequence cautioni

The sequence CAI17665 differs from that shown. Reason: Erroneous gene model prediction.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti289Q → R in BAD96632 (Ref. 3) Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_026347114V → VYLGRVLGRGFWLGLV in isoform 2. Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z37166 mRNA Translation: CAA85523.1
BT009909 mRNA Translation: AAP88911.1
AK222912 mRNA Translation: BAD96632.1
AB088115 Genomic DNA Translation: BAC54953.1
AB103621 Genomic DNA Translation: BAF31287.1
AB202112 Genomic DNA Translation: BAE78637.1
BA000025 Genomic DNA Translation: BAB63306.1
AL662847 Genomic DNA Translation: CAI17664.2
AL662847 Genomic DNA Translation: CAI17665.2 Sequence problems.
AL662801 Genomic DNA Translation: CAI18279.2
AL662801 Genomic DNA Translation: CAI18280.1
AL662801 Genomic DNA Translation: CAI18281.2
AL662801 Genomic DNA Translation: CAI18282.2
AL662801 Genomic DNA Translation: CAI18283.2
BX001040 Genomic DNA Translation: CAI18634.1
BX248516 Genomic DNA Translation: CAI41922.1
BX927320 Genomic DNA Translation: CAQ09974.1
CR753820 Genomic DNA Translation: CAQ07176.1
CR753864 Genomic DNA Translation: CAQ10634.1
CH471081 Genomic DNA Translation: EAX03404.1
BC000361 mRNA Translation: AAH00361.1
BC013006 mRNA Translation: AAH13006.1
AF029061 Genomic DNA Translation: AAB94615.1
AF029062 Genomic DNA Translation: AAC63046.1
CCDSiCCDS4697.1 [Q13838-1]
PIRiI37201
RefSeqiNP_004631.1, NM_004640.6 [Q13838-1]
NP_542165.1, NM_080598.5 [Q13838-1]
UniGeneiHs.254042
Hs.730849

Genome annotation databases

EnsembliENST00000383508; ENSP00000373000; ENSG00000215425 [Q13838-1]
ENST00000396172; ENSP00000379475; ENSG00000198563 [Q13838-1]
ENST00000400295; ENSP00000383151; ENSG00000215425 [Q13838-1]
ENST00000400296; ENSP00000383152; ENSG00000215425 [Q13838-1]
ENST00000412106; ENSP00000393712; ENSG00000225073 [Q13838-1]
ENST00000412330; ENSP00000398775; ENSG00000225859 [Q13838-1]
ENST00000413678; ENSP00000391463; ENSG00000229496 [Q13838-1]
ENST00000414440; ENSP00000411853; ENSG00000229496 [Q13838-1]
ENST00000415689; ENSP00000390999; ENSG00000225073 [Q13838-1]
ENST00000416863; ENSP00000407419; ENSG00000229496 [Q13838-1]
ENST00000430784; ENSP00000399030; ENSG00000235439 [Q13838-1]
ENST00000431360; ENSP00000404695; ENSG00000235439 [Q13838-1]
ENST00000441425; ENSP00000388880; ENSG00000230624 [Q13838-1]
ENST00000445218; ENSP00000411136; ENSG00000225859 [Q13838-1]
ENST00000448296; ENSP00000405560; ENSG00000225859 [Q13838-1]
ENST00000453138; ENSP00000387994; ENSG00000230624 [Q13838-1]
ENST00000456476; ENSP00000400326; ENSG00000225073 [Q13838-1]
ENST00000456666; ENSP00000394160; ENSG00000230624 [Q13838-1]
ENST00000458640; ENSP00000416269; ENSG00000198563 [Q13838-1]
GeneIDi7919
KEGGihsa:7919
UCSCiuc003ntt.4 human [Q13838-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiDX39B_HUMAN
AccessioniPrimary (citable) accession number: Q13838
Secondary accession number(s): B0S8C0
, O43496, Q0EFA1, Q2L6F9, Q53GL9, Q5RJ64, Q5RJ66, Q5ST94, Q5STB4, Q5STB5, Q5STB7, Q5STB8, Q5STU4, Q5STU5, Q5STU6, Q5STU8, Q71V76
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: July 18, 2018
This is version 191 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

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