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Protein

ATP-dependent RNA helicase DDX39A

Gene

DDX39A

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Isoform 1: Involved in pre-mRNA splicing. Required for the export of mRNA out of the nucleus.2 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi88 – 95ATPPROSITE-ProRule annotation8

GO - Molecular functioni

GO - Biological processi

  • cellular response to DNA damage stimulus Source: GO_Central
  • mRNA 3'-end processing Source: Reactome
  • mRNA export from nucleus Source: UniProtKB
  • mRNA splicing, via spliceosome Source: UniProtKB
  • regulation of gene expression Source: GO_Central
  • RNA export from nucleus Source: Reactome
  • RNA secondary structure unwinding Source: GO_Central
  • termination of RNA polymerase II transcription Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Helicase, Hydrolase

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

ATP-binding, Nucleotide-binding, RNA-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.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent RNA helicase DDX39A (EC:3.6.4.13)
Alternative name(s):
DEAD box protein 39
Nuclear RNA helicase URH49
Gene namesi
Name:DDX39A
Synonyms:DDX39
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 19

Organism-specific databases

HGNCiHGNC:17821. DDX39A.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • membrane Source: UniProtKB
  • nucleoplasm Source: Reactome
  • nucleus Source: UniProtKB
  • spliceosomal complex Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi10212.
OpenTargetsiENSG00000123136.
PharmGKBiPA27226.

Polymorphism and mutation databases

BioMutaiDDX39A.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00000550672 – 427ATP-dependent RNA helicase DDX39AAdd BLAST426

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineCombined sources1
Modified residuei35N6-acetyllysine; alternateCombined sources1
Cross-linki35Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Modified residuei37PhosphoserineCombined sources1
Modified residuei171PhosphothreonineCombined sources1
Modified residuei426PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiO00148.
MaxQBiO00148.
PaxDbiO00148.
PeptideAtlasiO00148.
PRIDEiO00148.

PTM databases

iPTMnetiO00148.
PhosphoSitePlusiO00148.
SwissPalmiO00148.

Expressioni

Tissue specificityi

Detected in testis, and at lower levels in brain, kidney, lung, thymus, spleen and salivary gland.1 Publication

Inductioni

Up-regulated in proliferating cells. Present at low levels in quiescent cells.1 Publication

Gene expression databases

BgeeiENSG00000123136.
CleanExiHS_DDX39.
ExpressionAtlasiO00148. baseline and differential.
GenevisibleiO00148. HS.

Organism-specific databases

HPAiHPA055334.

Interactioni

Subunit structurei

Binds ALYREF/THOC4 and DDX39B/BAT1. Interacts with SARNP. Interacts with human cytomegalovirus/HHV-5 protein UL69. Interacts with MX1.5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself3EBI-348253,EBI-348253
H0YHG03EBI-348253,EBI-6190012
DDX39BQ138389EBI-348253,EBI-348622
SARNPP829794EBI-348253,EBI-347495
SATQ6ICU93EBI-348253,EBI-10178867
TERF1P542742EBI-348253,EBI-710997

Protein-protein interaction databases

BioGridi115507. 81 interactors.
IntActiO00148. 47 interactors.
MINTiMINT-1035991.
STRINGi9606.ENSP00000242776.

Structurei

3D structure databases

ProteinModelPortaliO00148.
SMRiO00148.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini75 – 248Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST174
Domaini260 – 421Helicase C-terminalPROSITE-ProRule annotationAdd BLAST162

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi44 – 72Q motifAdd BLAST29
Motifi195 – 198DECD box4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi15 – 18Poly-Glu4

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.
HOGENOMiHOG000268797.
HOVERGENiHBG107334.
InParanoidiO00148.
KOiK13182.
OMAiAMRESPT.
OrthoDBiEOG091G0H5W.
PhylomeDBiO00148.
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]

Sequences (3)i

Sequence statusi: Complete.

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

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: O00148-1) [UniParc]FASTAAdd to basket
Also known as: L

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
MAEQDVENDL LDYDEEEEPQ APQESTPAPP KKDIKGSYVS IHSSGFRDFL
60 70 80 90 100
LKPELLRAIV DCGFEHPSEV QHECIPQAIL GMDVLCQAKS GMGKTAVFVL
110 120 130 140 150
ATLQQIEPVN GQVTVLVMCH TRELAFQISK EYERFSKYMP SVKVSVFFGG
160 170 180 190 200
LSIKKDEEVL KKNCPHVVVG TPGRILALVR NRSFSLKNVK HFVLDECDKM
210 220 230 240 250
LEQLDMRRDV QEIFRLTPHE KQCMMFSATL SKDIRPVCRK FMQDPMEVFV
260 270 280 290 300
DDETKLTLHG LQQYYVKLKD SEKNRKLFDL LDVLEFNQVI IFVKSVQRCM
310 320 330 340 350
ALAQLLVEQN FPAIAIHRGM AQEERLSRYQ QFKDFQRRIL VATNLFGRGM
360 370 380 390 400
DIERVNIVFN YDMPEDSDTY LHRVARAGRF GTKGLAITFV SDENDAKILN
410 420
DVQDRFEVNV AELPEEIDIS TYIEQSR
Length:427
Mass (Da):49,130
Last modified:March 15, 2005 - v2
Checksum:i38D02D4234995574
GO
Isoform 2 (identifier: O00148-2) [UniParc]FASTAAdd to basket
Also known as: S

The sequence of this isoform differs from the canonical sequence as follows:
     289-322: VIIFVKSVQRCMALAQLLVEQNFPAIAIHRGMAQ → PVTLSAVQGFPAADPGGHQSVWPGDGHRASQHRL
     323-427: Missing.

Note: Probably devoid of RNA helicase activity.
Show »
Length:322
Mass (Da):36,577
Checksum:iD6E9E2A0B94B1995
GO
Isoform 3 (identifier: O00148-3) [UniParc]FASTAAdd to basket
Also known as: SS

The sequence of this isoform differs from the canonical sequence as follows:
     245-267: PMEVFVDDETKLTLHGLQQYYVK → VLWEVSHKGVAHWKVLGRRDAQR
     268-427: Missing.

Note: Probably devoid of RNA helicase activity.
Show »
Length:267
Mass (Da):30,488
Checksum:i59E8D24E3CEE81ED
GO

Sequence cautioni

The sequence BAB15509 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti38Y → H in BAB15509 (PubMed:14702039).Curated1
Sequence conflicti64F → L in AAB50231 (Ref. 1) Curated1
Sequence conflicti160L → M in AAB50231 (Ref. 1) Curated1
Sequence conflicti377A → G in AAB50231 (Ref. 1) Curated1
Sequence conflicti401D → H in AAB50231 (Ref. 1) Curated1
Sequence conflicti406F → C in AAB50231 (Ref. 1) Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_052166142V → I.Corresponds to variant rs36127505dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_057426245 – 267PMEVF…QYYVK → VLWEVSHKGVAHWKVLGRRD AQR in isoform 3. 1 PublicationAdd BLAST23
Alternative sequenceiVSP_057427268 – 427Missing in isoform 3. 1 PublicationAdd BLAST160
Alternative sequenceiVSP_046559289 – 322VIIFV…RGMAQ → PVTLSAVQGFPAADPGGHQS VWPGDGHRASQHRL in isoform 2. 1 PublicationAdd BLAST34
Alternative sequenceiVSP_046560323 – 427Missing in isoform 2. 1 PublicationAdd BLAST105

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U90426 mRNA. Translation: AAB50231.1.
AB254849 mRNA. Translation: BAG16272.1.
AK026614 mRNA. Translation: BAB15509.1. Different initiation.
AC008569 Genomic DNA. No translation available.
CH471106 Genomic DNA. Translation: EAW84417.1.
BC001009 mRNA. Translation: AAH01009.1.
BC032128 mRNA. Translation: AAH32128.1.
CCDSiCCDS12308.1. [O00148-1]
RefSeqiNP_005795.2. NM_005804.3. [O00148-1]
XP_011525922.1. XM_011527620.1. [O00148-1]
UniGeneiHs.311609.

Genome annotation databases

EnsembliENST00000242776; ENSP00000242776; ENSG00000123136. [O00148-1]
ENST00000324340; ENSP00000322749; ENSG00000123136. [O00148-2]
ENST00000454233; ENSP00000392929; ENSG00000123136. [O00148-3]
ENST00000588692; ENSP00000467862; ENSG00000123136. [O00148-3]
GeneIDi10212.
KEGGihsa:10212.
UCSCiuc002myo.4. human. [O00148-1]
uc010dzm.2. human.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U90426 mRNA. Translation: AAB50231.1.
AB254849 mRNA. Translation: BAG16272.1.
AK026614 mRNA. Translation: BAB15509.1. Different initiation.
AC008569 Genomic DNA. No translation available.
CH471106 Genomic DNA. Translation: EAW84417.1.
BC001009 mRNA. Translation: AAH01009.1.
BC032128 mRNA. Translation: AAH32128.1.
CCDSiCCDS12308.1. [O00148-1]
RefSeqiNP_005795.2. NM_005804.3. [O00148-1]
XP_011525922.1. XM_011527620.1. [O00148-1]
UniGeneiHs.311609.

3D structure databases

ProteinModelPortaliO00148.
SMRiO00148.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115507. 81 interactors.
IntActiO00148. 47 interactors.
MINTiMINT-1035991.
STRINGi9606.ENSP00000242776.

PTM databases

iPTMnetiO00148.
PhosphoSitePlusiO00148.
SwissPalmiO00148.

Polymorphism and mutation databases

BioMutaiDDX39A.

Proteomic databases

EPDiO00148.
MaxQBiO00148.
PaxDbiO00148.
PeptideAtlasiO00148.
PRIDEiO00148.

Protocols and materials databases

DNASUi10212.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000242776; ENSP00000242776; ENSG00000123136. [O00148-1]
ENST00000324340; ENSP00000322749; ENSG00000123136. [O00148-2]
ENST00000454233; ENSP00000392929; ENSG00000123136. [O00148-3]
ENST00000588692; ENSP00000467862; ENSG00000123136. [O00148-3]
GeneIDi10212.
KEGGihsa:10212.
UCSCiuc002myo.4. human. [O00148-1]
uc010dzm.2. human.

Organism-specific databases

CTDi10212.
DisGeNETi10212.
GeneCardsiDDX39A.
HGNCiHGNC:17821. DDX39A.
HPAiHPA055334.
neXtProtiNX_O00148.
OpenTargetsiENSG00000123136.
PharmGKBiPA27226.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0329. Eukaryota.
COG0513. LUCA.
GeneTreeiENSGT00830000128348.
HOGENOMiHOG000268797.
HOVERGENiHBG107334.
InParanoidiO00148.
KOiK13182.
OMAiAMRESPT.
OrthoDBiEOG091G0H5W.
PhylomeDBiO00148.
TreeFamiTF300442.

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.

Miscellaneous databases

ChiTaRSiDDX39A. human.
GeneWikiiDDX39.
GenomeRNAii10212.
PROiO00148.

Gene expression databases

BgeeiENSG00000123136.
CleanExiHS_DDX39.
ExpressionAtlasiO00148. baseline and differential.
GenevisibleiO00148. HS.

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...

Entry informationi

Entry nameiDX39A_HUMAN
AccessioniPrimary (citable) accession number: O00148
Secondary accession number(s): B1Q2N1
, Q8N5M0, Q9BVP6, Q9H5W0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 15, 2005
Last sequence update: March 15, 2005
Last modified: November 30, 2016
This is version 150 of the entry and version 2 of the sequence. [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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. 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.