ATP-dependent RNA helicase DDX3X - Homo sapiens (Human)

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Reviewed, UniProtKB/Swiss-Prot O00571 (DDX3X_HUMAN)

Last modified June 16, 2009. Version 108. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    ATP-dependent RNA helicase DDX3X
    EC=3.6.1.-
Alternative name(s):
    DEAD box protein 3, X-chromosomal
    Helicase-like protein 2
      Short name=HLP2
    DEAD box, X isoform

Gene names

Name:	DDX3X
Synonyms:	DBX, DDX3

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

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Protein attributes

Sequence length	662 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	ATP-dependent RNA helicase. Acts as a cofactor for XPO1-mediated nuclear export of incompletely spliced HIV-1 Rev RNAs. Also involved in HIV-1 replication. Interacts specifically with hepatitis C virus core protein resulting in a change in intracellular location. Ref.2 Ref.6
Subunit structure	Found in a complex with Rev and XPO1. Interacts with XPO1 and TDRD3. Interacts with HCV core protein. Ref.2 Ref.6 Ref.12
Subcellular location	Nucleus speckle. Cytoplasm. Note: Located predominantly in nuclear speckles and, at low levels, throughout the cytoplasm. Located to the outer side of nuclear pore complexes (NPC). Shuttles between the nucleus and the cytoplasm in a XPO1-dependent manner. Ref.2 Ref.6
Sequence similarities	Belongs to the DEAD box helicase family. DDX3/DED1 subfamily. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain.

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Ontologies

Keywords
Biological process	Host-virus interaction
Cellular component	Cytoplasm Nucleus
Coding sequence diversity	Polymorphism
Ligand	ATP-binding DNA-binding Nucleotide-binding RNA-binding
Molecular function	Helicase Hydrolase
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	interspecies interaction between organisms Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Ref.2 Inferred from direct assay. Source: UniProtKB nuclear speck Inferred from electronic annotation. Source: UniProtKB-SubCell plasma membrane Inferred from direct assay. Source: HPA
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent RNA helicase activity Ref.3 Traceable author statement. Source: ProtInc DNA binding Inferred from electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct	Notes
TOB1	P50616	1	EBI-353779,EBI-723281

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.5

Chain

2 – 662

661

ATP-dependent RNA helicase DDX3X

PRO_0000055009

Regions

Domain

211 – 403

193

Helicase ATP-binding

Domain

414 – 575

162

Helicase C-terminal

Nucleotide binding

200 – 207

ATP

Nucleotide binding

224 – 231

ATP

Region

260 – 517

258

Necessary for interaction with XPO1

Motif

180 – 208

Q motif

Motif

347 – 350

DEAD box

Compositional bias

582 – 662

Gly/Ser-rich

Amino acid modifications

Modified residue

N-acetylserine Ref.5

Modified residue

Phosphotyrosine Ref.7 Ref.8

Modified residue

Phosphoserine Ref.11

Modified residue

Phosphoserine Ref.11

Modified residue

Phosphoserine Ref.11

Modified residue

104

Phosphotyrosine Ref.7

Modified residue

125

Phosphoserine Ref.11

Modified residue

343

Phosphotyrosine Ref.9 Ref.10

Modified residue

590

Phosphoserine Ref.10

Modified residue

594

Phosphoserine Ref.10 Ref.13

Modified residue

612

Phosphoserine Ref.13

Natural variations

Natural variant

294

R → T in a breast cancer sample; somatic mutation. Ref.17

VAR_035839

Experimental info

Mutagenesis

230

K → E: Abolishes ATPase activity and RNA-unwinding activity. Ref.6

Mutagenesis

382

S → L: Abolishes ATPase activity and RNA-unwinding activity. Ref.6

Sequence conflict

K → R in AAC51830. Ref.3

Sequence conflict

K → R in AAC51829. Ref.3

Secondary structure

662

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

O00571-1 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 7074D2B8A6EBBF09
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FASTA

662

73,243

        10         20         30         40         50         60 
MSHVAVENAL GLDQQFAGLD LNSSDNQSGG STASKGRYIP PHLRNREATK GFYDKDSSGW 

        70         80         90        100        110        120 
SSSKDKDAYS SFGSRSDSRG KSSFFSDRGS GSRGRFDDRG RSDYDGIGSR GDRSGFGKFE 

       130        140        150        160        170        180 
RGGNSRWCDK SDEDDWSKPL PPSERLEQEL FSGGNTGINF EKYDDIPVEA TGNNCPPHIE 

       190        200        210        220        230        240 
SFSDVEMGEI IMGNIELTRY TRPTPVQKHA IPIIKEKRDL MACAQTGSGK TAAFLLPILS 

       250        260        270        280        290        300 
QIYSDGPGEA LRAMKENGRY GRRKQYPISL VLAPTRELAV QIYEEARKFS YRSRVRPCVV 

       310        320        330        340        350        360 
YGGADIGQQI RDLERGCHLL VATPGRLVDM MERGKIGLDF CKYLVLDEAD RMLDMGFEPQ 

       370        380        390        400        410        420 
IRRIVEQDTM PPKGVRHTMM FSATFPKEIQ MLARDFLDEY IFLAVGRVGS TSENITQKVV 

       430        440        450        460        470        480 
WVEESDKRSF LLDLLNATGK DSLTLVFVET KKGADSLEDF LYHEGYACTS IHGDRSQRDR 

       490        500        510        520        530        540 
EEALHQFRSG KSPILVATAV AARGLDISNV KHVINFDLPS DIEEYVHRIG RTGRVGNLGL 

       550        560        570        580        590        600 
ATSFFNERNI NITKDLLDLL VEAKQEVPSW LENMAYEHHY KGSSRGRSKS SRFSGGFGAR 

       610        620        630        640        650        660 
DYRQSSGASS SSFSSSRASS SRSGGGGHGS SRGFGGGGYG GFYNSDGYGG NYNSQGVDWW 


GN

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification of a human homolog of a putative RNA helicase gene (mDEAD3) expressed in mouse erythroid cells." Chung J., Lee S.-G., Song K. Korean J. Biochem. 27:193-197(1995) Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Tissue: Hippocampus and Liver.
[2]	"Hepatitis C virus core protein interacts with a human DEAD box protein DDX3." Owsianka A.M., Patel A.H. Virology 257:330-340(1999) [PubMed: 10329544] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH HCV CORE PROTEIN. Tissue: Liver.
[3]	"Functional coherence of the human Y chromosome." Lahn B.T., Page D.C. Science 278:675-680(1997) [PubMed: 9381176] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Skin.
[5]	"An N-acetylated natural ligand of human histocompatibility leukocyte antigen (HLA)-B39. Classical major histocompatibility complex class I proteins bind peptides with a blocked NH(2) terminus in vivo." Yaguee J., Alvarez I., Rognan D., Ramos M., Vazquez J., Lopez de Castro J.A. J. Exp. Med. 191:2083-2092(2000) [PubMed: 10859333] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-10, ACETYLATION AT SER-2.
[6]	"Requirement of DDX3 DEAD box RNA helicase for HIV-1 Rev-RRE export function." Yedavalli V.S., Neuveut C., Chi Y.-H., Kleiman L., Jeang K.-T. Cell 119:381-392(2004) [PubMed: 15507209] [Abstract] Cited for: FUNCTION IN HIV-1 RNA EXPORT/REPLICATION, IDENTIFICATION IN A COMPLEX WITH XPO1 AND REV, INTERACTION WITH XPO1, MUTAGENESIS OF LYS-230 AND SER-382, SUBCELLULAR LOCATION.
[7]	"Immunoaffinity profiling of tyrosine phosphorylation in cancer cells." Rush J., Moritz A., Lee K.A., Guo A., Goss V.L., Spek E.J., Zhang H., Zha X.-M., Polakiewicz R.D., Comb M.J. Nat. Biotechnol. 23:94-101(2005) [PubMed: 15592455] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-69 AND TYR-104, MASS SPECTROMETRY.
[8]	"Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry." Tao W.A., Wollscheid B., O'Brien R., Eng J.K., Li X.-J., Bodenmiller B., Watts J.D., Hood L., Aebersold R. Nat. Methods 2:591-598(2005) [PubMed: 16094384] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-69, MASS SPECTROMETRY. Tissue: T-cell.
[9]	"Global phosphoproteome analysis on human HepG2 hepatocytes using reversed-phase diagonal LC." Gevaert K., Staes A., Van Damme J., De Groot S., Hugelier K., Demol H., Martens L., Goethals M., Vandekerckhove J. Proteomics 5:3589-3599(2005) [PubMed: 16097034] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-343, MASS SPECTROMETRY. Tissue: Hepatocyte.
[10]	"Improved titanium dioxide enrichment of phosphopeptides from HeLa cells and high confident phosphopeptide identification by cross-validation of MS/MS and MS/MS/MS spectra." Yu L.-R., Zhu Z., Chan K.C., Issaq H.J., Dimitrov D.S., Veenstra T.D. J. Proteome Res. 6:4150-4162(2007) [PubMed: 17924679] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-343; SER-590 AND SER-594, MASS SPECTROMETRY. Tissue: Epithelium.
[11]	"Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry." Molina H., Horn D.M., Tang N., Mathivanan S., Pandey A. Proc. Natl. Acad. Sci. U.S.A. 104:2199-2204(2007) [PubMed: 17287340] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-74; SER-76; SER-78 AND SER-125, MASS SPECTROMETRY.
[12]	"TDRD3, a novel Tudor domain-containing protein, localizes to cytoplasmic stress granules." Goulet I., Boisvenue S., Mokas S., Mazroui R., Cote J. Hum. Mol. Genet. 17:3055-3074(2008) [PubMed: 18632687] [Abstract] Cited for: INTERACTION WITH TDRD3.
[13]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-594 AND SER-612, MASS SPECTROMETRY.
[14]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[15]	"Expression, purification, crystallization and preliminary X-ray diffraction analysis of the DDX3 RNA helicase domain." Rodamilans B., Montoya G. Acta Crystallogr. F 63:283-286(2007) [PubMed: 17401195] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.91 ANGSTROMS) OF 409-580.
[16]	"Crystal structure of conserved domains 1 and 2 of the human DEAD-box helicase DDX3X in complex with the mononucleotide AMP." Hoegbom M., Collins R., van den Berg S., Jenvert R.-M., Karlberg T., Kotenyova T., Flores A., Karlsson Hedestam G.B., Schiavone L.H. J. Mol. Biol. 372:150-159(2007) [PubMed: 17631897] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 168-582 IN COMPLEX WITH AMP.
[17]	"The consensus coding sequences of human breast and colorectal cancers." Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D., Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S., Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J., Dawson D., Willson J.K.V. Velculescu V.E. Science 314:268-274(2006) [PubMed: 16959974] [Abstract] Cited for: VARIANT [LARGE SCALE ANALYSIS] THR-294.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

U50553 mRNA. Translation: AAB95637.1.
AF061337 mRNA. Translation: AAC34298.1.
AF000983 mRNA. Translation: AAC51830.1.
AF000982 mRNA. Translation: AAC51829.1.
BC011819 mRNA. Translation: AAH11819.1.

IPI

IPI00215637.

RefSeq

NP_001347.3.

UniGene

Hs.380774

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2I4I	X-ray	2.20	A	168-581	[»]
2JGN	X-ray	1.91	A/B/C	409-579	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

O00571. 16 interactions.

PTM databases

PhosphoSite

O00571.

2-D gel databases

SWISS-2DPAGE

O00571.

REPRODUCTION-2DPAGE

IPI00215637.

Proteomic databases

PeptideAtlas

O00571.

PRIDE

O00571.

Genome annotation databases

Ensembl

ENSG00000215301. Homo sapiens. [Contig view]

GeneID

1654.

KEGG

hsa:1654.

Organism-specific databases

GeneCards

GC0XP041077.

H-InvDB

HIX0016737.

HGNC

HGNC:2745. DDX3X.

HPA

HPA001648.
HPA005631.

MIM

300160. gene.

PharmGKB

PA27216.

GenAtlas

Search...

Phylogenomic databases

HOVERGEN

O00571.

OMA

O00571. KYERGGN.

Gene expression databases

ArrayExpress

O00571.

Bgee

O00571.

CleanEx

HS_DDX3X.

GermOnline

ENSG00000124487. Homo sapiens.

Family and domain databases

InterPro

IPR014001. DEAD-like_N.
IPR001650. DNA/RNA_helicase_C.
IPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
IPR014021. Helicase_SF1/SF2_ATP-bd.
IPR000629. RNA-helicase_DEAD-box_CS.
IPR014014. RNA_helicase_DEAD_Q_motif.
[Graphical view]

Pfam

PF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
[Graphical view]

SMART

SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]

PROSITE

PS00039. DEAD_ATP_HELICASE. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

6810.

SOURCE

Search...

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Entry information

Entry name

DDX3X_HUMAN

Accession

Primary (citable) accession number: O00571
Secondary accession number(s): O15536

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 15, 1998
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 108 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

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Relevant documents

Human chromosome X

Human chromosome X: entries, gene names and cross-references to MIM

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Amino acid modifications

Natural variations

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

PTM databases

2-D gel databases

Proteomic databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other Resources

Entry information

Relevant documents