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Protein

ATP-dependent RNA helicase DDX1

Gene

DDX1

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

Functioni

Acts as an ATP-dependent RNA helicase, able to unwind both RNA-RNA and RNA-DNA duplexes. Possesses 5' single-stranded RNA overhang nuclease activity. Possesses ATPase activity on various RNA, but not DNA polynucleotides. May play a role in RNA clearance at DNA double-strand breaks (DSBs), thereby facilitating the template-guided repair of transcriptionally active regions of the genome. Together with RELA, acts as a coactivator to enhance NF-kappa-B-mediated transcriptional activation. Acts as a positive transcriptional regulator of cyclin CCND2 expression. Binds to the cyclin CCND2 promoter region. Associates with chromatin at the NF-kappa-B promoter region via association with RELA. Binds to poly(A) RNA. May be involved in 3'-end cleavage and polyadenylation of pre-mRNAs. Component of the tRNA-splicing ligase complex required to facilitate the enzymatic turnover of catalytic subunit RTCB: together with archease (ZBTB8OS), acts by facilitating the guanylylation of RTCB, a key intermediate step in tRNA ligation (PubMed:24870230).6 Publications
(Microbial infection) Required for HIV-1 Rev function as well as for HIV-1 and coronavirus IBV replication. Binds to the RRE sequence of HIV-1 mRNAs.1 Publication
(Microbial infection) Required for Coronavirus IBV replication.1 Publication

Caution

According to some authors the unwinding activity is ADP-dependent and not ATP-dependent.1 Publication

Catalytic activityi

ATP + H2O = ADP + phosphate.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi46 – 53ATPCurated8

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ATP-dependent helicase activity Source: UniProtKB
  • ATP-dependent RNA helicase activity Source: GO_Central
  • chromatin binding Source: UniProtKB
  • DNA/RNA helicase activity Source: UniProtKB
  • DNA binding Source: UniProtKB-KW
  • double-stranded RNA binding Source: Ensembl
  • exonuclease activity Source: UniProtKB-KW
  • nuclease activity Source: UniProtKB
  • poly(A) binding Source: UniProtKB
  • RNA binding Source: UniProtKB
  • RNA helicase activity Source: ProtInc
  • transcription coregulator activity Source: UniProtKB

GO - Biological processi

  • DNA duplex unwinding Source: UniProtKB
  • double-strand break repair Source: UniProtKB
  • multicellular organism development Source: UniProtKB
  • nucleic acid phosphodiester bond hydrolysis Source: UniProtKB
  • protein localization to cytoplasmic stress granule Source: AgBase
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • regulation of translational initiation Source: UniProtKB
  • response to exogenous dsRNA Source: Ensembl
  • response to virus Source: Ensembl
  • RNA secondary structure unwinding Source: GO_Central
  • spliceosomal complex assembly Source: UniProtKB
  • transcription, DNA-templated Source: UniProtKB-KW
  • tRNA splicing, via endonucleolytic cleavage and ligation Source: UniProtKB

Keywordsi

Molecular functionActivator, DNA-binding, Exonuclease, Helicase, Hydrolase, Nuclease, RNA-binding
Biological processmRNA processing, Transcription, Transcription regulation, tRNA processing
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:ENSG00000079785-MONOMER
ReactomeiR-HSA-6784531 tRNA processing in the nucleus

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent RNA helicase DDX1 (EC:3.6.4.13)
Alternative name(s):
DEAD box protein 1
DEAD box protein retinoblastoma
Short name:
DBP-RB
Gene namesi
Name:DDX1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

EuPathDBiHostDB:ENSG00000079785.14
HGNCiHGNC:2734 DDX1
MIMi601257 gene
neXtProtiNX_Q92499

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

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi52K → N: Abolishes ability to promote guanylylation of RTCB. 1 Publication1
Mutagenesisi371E → G: Inhibits the transcriptional activity of RELA and attenuates NF-kappa-B-mediated gene expression. 2 Publications1
Mutagenesisi371E → Q: Abolishes ability to promote guanylylation of RTCB. 2 Publications1

Organism-specific databases

DisGeNETi1653
OpenTargetsiENSG00000079785
PharmGKBiPA27199

Chemistry databases

ChEMBLiCHEMBL2010634

Polymorphism and mutation databases

BioMutaiDDX1
DMDMi6919862

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000549861 – 740ATP-dependent RNA helicase DDX1Add BLAST740

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei239N6-acetyllysineCombined sources1
Modified residuei268N6-acetyllysineCombined sources1
Modified residuei281N6-acetyllysine; alternateCombined sources1
Cross-linki281Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateCombined sources
Modified residuei481PhosphoserineCombined sources1

Post-translational modificationi

Phosphorylated. Phosphorylated by ATM kinase; phosphorylation is increased in response to ionizing radiation (IR).1 Publication

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ92499
MaxQBiQ92499
PaxDbiQ92499
PeptideAtlasiQ92499
PRIDEiQ92499
ProteomicsDBi75269

2D gel databases

REPRODUCTION-2DPAGEiIPI00293655

PTM databases

iPTMnetiQ92499
PhosphoSitePlusiQ92499
SwissPalmiQ92499

Expressioni

Tissue specificityi

Highest levels of transcription in 2 retinoblastoma cell lines and in tissues of neuroectodermal origin including the retina, brain, and spinal cord.1 Publication

Gene expression databases

BgeeiENSG00000079785
CleanExiHS_DDX1
ExpressionAtlasiQ92499 baseline and differential
GenevisibleiQ92499 HS

Organism-specific databases

HPAiCAB012280
HPA034502
HPA034503

Interactioni

Subunit structurei

Interacts with FAM98A (via N- and C-terminus) (PubMed:28040436). Interacts with MBNL1 (PubMed:18335541). Interacts with CSTF2 (PubMed:11598190). Interacts with HNRNPK (PubMed:12183465). Interacts with ATM (PubMed:18710941). Interacts with RELA (via C-terminus) (PubMed:19058135). Component of the tRNA-splicing ligase complex (PubMed:21311021, PubMed:24870230). Interacts with PQBP1 (PubMed:21933836). Interacts with PHF5A (via C-terminus) (By similarity).By similarity9 Publications
(Microbial infection) Interacts with Rev of HIV-1.1 Publication
(Microbial infection) Interacts with Severe acute respiratory syndrome coronavirus (SARS-CoV) (via N-terminus) (PubMed:20573827). Interacts (via C-terminus) with the replicase polyprotein 1ab Nsp14 of the Avian infectious bronchitis virus (IBV).1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
revP046186EBI-15532186,EBI-6164309From Human immunodeficiency virus type 1 group M subtype B (isolate HXB2).

Protein-protein interaction databases

BioGridi108019, 221 interactors
CORUMiQ92499
DIPiDIP-38163N
IntActiQ92499, 46 interactors
MINTiQ92499
STRINGi9606.ENSP00000233084

Chemistry databases

BindingDBiQ92499

Structurei

Secondary structure

1740
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi90 – 98Combined sources9
Beta strandi102 – 104Combined sources3
Beta strandi110 – 113Combined sources4
Beta strandi120 – 139Combined sources20
Beta strandi141 – 150Combined sources10
Beta strandi164 – 168Combined sources5
Turni169 – 171Combined sources3
Beta strandi172 – 175Combined sources4
Beta strandi178 – 181Combined sources4
Beta strandi191 – 197Combined sources7
Turni198 – 201Combined sources4
Beta strandi202 – 207Combined sources6
Beta strandi210 – 217Combined sources8
Helixi220 – 222Combined sources3
Beta strandi227 – 245Combined sources19
Helixi258 – 260Combined sources3
Helixi263 – 265Combined sources3
Beta strandi266 – 268Combined sources3

3D structure databases

ProteinModelPortaliQ92499
SMRiQ92499
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini2 – 428Helicase ATP-bindingPROSITE-ProRule annotationAdd BLAST427
Domaini70 – 247B30.2/SPRYPROSITE-ProRule annotationAdd BLAST178
Domaini493 – 681Helicase C-terminalPROSITE-ProRule annotationAdd BLAST189

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 525Necessary for interaction with RELA1 PublicationAdd BLAST525
Regioni1 – 295Necessary for interaction with HNRNPK1 PublicationAdd BLAST295
Regioni525 – 740Necessary for interaction with HNRNPK1 PublicationAdd BLAST216
Regioni536 – 631Necessary for interaction with replicase polyprotein 1ab nsp14 of IBVAdd BLAST96

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi370 – 373DEAD box4

Domaini

The helicase domain is involved in the stimulation of RELA transcriptional activity.

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG0349 Eukaryota
COG0513 LUCA
GeneTreeiENSGT00900000140933
HOGENOMiHOG000251633
HOVERGENiHBG005462
InParanoidiQ92499
KOiK13177
OMAiTLNNVKQ
OrthoDBiEOG091G03WJ
PhylomeDBiQ92499
TreeFamiTF106114

Family and domain databases

CDDicd00079 HELICc, 1 hit
InterProiView protein in InterPro
IPR001870 B30.2/SPRY
IPR013320 ConA-like_dom_sf
IPR011545 DEAD/DEAH_box_helicase_dom
IPR014001 Helicase_ATP-bd
IPR001650 Helicase_C
IPR027417 P-loop_NTPase
IPR014014 RNA_helicase_DEAD_Q_motif
IPR003877 SPRY_dom
PfamiView protein in Pfam
PF00270 DEAD, 1 hit
PF00271 Helicase_C, 1 hit
PF00622 SPRY, 1 hit
SMARTiView protein in SMART
SM00487 DEXDc, 1 hit
SM00490 HELICc, 1 hit
SM00449 SPRY, 1 hit
SUPFAMiSSF49899 SSF49899, 1 hit
SSF52540 SSF52540, 3 hits
PROSITEiView protein in PROSITE
PS50188 B302_SPRY, 1 hit
PS51192 HELICASE_ATP_BIND_1, 2 hits
PS51194 HELICASE_CTER, 1 hit
PS51195 Q_MOTIF, 1 hit

Sequences (3)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: Q92499-1) [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
MAAFSEMGVM PEIAQAVEEM DWLLPTDIQA ESIPLILGGG DVLMAAETGS
60 70 80 90 100
GKTGAFSIPV IQIVYETLKD QQEGKKGKTT IKTGASVLNK WQMNPYDRGS
110 120 130 140 150
AFAIGSDGLC CQSREVKEWH GCRATKGLMK GKHYYEVSCH DQGLCRVGWS
160 170 180 190 200
TMQASLDLGT DKFGFGFGGT GKKSHNKQFD NYGEEFTMHD TIGCYLDIDK
210 220 230 240 250
GHVKFSKNGK DLGLAFEIPP HMKNQALFPA CVLKNAELKF NFGEEEFKFP
260 270 280 290 300
PKDGFVALSK APDGYIVKSQ HSGNAQVTQT KFLPNAPKAL IVEPSRELAE
310 320 330 340 350
QTLNNIKQFK KYIDNPKLRE LLIIGGVAAR DQLSVLENGV DIVVGTPGRL
360 370 380 390 400
DDLVSTGKLN LSQVRFLVLD EADGLLSQGY SDFINRMHNQ IPQVTSDGKR
410 420 430 440 450
LQVIVCSATL HSFDVKKLSE KIMHFPTWVD LKGEDSVPDT VHHVVVPVNP
460 470 480 490 500
KTDRLWERLG KSHIRTDDVH AKDNTRPGAN SPEMWSEAIK ILKGEYAVRA
510 520 530 540 550
IKEHKMDQAI IFCRTKIDCD NLEQYFIQQG GGPDKKGHQF SCVCLHGDRK
560 570 580 590 600
PHERKQNLER FKKGDVRFLI CTDVAARGID IHGVPYVINV TLPDEKQNYV
610 620 630 640 650
HRIGRVGRAE RMGLAISLVA TEKEKVWYHV CSSRGKGCYN TRLKEDGGCT
660 670 680 690 700
IWYNEMQLLS EIEEHLNCTI SQVEPDIKVP VDEFDGKVTY GQKRAAGGGS
710 720 730 740
YKGHVDILAP TVQELAALEK EAQTSFLHLG YLPNQLFRTF
Length:740
Mass (Da):82,432
Last modified:August 1, 1998 - v2
Checksum:iC6D0179F83BD8C73
GO
Isoform 2 (identifier: Q92499-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     98-113: Missing.
     630-740: VCSSRGKGCY...YLPNQLFRTF → MVQRDAVTI

Note: No experimental confirmation available.
Show »
Length:622
Mass (Da):69,556
Checksum:iF0DC36DB1DAA09F8
GO
Isoform 3 (identifier: Q92499-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-128: Missing.

Note: No experimental confirmation available.
Show »
Length:612
Mass (Da):68,712
Checksum:i511B121802355812
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0554531 – 128Missing in isoform 3. 1 PublicationAdd BLAST128
Alternative sequenceiVSP_05545498 – 113Missing in isoform 2. 1 PublicationAdd BLAST16
Alternative sequenceiVSP_055455630 – 740VCSSR…LFRTF → MVQRDAVTI in isoform 2. 1 PublicationAdd BLAST111

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X70649 mRNA Translation: CAA49992.1
AK297432 mRNA Translation: BAG59860.1
AK298426 mRNA Translation: BAG60648.1
BC012132 mRNA Translation: AAH12132.1
BC053673 mRNA Translation: AAH53673.1
CCDSiCCDS1686.1 [Q92499-1]
RefSeqiNP_004930.1, NM_004939.2 [Q92499-1]
UniGeneiHs.440599

Genome annotation databases

EnsembliENST00000233084; ENSP00000233084; ENSG00000079785 [Q92499-1]
ENST00000381341; ENSP00000370745; ENSG00000079785 [Q92499-1]
GeneIDi1653
KEGGihsa:1653
UCSCiuc002rce.5 human [Q92499-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiDDX1_HUMAN
AccessioniPrimary (citable) accession number: Q92499
Secondary accession number(s): B4DME8, B4DPN6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: August 1, 1998
Last modified: July 18, 2018
This is version 177 of the entry and version 2 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 2
    Human chromosome 2: 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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