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Protein

ATP-dependent RNA helicase DDX1

Gene

DDX1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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). Required for HIV-1 Rev function as well as for HIV-1 replication. Binds to the RRE sequence of HIV-1 mRNAs.6 Publications

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
  • poly(A) RNA binding Source: UniProtKB
  • RNA helicase activity Source: ProtInc
  • transcription cofactor activity Source: UniProtKB

GO - Biological processi

  • DNA duplex unwinding Source: UniProtKB
  • double-strand break repair Source: UniProtKB
  • multicellular organism development 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
Complete GO annotation...

Keywords - Molecular functioni

Activator, Exonuclease, Helicase, Hydrolase, Nuclease

Keywords - Biological processi

mRNA processing, Transcription, Transcription regulation, tRNA processing

Keywords - Ligandi

ATP-binding, DNA-binding, Nucleotide-binding, RNA-binding

Enzyme and pathway databases

BioCyciZFISH: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

HGNCiHGNC:2734. DDX1.

Subcellular locationi

  • Nucleus
  • Cytoplasm
  • Cytoplasmic granule

  • Note: Localized with MBNL1, TIAL1 and YBX1 in stress granules upon stress. Localized with CSTF2 in cleavage bodies. Forms large aggregates called DDX1 bodies. Relocalized into multiple foci (IR-induced foci or IRIF) after IR treatment, a process that depends on the presence of chromosomal DNA and/or RNA-DNA duplexes. Relocalized at sites of DNA double-strand breaks (DSBs) in an ATM-dependent manner after IR treatment. Colocalized with RELA in the nucleus upon TNF-alpha induction. Relocalized to the cytoplasm with a perinuclear staining pattern in avian infectious bronchitis virus (IBV)-infected cells. Required for proper localization of HIV-1 Rev. Enters into the nucleus in case of active transcription while it accumulates in cytosol when transcription level is low (PubMed:24608264).1 Publication

GO - Cellular componenti

  • cleavage body Source: UniProtKB
  • cytoplasm Source: UniProtKB
  • cytoplasmic stress granule Source: UniProtKB
  • intracellular ribonucleoprotein complex Source: MGI
  • membrane Source: UniProtKB
  • nucleoplasm Source: HPA
  • nucleus Source: UniProtKB
  • tRNA-splicing ligase complex Source: UniProtKB
Complete GO annotation...

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-acetyllysineCombined sources1
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, Phosphoprotein

Proteomic databases

EPDiQ92499.
MaxQBiQ92499.
PaxDbiQ92499.
PeptideAtlasiQ92499.
PRIDEiQ92499.

2D gel databases

REPRODUCTION-2DPAGEIPI00293655.

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 PHF5A (via C-terminus) (By similarity). Interacts with MBNL1. Interacts with CSTF2. Interacts with HNRNPK. Interacts with ATM. Interacts with RELA (via C-terminus). Interacts (via C-terminus) with the replicase polyprotein 1ab Nsp14 of the avian infectious bronchitis virus (IBV). Interacts with Rev of HIV-1. Interacts with severe acute respiratory syndrome coronavirus (SARS-CoV) (via N-terminus). Component of the tRNA-splicing ligase complex.By similarity9 Publications

Protein-protein interaction databases

BioGridi108019. 136 interactors.
DIPiDIP-38163N.
IntActiQ92499. 31 interactors.
MINTiMINT-5005493.
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

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4XW3X-ray2.00A/B72-283[»]
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

Contains 1 B30.2/SPRY domain.PROSITE-ProRule annotation
Contains 1 helicase ATP-binding domain.PROSITE-ProRule annotation
Contains 1 helicase C-terminal domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0349. Eukaryota.
COG0513. LUCA.
GeneTreeiENSGT00770000120531.
HOGENOMiHOG000251633.
HOVERGENiHBG005462.
InParanoidiQ92499.
KOiK13177.
OMAiTLNNVKQ.
OrthoDBiEOG091G03WJ.
PhylomeDBiQ92499.
TreeFamiTF106114.

Family and domain databases

Gene3Di3.40.50.300. 4 hits.
InterProiIPR001870. B30.2/SPRY.
IPR013320. ConA-like_dom.
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.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
PF00622. SPRY. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
SM00449. SPRY. 1 hit.
[Graphical view]
SUPFAMiSSF49899. SSF49899. 1 hit.
SSF52540. SSF52540. 3 hits.
PROSITEiPS50188. B302_SPRY. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 2 hits.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]

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

Cross-referencesi

Web resourcesi

Atlas of Genetics and Cytogenetics in Oncology and Haematology

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4XW3X-ray2.00A/B72-283[»]
ProteinModelPortaliQ92499.
SMRiQ92499.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi108019. 136 interactors.
DIPiDIP-38163N.
IntActiQ92499. 31 interactors.
MINTiMINT-5005493.
STRINGi9606.ENSP00000233084.

Chemistry databases

BindingDBiQ92499.
ChEMBLiCHEMBL2010634.

PTM databases

iPTMnetiQ92499.
PhosphoSitePlusiQ92499.
SwissPalmiQ92499.

Polymorphism and mutation databases

BioMutaiDDX1.
DMDMi6919862.

2D gel databases

REPRODUCTION-2DPAGEIPI00293655.

Proteomic databases

EPDiQ92499.
MaxQBiQ92499.
PaxDbiQ92499.
PeptideAtlasiQ92499.
PRIDEiQ92499.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi1653.
DisGeNETi1653.
GeneCardsiDDX1.
HGNCiHGNC:2734. DDX1.
HPAiCAB012280.
HPA034502.
HPA034503.
MIMi601257. gene.
neXtProtiNX_Q92499.
OpenTargetsiENSG00000079785.
PharmGKBiPA27199.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0349. Eukaryota.
COG0513. LUCA.
GeneTreeiENSGT00770000120531.
HOGENOMiHOG000251633.
HOVERGENiHBG005462.
InParanoidiQ92499.
KOiK13177.
OMAiTLNNVKQ.
OrthoDBiEOG091G03WJ.
PhylomeDBiQ92499.
TreeFamiTF106114.

Enzyme and pathway databases

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

Miscellaneous databases

ChiTaRSiDDX1. human.
GeneWikiiDDX1.
GenomeRNAii1653.
PROiQ92499.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000079785.
CleanExiHS_DDX1.
ExpressionAtlasiQ92499. baseline and differential.
GenevisibleiQ92499. HS.

Family and domain databases

Gene3Di3.40.50.300. 4 hits.
InterProiIPR001870. B30.2/SPRY.
IPR013320. ConA-like_dom.
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.
[Graphical view]
PfamiPF00270. DEAD. 1 hit.
PF00271. Helicase_C. 1 hit.
PF00622. SPRY. 1 hit.
[Graphical view]
SMARTiSM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
SM00449. SPRY. 1 hit.
[Graphical view]
SUPFAMiSSF49899. SSF49899. 1 hit.
SSF52540. SSF52540. 3 hits.
PROSITEiPS50188. B302_SPRY. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 2 hits.
PS51194. HELICASE_CTER. 1 hit.
PS51195. Q_MOTIF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDDX1_HUMAN
AccessioniPrimary (citable) accession number: Q92499
Secondary accession number(s): B4DME8, B4DPN6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: August 1, 1998
Last modified: November 30, 2016
This is version 162 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

Caution

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

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

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.