InnateDB: Systems Biology of the Innate Immune Response

Homo sapiens Protein: DDX1

Summary

InnateDB Protein

IDBP-30765.6

Last Modified

2014-10-13 [Report errors or provide feedback]

Gene Symbol

DDX1

Protein Name

DEAD (Asp-Glu-Ala-Asp) box polypeptide 1

Synonyms

DBP-RB; UKVH5d;

Species

Homo sapiens

Ensembl Protein

ENSP00000233084

InnateDB Gene

IDBG-30761 (DDX1)

Protein Structure

UniProt Annotation

Function

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. {ECO:0000269PubMed:12183465, ECO:0000269PubMed:15567440, ECO:0000269PubMed:18335541, ECO:0000269PubMed:18710941, ECO:0000269PubMed:20573827, ECO:0000269PubMed:24870230}.

Subcellular Localization

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). {ECO:0000269PubMed:24608264}.

Disease Associations

Tissue Specificity

Highest levels of transcription in 2 retinoblastoma cell lines and in tissues of neuroectodermal origin including the retina, brain, and spinal cord. {ECO:0000269PubMed:7689221}.

Comments

Interactions

Number of Interactions

This gene and/or its encoded proteins are associated with 130 experimentally validated interaction(s) in this database.
They are also associated with 6 interaction(s) predicted by orthology.

Experimentally validated
Total	130 [view]
Protein-Protein	128 [view]
Protein-DNA	2 [view]
Protein-RNA	0
DNA-DNA	0
RNA-RNA	0
DNA-RNA	0

Predicted by orthology
Total	6 [view]

Gene Ontology

Molecular Function

Accession	GO Term
GO:0003676	nucleic acid binding
GO:0003677	DNA binding
GO:0003682	chromatin binding
GO:0003712	transcription cofactor activity
GO:0003724	RNA helicase activity
GO:0004518	nuclease activity
GO:0004527	exonuclease activity
GO:0005515	protein binding
GO:0005524	ATP binding
GO:0008026	ATP-dependent helicase activity
GO:0008143	poly(A) binding
GO:0033677	DNA/RNA helicase activity
GO:0044822	poly(A) RNA binding

Biological Process

GO:0000245	spliceosomal complex assembly
GO:0006200	ATP catabolic process
GO:0006302	double-strand break repair
GO:0006351	transcription, DNA-templated
GO:0006355	regulation of transcription, DNA-templated
GO:0006446	regulation of translational initiation
GO:0007275	multicellular organismal development
GO:0032508	DNA duplex unwinding
GO:0045087	innate immune response (InnateDB)
GO:0090305	nucleic acid phosphodiester bond hydrolysis

Cellular Component

GO:0005634	nucleus
GO:0005737	cytoplasm
GO:0010494	cytoplasmic stress granule
GO:0016020	membrane
GO:0030529	ribonucleoprotein complex
GO:0071920	cleavage body
GO:0072669	tRNA-splicing ligase complex

Protein Structure and Domains

PDB ID

InterPro

IPR001650 Helicase, C-terminal
IPR001870 B30.2/SPRY domain
IPR003877 SPRY domain
IPR008985 Concanavalin A-like lectin/glucanases superfamily
IPR011545 DEAD/DEAH box helicase domain
IPR014001 Helicase, superfamily 1/2, ATP-binding domain
IPR014014 RNA helicase, DEAD-box type, Q motif
IPR027417 P-loop containing nucleoside triphosphate hydrolase

PFAM

PF00271
PF00622
PF00270

PRINTS

PIRSF

SMART

SM00490
SM00449
SM00487

TIGRFAMs

Post-translational Modifications

Modification

Cross-References

SwissProt

Q92499