Q9NY93 · DDX56_HUMAN
- ProteinProbable ATP-dependent RNA helicase DDX56
- GeneDDX56
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids547 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
Nucleolar RNA helicase that plays a role in various biological processes including innate immunity, ribosome biogenesis or nucleolus organization (PubMed:31340999, PubMed:33789112).
Plays an essential role in maintaining nucleolar integrity in planarian stem cells (PubMed:33789112).
Maintains embryonic stem cells proliferation by conventional regulation of ribosome assembly and interaction with OCT4 and POU5F1 complex (By similarity).
Regulates antiviral innate immunity by inhibiting the virus-triggered signaling nuclear translocation of IRF3 (PubMed:31340999).
Mechanistically, acts by disrupting the interaction between IRF3 and importin IPO5 (PubMed:31340999).
May play a role in later stages of the processing of the pre-ribosomal particles leading to mature 60S ribosomal subunits. Has intrinsic ATPase activity
Plays an essential role in maintaining nucleolar integrity in planarian stem cells (PubMed:33789112).
Maintains embryonic stem cells proliferation by conventional regulation of ribosome assembly and interaction with OCT4 and POU5F1 complex (By similarity).
Regulates antiviral innate immunity by inhibiting the virus-triggered signaling nuclear translocation of IRF3 (PubMed:31340999).
Mechanistically, acts by disrupting the interaction between IRF3 and importin IPO5 (PubMed:31340999).
May play a role in later stages of the processing of the pre-ribosomal particles leading to mature 60S ribosomal subunits. Has intrinsic ATPase activity
(Microbial infection) Helicase activity is important for packaging viral RNA into virions during West Nile virus infection.
(Microbial infection) Plays a positive role in foot-and-mouth disease virus replication by inhibiting the phosphorylation of IRF3 leading to inhibition of type I interferon.
(Microbial infection) Plays a positive role in EMCV replication by interrupting IRF3 phosphorylation and its nucleus translocation.
Catalytic activity
- ATP + H2O = ADP + H+ + phosphate
Features
Showing features for binding site.
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | cytosol | |
Cellular Component | membrane | |
Cellular Component | nucleolus | |
Cellular Component | nucleus | |
Molecular Function | ATP binding | |
Molecular Function | ATP hydrolysis activity | |
Molecular Function | protein sequestering activity | |
Molecular Function | RNA binding | |
Molecular Function | RNA helicase activity | |
Molecular Function | RNA stem-loop binding | |
Biological Process | defense response to virus | |
Biological Process | modulation by host of viral RNA genome replication | |
Biological Process | negative regulation of type I interferon production | |
Biological Process | positive regulation of neuron projection development | |
Biological Process | rRNA processing |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameProbable ATP-dependent RNA helicase DDX56
- EC number
- Alternative names
Gene names
Organism names
- Organism
- Taxonomic lineageEukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Primates > Haplorrhini > Catarrhini > Hominidae > Homo
Accessions
- Primary accessionQ9NY93
- Secondary accessions
Proteomes
Organism-specific databases
Subcellular Location
Disease & Variants
Features
Showing features for mutagenesis.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 166 | Complete loss of interaction with IRF3. About 3-4 times less genomic RNA in West Nile virus particles. | ||||
Sequence: D → N | ||||||
Mutagenesis | 167 | Complete loss of interaction with IRF3. About 3-4 times less genomic RNA in West Nile virus particles. | ||||
Sequence: E → Q |
Variants
We now provide the "Disease & Variants" viewer in its own tab.
The viewer provides 680 variants from UniProt as well as other sources including ClinVar and dbSNP.
Organism-specific databases
Miscellaneous
Genetic variation databases
PTM/Processing
Features
Showing features for chain, modified residue, modified residue (large scale data).
Type | ID | Position(s) | Source | Description | |||
---|---|---|---|---|---|---|---|
Chain | PRO_0000055058 | 1-547 | UniProt | Probable ATP-dependent RNA helicase DDX56 | |||
Sequence: MEDSEALGFEHMGLDPRLLQAVTDLGWSRPTLIQEKAIPLALEGKDLLARARTGSGKTAAYAIPMLQLLLHRKATGPVVEQAVRGLVLVPTKELARQAQSMIQQLATYCARDVRVANVSAAEDSVSQRAVLMEKPDVVVGTPSRILSHLQQDSLKLRDSLELLVVDEADLLFSFGFEEELKSLLCHLPRIYQAFLMSATFNEDVQALKELILHNPVTLKLQESQLPGPDQLQQFQVVCETEEDKFLLLYALLKLSLIRGKSLLFVNTLERSYRLRLFLEQFSIPTCVLNGELPLRSRCHIISQFNQGFYDCVIATDAEVLGAPVKGKRRGRGPKGDKASDPEAGVARGIDFHHVSAVLNFDLPPTPEAYIHRAGRTARANNPGIVLTFVLPTEQFHLGKIEELLSGENRGPILLPYQFRMEEIEGFRYRCRDAMRSVTKQAIREARLKEIKEELLHSEKLKTYFEDNPRDLQLLRHDLPLHPAVVKPHLGHVPDYLVPPALRGLVRPHKKRKKLSSSCRKAKRAKSQNPLRSFKHKGKKFRPTAKPS | |||||||
Modified residue | 126 | UniProt | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue | 141 | UniProt | Phosphothreonine | ||||
Sequence: T | |||||||
Modified residue (large scale data) | 141 | PRIDE | Phosphothreonine | ||||
Sequence: T | |||||||
Modified residue | 532 | UniProt | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 532 | PRIDE | Phosphoserine | ||||
Sequence: S |
Keywords
- PTM
Proteomic databases
PTM databases
Expression
Tissue specificity
Detected in heart, brain, liver, pancreas, placenta and lung.
Gene expression databases
Organism-specific databases
Interaction
Subunit
May form homooligomeric complexes. Interacts with IRF3 (PubMed:31340999).
Interacts with OCT4 and POU5F1 (By similarity).
Interacts with OCT4 and POU5F1 (By similarity).
(Microbial infection) Interacts with West Nile virus capsid protein C.
(Microbial infection) Interacts with foot-and-mouth disease virus protein 3A; this interaction leads to inhibition of type I interferon production.
(Microbial infection) Interacts with EMCV protein 3C; this interaction leads to inhibition of type I interferon production.
Binary interactions
Type | Entry 1 | Entry 2 | Number of experiments | Intact | |
---|---|---|---|---|---|
BINARY | Q9NY93 | EIF4A3 P38919 | 3 | EBI-372376, EBI-299104 |
Protein-protein interaction databases
Miscellaneous
Structure
Family & Domains
Features
Showing features for motif, domain, region.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Motif | 7-35 | Q motif | ||||
Sequence: LGFEHMGLDPRLLQAVTDLGWSRPTLIQE | ||||||
Domain | 38-218 | Helicase ATP-binding | ||||
Sequence: IPLALEGKDLLARARTGSGKTAAYAIPMLQLLLHRKATGPVVEQAVRGLVLVPTKELARQAQSMIQQLATYCARDVRVANVSAAEDSVSQRAVLMEKPDVVVGTPSRILSHLQQDSLKLRDSLELLVVDEADLLFSFGFEEELKSLLCHLPRIYQAFLMSATFNEDVQALKELILHNPVTL | ||||||
Motif | 166-169 | DEAD box | ||||
Sequence: DEAD | ||||||
Domain | 230-424 | Helicase C-terminal | ||||
Sequence: QLQQFQVVCETEEDKFLLLYALLKLSLIRGKSLLFVNTLERSYRLRLFLEQFSIPTCVLNGELPLRSRCHIISQFNQGFYDCVIATDAEVLGAPVKGKRRGRGPKGDKASDPEAGVARGIDFHHVSAVLNFDLPPTPEAYIHRAGRTARANNPGIVLTFVLPTEQFHLGKIEELLSGENRGPILLPYQFRMEEIE | ||||||
Region | 506-547 | Disordered | ||||
Sequence: RPHKKRKKLSSSCRKAKRAKSQNPLRSFKHKGKKFRPTAKPS |
Sequence similarities
Belongs to the DEAD box helicase family. DDX56/DBP9 subfamily.
Phylogenomic databases
Family and domain databases
Sequence & Isoform
- Sequence statusComplete
This entry describes 2 isoforms produced by Alternative splicing.
Q9NY93-1
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.
- Name1
- Length547
- Mass (Da)61,590
- Last updated2000-10-01 v1
- Checksum6D127CDAA73610D2
Q9NY93-2
- Name2
- Differences from canonical
- 298-337: Missing
Computationally mapped potential isoform sequences
There are 5 potential isoforms mapped to this entry
Features
Showing features for sequence conflict, alternative sequence.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Sequence conflict | 30 | in Ref. 5; CAG33494 | ||||
Sequence: P → S | ||||||
Sequence conflict | 145 | in Ref. 4; BAB14238 | ||||
Sequence: I → T | ||||||
Alternative sequence | VSP_044869 | 298-337 | in isoform 2 | |||
Sequence: Missing | ||||||
Sequence conflict | 402 | in Ref. 4; AK315363 | ||||
Sequence: E → D | ||||||
Sequence conflict | 518 | in Ref. 5; CAG33494 | ||||
Sequence: C → Y |
Keywords
- Coding sequence diversity
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
AJ131712 EMBL· GenBank· DDBJ | CAB87992.1 EMBL· GenBank· DDBJ | mRNA | ||
AF247666 EMBL· GenBank· DDBJ | AAG36876.1 EMBL· GenBank· DDBJ | mRNA | ||
AL136700 EMBL· GenBank· DDBJ | CAB66635.1 EMBL· GenBank· DDBJ | mRNA | ||
AK022774 EMBL· GenBank· DDBJ | BAB14238.1 EMBL· GenBank· DDBJ | mRNA | ||
AK315363 EMBL· GenBank· DDBJ | - | mRNA | No translation available. | |
CR457213 EMBL· GenBank· DDBJ | CAG33494.1 EMBL· GenBank· DDBJ | mRNA | ||
AC004938 EMBL· GenBank· DDBJ | - | Genomic DNA | No translation available. | |
CH236960 EMBL· GenBank· DDBJ | EAL23752.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
CH471128 EMBL· GenBank· DDBJ | EAW61094.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
BC001235 EMBL· GenBank· DDBJ | AAH01235.1 EMBL· GenBank· DDBJ | mRNA |