Details of Host Protein

 Host Protein General Information (ID: PT0206)
  Protein Name
Leukophysin (LKP)
  Gene Name
DDX1
  Host Species
Homo sapiens
  Uniprot Entry Name
DDX1_HUMAN
  Protein Families
DEAD box helicase family
  EC Number
3.6.4.13
  Subcellular Location
Nucleus
  External Link
NCBI Gene ID
1653
Uniprot ID
Q92499
Ensembl ID
ENSG00000079785
HGNC ID
HGNC:2734
  Function in Host
Acts as an ATP-dependent RNA helicase, able to unwind bothRNA-RNA and RNA-DNA duplexes. Possesses 5' single-stranded RNA overhangnuclease activity. Possesses ATPase activity on various RNA, but notDNA polynucleotides. May play a role in RNA clearance at DNA double-strand breaks (DSBs), thereby facilitating the template-guided repairof transcriptionally active regions of the genome. Together with RELA, acts as a coactivator to enhance NF-kappa-B-mediated transcriptionalactivation. Acts as a positive transcriptional regulator of cyclinCCND2 expression. Binds to the cyclin CCND2 promoter region. Associateswith chromatin at the NF-kappa-B promoter region via association withRELA. Binds to poly (A) RNA. May be involved in 3'-end cleavage andpolyadenylation of pre-mRNAs. Component of the tRNA-splicing ligasecomplex required to facilitate the enzymatic turnover of catalyticsubunit RTCB: together with archease (ZBTB8OS), acts by facilitatingthe guanylylation of RTCB, a key intermediate step in tRNA ligation. Component of a multi-helicase-TICAM1 complex thatacts as a cytoplasmic sensor of viral double-stranded RNA (dsRNA) andplays a role in the activation of a cascade of antiviral responsesincluding the induction of pro-inflammatory cytokines via the adaptermolecule TICAM1. Specifically binds (via helicase ATP-binding domain) on both short and long poly (I:C) dsRNA. [1-6]
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  3D Structure
PDB ID: 4XW3 
FASTA   Download
  2D PNG Download  
PDB File Download

Function of This Protein During Virus Infection
Virus NameHCoV-229E Protein Function Anti-viral [7]
Infected TissueLiver Infection Time4 days
Infected CellHuh-7.5 Cells (Human hepatocellular carcinoma cells) Cellosaurus IDCVCL_7927 
Method DescriptionTo detect the role of host protein DDX1 in viral infection, DDX1 protein knockout Huh-7.5 Cells were infected with HCoV-229E for 4 days , and the effects on infection was detected through kit.
ResultsIt is reported that Knockout of DDX1 increases infection compared with control group.
Virus NameHCoV-NL63 Protein Function Anti-viral [7]
Infected TissueLiver Infection Time4 days
Infected CellHuh-7.5 Cells (Human hepatocellular carcinoma cells) Cellosaurus IDCVCL_7927 
Method DescriptionTo detect the role of host protein DDX1 in viral infection, DDX1 protein knockout Huh-7.5 Cells were infected with HCoV-NL63 for 4 days , and the effects on infection was detected through kit.
ResultsIt is reported that Knockout of DDX1 increases infection compared with control group.
Virus NameSARS-COV-2 Protein Function Anti-viral [7]
Infected TissueLiver Infection Time4 days
Infected CellHuh-7.5 Cells (Human hepatocellular carcinoma cells) Cellosaurus IDCVCL_7927 
Method DescriptionTo detect the role of host protein DDX1 in viral infection, DDX1 protein knockout Huh-7.5 Cells were infected with SARS-COV-2 for 4 days , and the effects on infection was detected through kit.
ResultsIt is reported that Knockout of DDX1 increases infection compared with control group.

Host Protein - Virus RNA Network
  Network Download  

 Full List of Virus RNA Interacting with This Protien
            RNA Region: Not Specified Virus Region (hCoV-19/Not Specified Virus Strain )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [8]
              Strains Name
hCoV-19/Not Specified Virus Strain
              RNA Binding Region
Not Specified Virus Region
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Infection Cells Huh7 cells (liver carcinoma cell)  (CVCL_0336 )
              Cell Originated Tissue Liver
              Infection Time 24h
              Interaction Score log2FC = 4.43074E+14
              Method Description RNA antisense purification and quantitative mass spectrometry (RAP-MS); Tandem mass tag (TMT) labelling; liquid chromatography tandem mass spectrometry (LC-MS/MS); Westernblot
           RNA Region: Not Specified Virus Region (hCoV-19/France/IDF-220-95/2020 )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [9]
              Strains Name
hCoV-19/France/IDF-220-95/2020
              RNA Binding Region
Not Specified Virus Region
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Interaction Type Direct interaction
              Infection Cells HEK293 Cells (Human embryonic kidney cell) HEK293 Cells (Human embryonic kidney cell)  (CVCL_0045 )
              Cell Originated Tissue Kidney
              Infection Time 48 h
              Interaction Score SAINT score ≥ 0.79
              Method Description comprehensive identification of RNA-binding proteins by massspectrometry (ChIRP-MS)
           RNA Region: Not Specified Virus Region (hCoV-19/England/02/2020 )
              RNA Region Details RNA Info Click to show the detail information of this RNA binding region [10]
              Strains Name
hCoV-19/England/02/2020
              Strains Family
Beta (B.1.351)
              RNA Binding Region
Not Specified Virus Region
              Virus Name
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
              Infection Cells Calu-3 cells (Human lung cancer cell) Calu-3 cells (Human lung cancer cell)  (CVCL_0609 )
              Cell Originated Tissue Lung
              Infection Time 24 h
              Interaction Score P-adjust = 0.037
              Method Description UV protein-RNA crosslinking; RNA interactome capture (cRIC); RNA antisense purification coupled with mass spectrometry (RAP-MS)

Differential Gene Expression During SARS-COV-2 Infection
GEO Accession: GSE152641
Sample Type: Blood
Samples Details: Healthy Control: 24; COVID-19: 62
Platform: GPL24676 Illumina NovaSeq 6000
  PNG Download  
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GEO Accession: GSE162835
Sample Type: Nasopharyngeal Swabs
Samples Details: COVID-19 (Mild Symptoms): 37; COVID-19 (Moderate Symptoms): 10; COVID-19 (Severe Symptoms): 3
Platform: GPL24676 Illumina NovaSeq 6000
  PNG Download  
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GEO Accession: GSE175779
Sample Type: Human Bronchial Epithelial Cells
Samples Details: Healthy Control: 4 (0, 24, 48, 72 and 96 h); COVID-19: 4 (24, 48, 72 and 96 h)
Platform: GPL18573 Illumina NextSeq 500
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Protein Phosphorylation after Virus Infection
S481 [11]
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Protein Sequence Information
MAAFSEMGVMPEIAQAVEEMDWLLPTDIQAESIPLILGGGDVLMAAETGSGKTGAFSIPVIQIVYETLKDQQEGKKGKTTIKTGASVLNKWQMNPYDRGSAFAIGSDGLCCQSREVKEWHGCRATKGLMKGKHYYEVSCHDQGLCRVGWSTMQASLDLGTDKFGFGFGGTGKKSHNKQFDNYGEEFTMHDTIGCYLDIDKGHVKFSKNGKDLGLAFEIPPHMKNQALFPACVLKNAELKFNFGEEEFKFPPKDGFVALSKAPDGYIVKSQHSGNAQVTQTKFLPNAPKALIVEPSRELAEQTLNNIKQFKKYIDNPKLRELLIIGGVAARDQLSVLENGVDIVVGTPGRLDDLVSTGKLNLSQVRFLVLDEADGLLSQGYSDFINRMHNQIPQVTSDGKRLQVIVCSATLHSFDVKKLSEKIMHFPTWVDLKGEDSVPDTVHHVVVPVNPKTDRLWERLGKSHIRTDDVHAKDNTRPGANSPEMWSEAIKILKGEYAVRAIKEHKMDQAIIFCRTKIDCDNLEQYFIQQGGGPDKKGHQFSCVCLHGDRKPHERKQNLERFKKGDVRFLICTDVAARGIDIHGVPYVINVTLPDEKQNYVHRIGRVGRAERMGLAISLVATEKEKVWYHVCSSRGKGCYNTRLKEDGGCTIWYNEMQLLSEIEEHLNCTISQVEPDIKVPVDEFDGKVTYGQKRAAGGGSYKGHVDILAPTVQELAALEKEAQTSFLHLGYLPNQLFRTF
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References
1 Analysis of orthologous groups reveals archease and DDX1 as tRNA splicing factors. Nature. 2014 Jul 3;511(7507):104-7.
2 The cellular RNA helicase DDX1 interacts with coronavirus nonstructural protein 14 and enhances viral replication. J Virol. 2010 Sep;84(17):8571-83.
3 A role for DEAD box 1 at DNA double-strand breaks. Mol Cell Biol. 2008 Oct;28(20):6413-25.
4 MBNL1 associates with YB-1 in cytoplasmic stress granules. J Neurosci Res. 2008 Jul;86(9):1994-2002.
5 A DEAD box protein facilitates HIV-1 replication as a cellular co-factor of Rev. Virology. 2004 Dec 20;330(2):471-80.
6 An RNA helicase, DDX1, interacting with poly(A) RNA and heterogeneous nuclear ribonucleoprotein K. J Biol Chem. 2002 Oct 25;277(43):40403-9.
7 Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks. Cell. 2021 Jan 7;184(1):120-132.e14.
8 The SARS-CoV-2 RNA-protein interactome in infected human cells. Nat Microbiol. 2021 Mar;6(3):339-353.
9 Characterization and functional interrogation of the SARS-CoV-2 RNA interactome. Cell Rep. 2022 Apr 26;39(4):110744.
10 Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection. Mol Cell. 2021 Jul 1;81(13):2851-2867.e7.
11 Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV. Nature. 2021 Jun;594(7862):246-252.