CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-015350
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Probable ATP-dependent RNA helicase DDX58 
Protein Synonyms/Alias
 DEAD box protein 58; RIG-I-like receptor 1; RLR-1; Retinoic acid-inducible gene 1 protein; RIG-1; Retinoic acid-inducible gene I protein; RIG-I 
Gene Name
 Ddx58 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Mus musculus (Mouse) 
NCBI Taxa ID
 10090 
Lysine Modification
Position
Peptide
Type
References
496DVSEELGKLFQIQNRubiquitination[1]
600EKLEELEKVSRDPSNubiquitination[1]
645RALVDALKKWIEENPubiquitination[1]
852CKPHPKPKIYDNFEKacetylation[2]
Reference
 [1] Proteomic analyses reveal divergent ubiquitylation site patterns in murine tissues.
 Wagner SA, Beli P, Weinert BT, Schölz C, Kelstrup CD, Young C, Nielsen ML, Olsen JV, Brakebusch C, Choudhary C.
 Mol Cell Proteomics. 2012 Dec;11(12):1578-85. [PMID: 22790023]
 [2] SIRT5-Mediated Lysine Desuccinylation Impacts Diverse Metabolic Pathways.
 Park J, Chen Y, Tishkoff DX, Peng C, Tan M, Dai L, Xie Z, Zhang Y, Zwaans BM, Skinner ME, Lombard DB, Zhao Y.
 Mol Cell. 2013 Jun 27;50(6):919-30. [PMID: 23806337] 
Functional Description
 Innate immune receptor which acts as a cytoplasmic sensor of viral nucleic acids and plays a major role in sensing viral infection and in the activation of a cascade of antiviral responses including the induction of type I interferons and proinflammatory cytokines. Its ligands include: 5'- triphosphorylated ssRNA and dsRNA and short dsRNA (<1 kb in length). In addition to the 5'-triphosphate moiety, blunt-end base pairing at the 5'-end of the RNA is very essential. Overhangs at the non-triphosphorylated end of the dsRNA RNA have no major impact on its activity. A 3'overhang at the 5'triphosphate end decreases and any 5'overhang at the 5' triphosphate end abolishes its activity. Upon ligand binding it associates with mitochondria antiviral signaling protein (MAVS/IPS1) which activates the IKK- related kinases: TBK1 and IKBKE which phosphorylate interferon regulatory factors: IRF3 and IRF7 which in turn activate transcription of antiviral immunological genes, including interferons (IFNs); IFN-alpha and IFN-beta. Detects both positive and negative strand RNA viruses including members of the families Paramyxoviridae: newcastle disease virus (NDV) and Sendai virus (SeV), Rhabdoviridae: vesicular stomatitis virus (VSV), Orthomyxoviridae: influenza A and B virus, Flaviviridae: Japanese encephalitis virus (JEV), hepatitis C virus (HCV), dengue virus (DENV) and west Nile virus (WNV). It also detects rotavirus and orthoreovirus. Also involved in antiviral signaling in response to viruses containing a dsDNA genome such as Epstein-Barr virus (EBV). Detects dsRNA produced from non-self dsDNA by RNA polymerase III, such as Epstein-Barr virus-encoded RNAs (EBERs). May play important roles in granulocyte production and differentiation, bacterial phagocytosis and in the regulation of cell migration. 
Sequence Annotation
 DOMAIN 1 87 CARD 1.
 DOMAIN 92 172 CARD 2.
 DOMAIN 252 431 Helicase ATP-binding.
 DOMAIN 611 777 Helicase C-terminal.
 NP_BIND 265 272 ATP (By similarity).
 REGION 219 926 Interaction with ZC3HAV1 (By similarity).
 REGION 736 926 Repressor domain (By similarity).
 MOTIF 373 376 DECH box.
 METAL 811 811 Zinc (By similarity).
 METAL 814 814 Zinc (By similarity).
 METAL 865 865 Zinc (By similarity).
 METAL 870 870 Zinc (By similarity).
 MOD_RES 771 771 Phosphothreonine; by CK2 (By similarity).
 MOD_RES 859 859 N6-acetyllysine (By similarity).
 CROSSLNK 154 154 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 164 164 Glycyl lysine isopeptide (Lys-Gly)  
Keyword
 3D-structure; Acetylation; Alternative splicing; Antiviral defense; ATP-binding; Cell junction; Cell membrane; Cell projection; Complete proteome; Cytoplasm; Cytoskeleton; Helicase; Hydrolase; Immunity; Innate immunity; Isopeptide bond; Membrane; Metal-binding; Nucleotide-binding; Phosphoprotein; Reference proteome; Repeat; RNA-binding; Tight junction; Ubl conjugation; Zinc. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 926 AA 
Protein Sequence
MTAEQRQNLQ AFRDYIKKIL DPTYILSYMS SWLEDEEVQY IQAEKNNKGP MEAASLFLQY 60
LLKLQSEGWF QAFLDALYHA GYCGLCEAIE SWDFQKIEKL EEHRLLLRRL EPEFKATVDP 120
NDILSELSEC LINQECEEIR QIRDTKGRMA GAEKMAECLI RSDKENWPKV LQLALEKDNS 180
KFSELWIVDK GFKRAESKAD EDDGAEASSI QIFIQEEPEC QNLSQNPGPP SEASSNNLHS 240
PLKPRNYQLE LALPAKKGKN TIICAPTGCG KTFVSLLICE HHLKKFPCGQ KGKVVFFANQ 300
IPVYEQQATV FSRYFERLGY NIASISGATS DSVSVQHIIE DNDIIILTPQ ILVNNLNNGA 360
IPSLSVFTLM IFDECHNTSK NHPYNQIMFR YLDHKLGESR DPLPQVVGLT ASVGVGDAKT 420
AEEAMQHICK LCAALDASVI ATVRDNVAEL EQVVYKPQKI SRKVASRTSN TFKCIISQLM 480
KETEKLAKDV SEELGKLFQI QNREFGTQKY EQWIVGVHKA CSVFQMADKE EESRVCKALF 540
LYTSHLRKYN DALIISEDAQ MTDALNYLKA FFHDVREAAF DETERELTRR FEEKLEELEK 600
VSRDPSNENP KLRDLYLVLQ EEYHLKPETK TILFVKTRAL VDALKKWIEE NPALSFLKPG 660
ILTGRGRTNR ATGMTLPAQK CVLEAFRASG DNNILIATSV ADEGIDIAEC NLVILYEYVG 720
NVIKMIQTRG RGRARDSKCF LLTSSADVIE KEKANMIKEK IMNESILRLQ TWDEMKFGKT 780
VHRIQVNEKL LRDSQHKPQP VPDKENKKLL CGKCKNFACY TADIRVVETS HYTVLGDAFK 840
ERFVCKPHPK PKIYDNFEKK AKIFCAKQNC SHDWGIFVRY KTFEIPVIKI ESFVVEDIVS 900
GVQNRHSKWK DFHFERIQFD PAEMSV 926 
Gene Ontology
 GO:0015629; C:actin cytoskeleton; ISS:UniProtKB.
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0032587; C:ruffle membrane; ISS:UniProtKB.
 GO:0005923; C:tight junction; ISS:UniProtKB.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0008026; F:ATP-dependent helicase activity; IEA:InterPro.
 GO:0003690; F:double-stranded DNA binding; IDA:MGI.
 GO:0003725; F:double-stranded RNA binding; IDA:UniProtKB.
 GO:0003727; F:single-stranded RNA binding; IDA:UniProtKB.
 GO:0008270; F:zinc ion binding; ISS:UniProtKB.
 GO:0009597; P:detection of virus; IEA:Compara.
 GO:0045087; P:innate immune response; IMP:UniProtKB.
 GO:0002230; P:positive regulation of defense response to virus by host; ISS:UniProtKB.
 GO:0032727; P:positive regulation of interferon-alpha production; ISS:UniProtKB.
 GO:0032728; P:positive regulation of interferon-beta production; IMP:UniProtKB.
 GO:0042993; P:positive regulation of transcription factor import into nucleus; IEA:Compara.
 GO:0045944; P:positive regulation of transcription from RNA polymerase II promoter; IEA:Compara.
 GO:0030334; P:regulation of cell migration; ISS:UniProtKB.
 GO:0043330; P:response to exogenous dsRNA; IMP:MGI.
 GO:0009615; P:response to virus; IMP:UniProtKB.
 GO:0039529; P:RIG-I signaling pathway; IEA:Compara. 
Interpro
 IPR011029; DEATH-like_dom.
 IPR011545; DNA/RNA_helicase_DEAD/DEAH_N.
 IPR014001; Helicase_ATP-bd.
 IPR001650; Helicase_C.
 IPR027417; P-loop_NTPase.
 IPR021673; RIG-I_C-RD. 
Pfam
 PF00270; DEAD
 PF00271; Helicase_C
 PF11648; RIG-I_C-RD 
SMART
 SM00487; DEXDc
 SM00490; HELICc 
PROSITE
 PS50209; CARD
 PS51192; HELICASE_ATP_BIND_1
 PS51194; HELICASE_CTER 
PRINTS