CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-001661
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
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
115KRLQPEFKTRIIPTDubiquitination[1]
172ENWPKTLKLALEKERubiquitination[1]
177TLKLALEKERNKFSEubiquitination[1]
292FPQGQKGKVVFFANQubiquitination[1]
307IPVYEQQKSVFSKYFubiquitination[1]
312QQKSVFSKYFERHGYubiquitination[1]
455ELEQVVYKPQKFFRKubiquitination[1]
644RALVDALKNWIEGNPubiquitination[1, 2, 3]
666GILTGRGKTNQNTGMubiquitination[1]
757KEQINMYKEKMMNDSubiquitination[1]
759QINMYKEKMMNDSILubiquitination[1]
788LHIQTHEKFIRDSQEubiquitination[1]
858KQFSSFEKRAKIFCAacetylation[4]
858KQFSSFEKRAKIFCAubiquitination[1]
880WGIHVKYKTFEIPVIubiquitination[1]
909QTLYSKWKDFHFEKIacetylation[4]
Reference
 [1] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [2] Systematic and quantitative assessment of the ubiquitin-modified proteome.
 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
 Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983]
 [3] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
 Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
 Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965]
 [4] Lysine acetylation targets protein complexes and co-regulates major cellular functions.
 Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M.
 Science. 2009 Aug 14;325(5942):834-40. [PMID: 19608861] 
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: Human respiratory syncytial virus and measles virus (MeV), 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 reovirus. 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 251 430 Helicase ATP-binding.
 DOMAIN 610 776 Helicase C-terminal.
 NP_BIND 264 271 ATP (Probable).
 REGION 218 925 Interaction with ZC3HAV1.
 REGION 735 925 Repressor domain.
 MOTIF 372 375 DECH box.
 METAL 810 810 Zinc.
 METAL 813 813 Zinc.
 METAL 864 864 Zinc.
 METAL 869 869 Zinc.
 MOD_RES 770 770 Phosphothreonine; by CK2.
 MOD_RES 854 854 Phosphoserine; by CK2.
 MOD_RES 855 855 Phosphoserine; by CK2.
 MOD_RES 858 858 N6-acetyllysine.
 CROSSLNK 154 154 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 164 164 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 172 172 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; Host-virus interaction; Hydrolase; Immunity; Innate immunity; Isopeptide bond; Membrane; Metal-binding; Nucleotide-binding; Phosphoprotein; Polymorphism; Reference proteome; Repeat; RNA-binding; Tight junction; Ubl conjugation; Zinc. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 925 AA 
Protein Sequence
MTTEQRRSLQ AFQDYIRKTL DPTYILSYMA PWFREEEVQY IQAEKNNKGP MEAATLFLKF 60
LLELQEEGWF RGFLDALDHA GYSGLYEAIE SWDFKKIEKL EEYRLLLKRL QPEFKTRIIP 120
TDIISDLSEC LINQECEEIL QICSTKGMMA GAEKLVECLL RSDKENWPKT LKLALEKERN 180
KFSELWIVEK GIKDVETEDL EDKMETSDIQ IFYQEDPECQ NLSENSCPPS EVSDTNLYSP 240
FKPRNYQLEL ALPAMKGKNT IICAPTGCGK TFVSLLICEH HLKKFPQGQK GKVVFFANQI 300
PVYEQQKSVF SKYFERHGYR VTGISGATAE NVPVEQIVEN NDIIILTPQI LVNNLKKGTI 360
PSLSIFTLMI FDECHNTSKQ HPYNMIMFNY LDQKLGGSSG PLPQVIGLTA SVGVGDAKNT 420
DEALDYICKL CASLDASVIA TVKHNLEELE QVVYKPQKFF RKVESRISDK FKYIIAQLMR 480
DTESLAKRIC KDLENLSQIQ NREFGTQKYE QWIVTVQKAC MVFQMPDKDE ESRICKALFL 540
YTSHLRKYND ALIISEHARM KDALDYLKDF FSNVRAAGFD EIEQDLTQRF EEKLQELESV 600
SRDPSNENPK LEDLCFILQE EYHLNPETIT ILFVKTRALV DALKNWIEGN PKLSFLKPGI 660
LTGRGKTNQN TGMTLPAQKC ILDAFKASGD HNILIATSVA DEGIDIAQCN LVILYEYVGN 720
VIKMIQTRGR GRARGSKCFL LTSNAGVIEK EQINMYKEKM MNDSILRLQT WDEAVFREKI 780
LHIQTHEKFI RDSQEKPKPV PDKENKKLLC RKCKALACYT ADVRVIEECH YTVLGDAFKE 840
CFVSRPHPKP KQFSSFEKRA KIFCARQNCS HDWGIHVKYK TFEIPVIKIE SFVVEDIATG 900
VQTLYSKWKD FHFEKIPFDP AEMSK 925 
Gene Ontology
 GO:0015629; C:actin cytoskeleton; IDA:UniProtKB.
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0032587; C:ruffle membrane; IDA:UniProtKB.
 GO:0005923; C:tight junction; IDA: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; IEA:Compara.
 GO:0003725; F:double-stranded RNA binding; IDA:UniProtKB.
 GO:0003727; F:single-stranded RNA binding; IMP:UniProtKB.
 GO:0008270; F:zinc ion binding; IDA:UniProtKB.
 GO:0009597; P:detection of virus; IDA:BHF-UCL.
 GO:0045087; P:innate immune response; IMP:UniProtKB.
 GO:0032480; P:negative regulation of type I interferon production; TAS:Reactome.
 GO:0002230; P:positive regulation of defense response to virus by host; IMP:UniProtKB.
 GO:0032727; P:positive regulation of interferon-alpha production; IDA:UniProtKB.
 GO:0032728; P:positive regulation of interferon-beta production; IMP:UniProtKB.
 GO:0051091; P:positive regulation of sequence-specific DNA binding transcription factor activity; IC:BHF-UCL.
 GO:0042993; P:positive regulation of transcription factor import into nucleus; IDA:BHF-UCL.
 GO:0045944; P:positive regulation of transcription from RNA polymerase II promoter; IDA:BHF-UCL.
 GO:0030334; P:regulation of cell migration; IDA:UniProtKB.
 GO:0034344; P:regulation of type III interferon production; TAS:UniProtKB.
 GO:0043330; P:response to exogenous dsRNA; IEA:Compara.
 GO:0039529; P:RIG-I signaling pathway; IMP:UniProtKB.
 GO:0019048; P:virus-host interaction; IEA:UniProtKB-KW. 
Interpro
 IPR003593; AAA+_ATPase.
 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
 SM00382; AAA
 SM00487; DEXDc
 SM00490; HELICc 
PROSITE
 PS50209; CARD
 PS51192; HELICASE_ATP_BIND_1
 PS51194; HELICASE_CTER 
PRINTS