| IED ID | IndEnz0002006029 |
| Enzyme Type ID | protease006029 |
| Protein Name |
Antiviral innate immune response receptor RIG-I DEAD box protein 58 Probable ATP-dependent RNA helicase DDX58 EC 3.6.4.13 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 |
| Organism | Homo sapiens (Human) |
| Taxonomic Lineage | cellular organisms Eukaryota Opisthokonta Metazoa Eumetazoa Bilateria Deuterostomia Chordata Craniata Vertebrata Gnathostomata (jawed vertebrates) Teleostomi Euteleostomi Sarcopterygii Dipnotetrapodomorpha Tetrapoda Amniota Mammalia Theria Eutheria Boreoeutheria Euarchontoglires Primates Haplorrhini Simiiformes Catarrhini Hominoidea (apes) Hominidae (great apes) Homininae Homo Homo sapiens (Human) |
| Enzyme Sequence | MTTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNNKGPMEAATLFLKFLLELQEEGWFRGFLDALDHAGYSGLYEAIESWDFKKIEKLEEYRLLLKRLQPEFKTRIIPTDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLALEKERNKFSELWIVEKGIKDVETEDLEDKMETSDIQIFYQEDPECQNLSENSCPPSEVSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHIQTHEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSK |
| Enzyme Length | 925 |
| Uniprot Accession Number | O95786 |
| Absorption | |
| Active Site | |
| Activity Regulation | |
| Binding Site | |
| Calcium Binding | |
| catalytic Activity | CATALYTIC ACTIVITY: Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13; |
| DNA Binding | |
| EC Number | 3.6.4.13 |
| Enzyme Function | FUNCTION: Innate immune receptor that senses cytoplasmic viral nucleic acids and activates a downstream signaling cascade leading to the production of type I interferons and proinflammatory cytokines (PubMed:15208624, PubMed:16125763, PubMed:15708988, PubMed:16127453, PubMed:16153868, PubMed:17190814, PubMed:18636086, PubMed:19122199, PubMed:19211564, PubMed:29117565, PubMed:28469175, PubMed:31006531). Forms a ribonucleoprotein complex with viral RNAs on which it homooligomerizes to form filaments (PubMed:15208624, PubMed:15708988). The homooligomerization allows the recruitment of RNF135 an E3 ubiquitin-protein ligase that activates and amplifies the RIG-I-mediated antiviral signaling in an RNA length-dependent manner through ubiquitination-dependent and -independent mechanisms (PubMed:28469175, PubMed:31006531). Upon activation, associates with mitochondria antiviral signaling protein (MAVS/IPS1) that activates the IKK-related kinases TBK1 and IKBKE which in turn phosphorylate the interferon regulatory factors IRF3 and IRF7, activating transcription of antiviral immunological genes including the IFN-alpha and IFN-beta interferons (PubMed:28469175, PubMed:31006531). Ligands include 5'-triphosphorylated ssRNAs and dsRNAs but also short dsRNAs (<1 kb in length) (PubMed:15208624, PubMed:15708988, PubMed:19576794, PubMed:19609254, PubMed:21742966). In addition to the 5'-triphosphate moiety, blunt-end base pairing at the 5'-end of the RNA is very essential (PubMed:15208624, PubMed:15708988, PubMed:19576794, PubMed:19609254, PubMed:21742966). Overhangs at the non-triphosphorylated end of the dsRNA RNA have no major impact on its activity (PubMed:15208624, PubMed:15708988, PubMed:19576794, PubMed:19609254, PubMed:21742966). A 3'overhang at the 5'triphosphate end decreases and any 5'overhang at the 5' triphosphate end abolishes its activity (PubMed:15208624, PubMed:15708988, PubMed:19576794, PubMed:19609254, PubMed:21742966). 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) (PubMed:21616437, PubMed:21884169). It also detects rotaviruses and reoviruses (PubMed:21616437, PubMed:21884169). Detects and binds to SARS-CoV-2 RNAs which is inhibited by m6A RNA modifications (Ref.65). Also involved in antiviral signaling in response to viruses containing a dsDNA genome such as Epstein-Barr virus (EBV) (PubMed:19631370). 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. {ECO:0000269|PubMed:15208624, ECO:0000269|PubMed:15708988, ECO:0000269|PubMed:16125763, ECO:0000269|PubMed:16127453, ECO:0000269|PubMed:16153868, ECO:0000269|PubMed:17190814, ECO:0000269|PubMed:18636086, ECO:0000269|PubMed:19122199, ECO:0000269|PubMed:19211564, ECO:0000269|PubMed:19576794, ECO:0000269|PubMed:19609254, ECO:0000269|PubMed:19631370, ECO:0000269|PubMed:21742966, ECO:0000269|PubMed:28469175, ECO:0000269|PubMed:29117565, ECO:0000269|PubMed:31006531, ECO:0000269|Ref.65, ECO:0000303|PubMed:21616437, ECO:0000303|PubMed:21884169}. |
| Temperature Dependency | |
| PH Dependency | |
| Pathway | |
| nucleotide Binding | NP_BIND 264..271; /note=ATP; /evidence=ECO:0000305 |
| Features | Alternative sequence (1); Beta strand (35); Chain (1); Cross-link (7); Domain (5); Helix (45); Metal binding (4); Modified residue (6); Motif (1); Mutagenesis (18); Natural variant (4); Nucleotide binding (1); Region (2); Turn (9) |
| Keywords | 3D-structure;ATP-binding;Acetylation;Alternative splicing;Antiviral defense;Cell junction;Cell membrane;Cell projection;Cytoplasm;Cytoskeleton;Disease variant;Helicase;Host-virus interaction;Hydrolase;Immunity;Innate immunity;Isopeptide bond;Membrane;Metal-binding;Nucleotide-binding;Phosphoprotein;RNA-binding;Reference proteome;Repeat;Tight junction;Ubl conjugation;Zinc |
| Interact With | Q9NQC7; O00571; Itself; Q7Z434; Q9NZM5; O75569; P42224; Q14258; Q96S55; Q7Z2W4; Q7Z2W4-2; P04543; Q920D5; P59596; P0DTC9; P21699; P04487; Q6IUF9; Q6IVU5; Q6UY62; Q6UY71; F1BA49; Q9H1Y0; Itself; Q7Z434-1; Q96EQ8; Q86WV6; Q99AU3 |
| Induction | INDUCTION: By bacterial lipopolysaccharides (LPS) in endothelial cells. By interferon (IFN). {ECO:0000269|PubMed:11890704, ECO:0000269|PubMed:15181474, ECO:0000269|PubMed:15208624, ECO:0000269|PubMed:15219805, ECO:0000269|PubMed:15708988}. |
| Subcellular Location | SUBCELLULAR LOCATION: Cytoplasm. Cell projection, ruffle membrane. Cytoplasm, cytoskeleton. Cell junction, tight junction. Note=Colocalized with TRIM25 at cytoplasmic perinuclear bodies. Associated with the actin cytoskeleton at membrane ruffles. |
| Modified Residue | MOD_RES 495; /note=(Microbial infection) Deamidated asparagine; by herpes simplex virus 1/HHV-1 UL37; /evidence=ECO:0000269|PubMed:27866900; MOD_RES 549; /note=(Microbial infection) Deamidated asparagine; by herpes simplex virus 1/HHV-1 UL37; /evidence=ECO:0000269|PubMed:27866900; MOD_RES 770; /note=Phosphothreonine; by CK2; /evidence=ECO:0000269|PubMed:21068236; MOD_RES 854; /note=Phosphoserine; by CK2; /evidence=ECO:0000269|PubMed:21068236; MOD_RES 855; /note=Phosphoserine; by CK2; /evidence=ECO:0000269|PubMed:21068236; MOD_RES 858; /note=N6-acetyllysine; /evidence=ECO:0007744|PubMed:19608861 |
| Post Translational Modification | PTM: Phosphorylated in resting cells and dephosphorylated in RNA virus-infected cells. Phosphorylation at Thr-770, Ser-854 and Ser-855 results in inhibition of its activity while dephosphorylation at these sites results in its activation. {ECO:0000269|PubMed:21068236}.; PTM: Ubiquitinated. 'Lys-63' ubiquitination by RNF135, which occurs after RNA-binding and homodimerization, releases the autoinhibition of the CARD domains by the RLR CTR domain, an essential step in the activation of the RIG-I signaling pathway (PubMed:23950712, PubMed:28469175, PubMed:31006531). Lys-172 is the critical site of ubiquitination for MAVS/IPS1 binding and to induce anti-viral signal transduction (PubMed:17392790, PubMed:30193849). Lys-154, Lys-164 and Lys-172 are shared sites for RNF135-mediated and TRIM4-mediated ubiquitination (PubMed:19017631, PubMed:19484123, PubMed:24755855). Also undergoes 'Lys-48' ubiquitination at Lys-181 by RNF125 that leads to proteasomal degradation (PubMed:17460044, PubMed:26471729). 'Lys-48' ubiquitination follows viral infection and is enhanced by 'Lys-63'-linked ubiquitination of the CARD domains that promotes interaction with VCP/p97 and subsequent recruitment of RNF125 (PubMed:17460044, PubMed:26471729). Within a negative feedback loop involving SIGLEC10 and PTPN11, 'Lys-48' ubiquitination at Lys-812 by CBL also elicits the proteasomal degradation of DDX58 (By similarity). Deubiquitinated by CYLD, a protease that selectively cleaves 'Lys-63'-linked ubiquitin chains (PubMed:18636086). Also probably deubiquitinated by USP17L2/USP17 that cleaves 'Lys-48'- and 'Lys-63'-linked ubiquitin chains and positively regulates the receptor (PubMed:20368735). Ubiquitinated by TRIM40 via 'Lys-48'-linked ubiquitination; leading to proteasomal degradation (PubMed:29117565). Deubiquitinated by USP27X that cleaves 'Lys-63'-linked ubiquitin chains and inhibits the innate immune receptor activity (PubMed:32027733). {ECO:0000250|UniProtKB:Q6Q899, ECO:0000269|PubMed:17392790, ECO:0000269|PubMed:17460044, ECO:0000269|PubMed:18636086, ECO:0000269|PubMed:19017631, ECO:0000269|PubMed:19484123, ECO:0000269|PubMed:20368735, ECO:0000269|PubMed:23950712, ECO:0000269|PubMed:24755855, ECO:0000269|PubMed:26471729, ECO:0000269|PubMed:29117565, ECO:0000269|PubMed:30193849, ECO:0000269|PubMed:31006531, ECO:0000269|PubMed:32027733}.; PTM: ISGylated. Conjugated to ubiquitin-like protein ISG15 upon IFN-beta stimulation. ISGylation negatively regulates its function in antiviral signaling response. {ECO:0000269|PubMed:16009940, ECO:0000269|PubMed:18057259, ECO:0000269|PubMed:20368735}.; PTM: Sumoylated, probably by MUL1; inhibiting its polyubiquitination. {ECO:0000269|PubMed:20368735, ECO:0000269|PubMed:23399697}.; PTM: (Microbial infection) Deamidated on 'Asn-495' and 'Asn-549' by herpes simplex virus 1 protein UL37. These modifications eliminate DDX58 detection of viral RNA and restriction of viral replication. {ECO:0000269|PubMed:27866900}.; PTM: (Microbial infection) Cleaved by the protease 3C of coxsackievirus B3, poliovirus and enterovirus 71 allowing the virus to disrupt the host type I interferon production. {ECO:0000269|PubMed:24390337}. |
| Signal Peptide | |
| Structure 3D | NMR spectroscopy (3); Electron microscopy (2); X-ray crystallography (20) |
| Cross Reference PDB | 2LWD; 2LWE; 2QFB; 2QFD; 2RMJ; 2YKG; 3LRN; 3LRR; 3NCU; 3OG8; 3ZD6; 3ZD7; 4AY2; 4BPB; 4NQK; 4ON9; 4P4H; 5E3H; 5F98; 5F9F; 5F9H; 6GPG; 6KYV; 7JL1; 7JL3; |
| Mapped Pubmed ID | 10421793; 10581243; 11002417; 11717445; 11788588; 12107169; 12133833; 12221085; 12582176; 12692549; 12884866; 14703513; 15361868; 15370293; 15737993; 15767399; 16116171; 16139798; 16177806; 16182584; 16306043; 16306936; 16585524; 16585540; 16618810; 16707574; 16797201; 16846591; 16858409; 16914100; 16946700; 17038589; 17038590; 17053203; 17079289; 17093192; 17182220; 17190786; 17307033; 17327220; 17403696; 17516545; 17526488; 17541283; 17709747; 17878351; 17911629; 17991829; 18021446; 18214119; 18250407; 18258269; 18268020; 18307765; 18428149; 18446221; 18467330; 18550535; 18591409; 18617992; 18632970; 18635538; 18650396; 18684960; 18761323; 18849341; 18948594; 18977754; 18981155; 18984593; 19044019; 19154402; 19164550; 19188362; 19201382; 19234166; 19324880; 19367725; 19374188; 19374189; 19454348; 19454678; 19478455; 19479062; 19574455; 19591957; 19615405; 19620789; 19628239; 19628240; 19666475; 19668221; 19846522; 19859543; 19881509; 19893624; 19902255; 19910467; 19922606; 19948350; 20001730; 20034464; 20042593; 20071582; 20130065; 20144762; 20167631; 20228808; 20331378; 20400512; 20403326; 20406818; 20410276; 20484300; 20492658; 20511549; 20519382; 20581823; 20637642; 20639488; 20805493; 20818395; 20926691; 20961956; 21084468; 21113677; 21187441; 21203974; 21224412; 21245912; 21248047; 21288362; 21292167; 21336305; 21501829; 21632559; 21659521; 21690088; 21691053; 21695051; 21811588; 21835791; 21899695; 21903422; 21910972; 21947008; 21971670; 21978001; 21979817; 22000018; 22000019; 22020100; 22067459; 22114345; 22235281; 22301134; 22328336; 22402283; 22430200; 22504413; 22607805; 22619329; 22623778; 22629479; 22705106; 22776165; 22787226; 22911572; 22912574; 22915805; 22992810; 23015697; 23022350; 23055530; 23056170; 23060457; 23063562; 23118418; 23185463; 23209422; 23262976; 23284052; 23325848; 23333445; 23385459; 23388719; 23390110; 23434273; 23453971; 23498958; 23499489; 23552410; 23592984; 23611287; 23671710; 23744645; 23772026; 23870315; 23897087; 23955621; 24039580; 24131985; 24260525; 24334410; 24360797; 24371060; 24391215; 24399297; 24412064; 24478431; 24478443; 24493797; 24590070; 24604766; 24623417; 24637767; 24692634; 24701034; 24719229; 24722368; 24729608; 24743923; 24763515; 24800889; 24821782; 24850742; 24886842; 24905199; 24918927; 24931123; 24942585; 24949794; 24992168; 25011106; 25056901; 25064677; 25084375; 25142601; 25146252; 25172485; 25288302; 25315416; 25359319; 25490387; 25552708; 25626059; 25658361; 25704008; 25721089; 25736886; 25752576; 25810557; 25833049; 25850761; 25878102; 25880109; 25891073; 25972545; 26093676; 26144659; 26187414; 26215161; 26223644; 26299329; 26311867; 26354181; 26355912; 26371557; 26378160; 26443454; 26446607; 26450567; 26454171; 26485346; 26496610; 26506431; 26518362; 26535695; 26608320; 26609812; 26612866; 26631910; 26725954; 26733676; 26746851; 26829212; 26862753; 26876165; 26992218; 26993858; 26996158; 26998762; 27210312; 27265729; 27267403; 27288441; 27318973; 27376632; 27387525; 27404108; 27425606; 27512060; 27572506; 27629939; 27633794; 27651356; 27707918; 27815826; 27956705; 28057020; 28077651; 28132841; 28148787; 28195391; 28248290; 28250012; 28273895; 28287082; 28377495; 28468914; 28475461; 28481620; 28507028; 28560754; 28594325; 28631605; 28656276; 28659477; 28710430; 28738907; 28768856; 28806404; 28865477; 28892164; 28928438; 28940253; 28948228; 29053956; 29098213; 29180807; 29186193; 29233916; 29235129; 29259080; 29263274; 29321315; 29453856; 29492454; 29496994; 29525183; 29669840; 29688572; 29698627; 29753657; 29949917; 29970461; 29996094; 30047865; 30097581; 30100205; 30177393; 30224800; 30258002; 30258449; 30270105; 30451863; 30558248; 30560918; 30563889; 30602605; 30633820; 30659926; 30804210; 30924966; 30974086; 31043531; 31068071; 31088527; 31139191; 31207307; 31299488; 31335993; 31364528; 31433974; 31575732; 31651197; 31656003; 31800094; 31806368; 31827077; 31843969; 31852354; 31881323; 32015498; 32023470; 32035159; 32092305; 32117232; 32152220; 32311159; 32357908; 32427578; 32471869; 32513696; 32560274; 32719095; 32824946; 32829203; 32878892; 32917214; 32917788; 32946572; 33177158; 33323678; 33360745; 33372174; 33373584; 33412226; 33459340; 33462384; 33486326; 33593967; 33713958; 33783003; 33785613; 33846346; 33849980; 33893074; 33913550; 33976430; 33986530; 34101213; 34170466; 34239945; 34249006; 34379517; 34445801; 34452305; 34487794; 34535668; 34619148; 34772806; 9008162; 9463386; 9689078; |
| Motif | MOTIF 372..375; /note=DECH box |
| Gene Encoded By | |
| Mass | 106,600 |
| Kinetics | |
| Metal Binding | METAL 810; /note=Zinc; /evidence=ECO:0000255|PROSITE-ProRule:PRU01125; METAL 813; /note=Zinc; /evidence=ECO:0000255|PROSITE-ProRule:PRU01125; METAL 864; /note=Zinc; /evidence=ECO:0000255|PROSITE-ProRule:PRU01125; METAL 869; /note=Zinc; /evidence=ECO:0000255|PROSITE-ProRule:PRU01125 |
| Rhea ID | RHEA:13065 |
| Cross Reference Brenda | 3.6.4.13; |