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Conserved domains on  [gi|1540347164|pdb|6DX3|A]
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Chain A, RNA-dependent RNA polymerase

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
OTU_RNAP_L_virus cd21880
OTU (ovarian tumor) domain of viral RNA-directed RNA polymerase L; RNA-directed RNA polymerase ...
 8-157 3.46e-59

OTU (ovarian tumor) domain of viral RNA-directed RNA polymerase L; RNA-directed RNA polymerase L is also called protein L, large structural protein, replicase, transcriptase, or ubiquitin thioesterase. It displays RNA-directed RNA polymerase (EC 2.7.7.48), deubiquitinase (DUB)/ubiquitin thiolesterase (EC 3.4.19.12), and deISGylating activities. It is a viral homolog of ovarian tumor protease (vOTU) that has been implicated in the downregulation of type I interferon immune response by removing post-translational modifying proteins ubiquitin (Ub) and the Ub-like interferon-simulated gene 15 (ISG15) from host cellular proteins. The attachment of Ub and ISG15 to cellular proteins mediates important innate antiviral responses, and their removal inhibits these antiviral pathways. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


:

Pssm-ID: 438580  Cd Length: 148  Bit Score: 181.26  E-value: 3.46e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6DX3_A        8 DWHLLLNGYYYSPVDLEVEDIFEIVNQPMDGNCLYHSLACGMIEEqqPDSYKLIKEQVREAAGLFWDTTEETKTTGEDLN 87
Cdd:cd21880   1 VWEEVGEGQYVSNPRFNLRDYFEIERVPGDGNCFFRSIAELLFDT--EDEWRLVKNTIESYARANWDECPEARLYYLSLE 78

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6DX3_A       88 GYLARIMKPNEWGSSLEVNFFSQKAKVTVYIWHEDASKHCDYVVRYGEDPMLESINIMHRRNHYDYLKPR 157
Cdd:cd21880  79 EYLRDAMKDGYWGGSLEAEILSKALGITIIIWVVDDSDWVTAAVRFGDGDVSTSLNLLHSGGHFDALRLK 148
 
Name Accession Description Interval E-value
OTU_RNAP_L_virus cd21880
OTU (ovarian tumor) domain of viral RNA-directed RNA polymerase L; RNA-directed RNA polymerase ...
 8-157 3.46e-59

OTU (ovarian tumor) domain of viral RNA-directed RNA polymerase L; RNA-directed RNA polymerase L is also called protein L, large structural protein, replicase, transcriptase, or ubiquitin thioesterase. It displays RNA-directed RNA polymerase (EC 2.7.7.48), deubiquitinase (DUB)/ubiquitin thiolesterase (EC 3.4.19.12), and deISGylating activities. It is a viral homolog of ovarian tumor protease (vOTU) that has been implicated in the downregulation of type I interferon immune response by removing post-translational modifying proteins ubiquitin (Ub) and the Ub-like interferon-simulated gene 15 (ISG15) from host cellular proteins. The attachment of Ub and ISG15 to cellular proteins mediates important innate antiviral responses, and their removal inhibits these antiviral pathways. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438580  Cd Length: 148  Bit Score: 181.26  E-value: 3.46e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6DX3_A        8 DWHLLLNGYYYSPVDLEVEDIFEIVNQPMDGNCLYHSLACGMIEEqqPDSYKLIKEQVREAAGLFWDTTEETKTTGEDLN 87
Cdd:cd21880   1 VWEEVGEGQYVSNPRFNLRDYFEIERVPGDGNCFFRSIAELLFDT--EDEWRLVKNTIESYARANWDECPEARLYYLSLE 78

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6DX3_A       88 GYLARIMKPNEWGSSLEVNFFSQKAKVTVYIWHEDASKHCDYVVRYGEDPMLESINIMHRRNHYDYLKPR 157
Cdd:cd21880  79 EYLRDAMKDGYWGGSLEAEILSKALGITIIIWVVDDSDWVTAAVRFGDGDVSTSLNLLHSGGHFDALRLK 148
 
Name Accession Description Interval E-value
OTU_RNAP_L_virus cd21880
OTU (ovarian tumor) domain of viral RNA-directed RNA polymerase L; RNA-directed RNA polymerase ...
 8-157 3.46e-59

OTU (ovarian tumor) domain of viral RNA-directed RNA polymerase L; RNA-directed RNA polymerase L is also called protein L, large structural protein, replicase, transcriptase, or ubiquitin thioesterase. It displays RNA-directed RNA polymerase (EC 2.7.7.48), deubiquitinase (DUB)/ubiquitin thiolesterase (EC 3.4.19.12), and deISGylating activities. It is a viral homolog of ovarian tumor protease (vOTU) that has been implicated in the downregulation of type I interferon immune response by removing post-translational modifying proteins ubiquitin (Ub) and the Ub-like interferon-simulated gene 15 (ISG15) from host cellular proteins. The attachment of Ub and ISG15 to cellular proteins mediates important innate antiviral responses, and their removal inhibits these antiviral pathways. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438580  Cd Length: 148  Bit Score: 181.26  E-value: 3.46e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6DX3_A        8 DWHLLLNGYYYSPVDLEVEDIFEIVNQPMDGNCLYHSLACGMIEEqqPDSYKLIKEQVREAAGLFWDTTEETKTTGEDLN 87
Cdd:cd21880   1 VWEEVGEGQYVSNPRFNLRDYFEIERVPGDGNCFFRSIAELLFDT--EDEWRLVKNTIESYARANWDECPEARLYYLSLE 78

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6DX3_A       88 GYLARIMKPNEWGSSLEVNFFSQKAKVTVYIWHEDASKHCDYVVRYGEDPMLESINIMHRRNHYDYLKPR 157
Cdd:cd21880  79 EYLRDAMKDGYWGGSLEAEILSKALGITIIIWVVDDSDWVTAAVRFGDGDVSTSLNLLHSGGHFDALRLK 148
OTU cd22744
OTU (ovarian tumor) domain family; The OTU family of cysteine proteases use a conserved ...
 30-154 8.69e-16

OTU (ovarian tumor) domain family; The OTU family of cysteine proteases use a conserved cysteine and histidine, and in most cases an aspartate, as the catalytic triad. OTU domains typically function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation.


Pssm-ID: 438581 [Multi-domain]  Cd Length: 128  Bit Score: 69.77  E-value: 8.69e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6DX3_A       30 EIVNQPMDGNCLYHSLACGMIEEQqpDSYKLIKEQV----REAAGLFWDTTEETKTTGEDLNGYLARIMKPNEWGSSLEV 105
Cdd:cd22744   1 RVVDVPGDGNCLFRALAHALYGDQ--ESHRELRQEVvdylRENPDLYEPAELADEDDGEDFDEYLQRMRKPGTWGGELEL 78

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
6DX3_A      106 NFFSQKAKVTVYIWHEDASKHCDYVVRYGEDPMLESINIMHR-RNHYDYL 154
Cdd:cd22744  79 QALANALNVPIVVYSEDGGFLPVSVFGPGPGPSGRPIHLLYTgGNHYDAL 128
OTU_232R-like cd22758
OTU (ovarian tumor) domain of Invertebrate iridescent virus putative ubiquitin thioesterase ...
 29-151 7.87e-08

OTU (ovarian tumor) domain of Invertebrate iridescent virus putative ubiquitin thioesterase 232R and similar proteins; This subfamily contains putative ubiquitin thioesterases 232R from Invertebrate iridescent virus and L96 from Tipula iridescent virus (TIV), Dictyostelium discoideum OTU domain-containing protein DDB_G0284757, and similar proteins. L96 may be involved in TIV genomic DNA packaging in a manner related to the Gag polyproteins of the mammalian viruses. Proteins in this subfamily contain an OTU domain. OTU domains typically function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438595 [Multi-domain]  Cd Length: 135  Bit Score: 48.80  E-value: 7.87e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6DX3_A       29 FEIVNQPMDGNCLYHSLACGMIEEQQPDSYKLIKEQV----REAAGLFWDTTEETKTTGEDLNGYLARIMKPNEWGSSLE 104
Cdd:cd22758   6 FEIRDVPGDGNCFFHAVSDQLYGNGIEHSHKELRQQAvnylRENPELYDGFFLSEFDEEESWEEYLNRMSKDGTWGDHII 85

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
6DX3_A      105 VNFFSQKAKVTVYIWHEDASkHCDYVVRYGEDPMLESINIMH-RRNHY 151
Cdd:cd22758  86 LQAAANLFNVRIVIISSDGS-DETTIIEPGNSKNGRTIYLGHiGENHY 132
OTU_RDRP-like cd22792
OTU (ovarian tumor) domain of the potexviruses/carlaviruses RNA replication protein family; ...
 35-157 7.15e-07

OTU (ovarian tumor) domain of the potexviruses/carlaviruses RNA replication protein family; RNA replication polyprotein (RDRP) is a viral homolog of ovarian tumor protease (vOTU), which displays RNA helicase (EC 3.6.4.13), RNA-directed RNA polymerase (EC 2.7.7.48), viral methyltransferase, Fe(2+) 2-oxoglutarate dioxygenase and protease activities. The central part of this protein possibly functions as an ATP-binding helicase. It is an RNA-directed RNA polymerase involved in viral RNA replication. It also acts as a thiol protease that cleaves the polyprotein. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438613 [Multi-domain]  Cd Length: 108  Bit Score: 45.68  E-value: 7.15e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6DX3_A       35 PMDGNCLYHSLAC--GMieeqqpdSYKLIKEQVREAAglfwdtteetkTTGEDLNGYLARIMKPNEWGSSLEVNFFSQKA 112
Cdd:cd22792   6 PGDGNCFWHSLGHflGL-------SALELKKLLRDSL-----------FDDPELDEELDEQLEPGVYAEDEAIAAAAKLF 67

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
6DX3_A      113 KVTVYIWHEDASKhcdyVVRYGEDPMLESINIMHRRNHYDYLKPR 157
Cdd:cd22792  68 GVNICVHDPDEGV----LYTFTPNESSKSIHLLLENEHFEPLVPK 108
OTU_OTUD3-like cd22756
OTU (ovarian tumor) domain of OTU domain-containing protein 3 and similar proteins; This ...
 37-137 9.51e-06

OTU (ovarian tumor) domain of OTU domain-containing protein 3 and similar proteins; This subfamily includes bilaterial OTU domain-containing protein 3 (OTUD3), Arabidopsis thaliana deubiquitinating enzyme OTU7, also called OTU domain-containing protein 7, and similar proteins. OTUD3 is a deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that hydrolyzes 'Lys-6'- and 'Lys-11'-linked polyubiquitin. It is an acetylation-dependent deubiquitinase that restricts innate antiviral immune signaling. It directly hydrolyzes lysine 63 (Lys63)-linked polyubiquitination of MAVS (mitochondrial antiviral-signaling protein) and shuts off innate antiviral immune response. OTUD3 can elicit tumor-suppressing or tumor-promoting activities in a cell- and tissue-dependent manner. It is a DUB for PTEN (phosphatase and tension homologue deleted on chromosome 10); the OTUD3-PTEN signaling axis plays a critical role in suppression of breast tumorigenesis. OTUD3 is also a DUB for glucose-regulated protein GRP78, stabilizing it and promoting lung tumorigenesis. OTU7 is a DUB that shows a preference for 'Lys-63' over 'Lys-48' over 'Met-1'-linked ubiquitin (UB) tetramers as substrates. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438593 [Multi-domain]  Cd Length: 131  Bit Score: 42.93  E-value: 9.51e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6DX3_A       37 DGNCLYHSLAcgmieEQ---QPDSYKLIKEQV----REAAGLFWDTTEETKTTGED--LNGYLARIMKPNEWGSSLEVNF 107
Cdd:cd22756   8 DGNCLFRALS-----DQlygDPDRHLEIRAEVveymRANPDDFKPFSEAATFAEDDeaFEDYLARMAKDGTYGDNLEIVA 82

                        90       100       110
                ....*....|....*....|....*....|
6DX3_A      108 FSQKAKVTVYIWHEDASkhcdYVVRYGEDP 137
Cdd:cd22756  83 FARAYNVDVKVYQPDPV----YVISAPEDG 108
OTU_plant_OTU3-like cd22759
OTU (ovarian tumor) domain of deubiquitinating enzyme OTU3 from plants and similar proteins; ...
 37-154 4.27e-04

OTU (ovarian tumor) domain of deubiquitinating enzyme OTU3 from plants and similar proteins; Deubiquitinating enzyme OTU3, also called OTU domain-containing protein 3, is a deubiquitinase (DUB) or ubiquitin thiolesterase (EC 3.4.19.12) that catalyzes the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. OTU3 may play an important regulatory role at the level of protein turnover by preventing degradation. OTU3 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438596  Cd Length: 159  Bit Score: 38.86  E-value: 4.27e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6DX3_A       37 DGNCLYHSLACGMI-----------EEQQPDSYKL-IKEQV-REAAGLFWDTTEETKTTGED-LNGYLARIMKPNEWGSS 102
Cdd:cd22759  11 DGRCMFRALVKGLAankgiflsgreEEQEADELRLaVAEALcRSEERRRDYEEALIAITVEGsLDRYCRRIQRPDFWGGE 90

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
6DX3_A      103 LEVNFFSQ--KAKVTVYI---WHEDASKHCDYV--VRYGEDPMLESINIMHRR---------NHYDYL 154
Cdd:cd22759  91 SELLVLSKmlKQPIIVYIpesEAKNGGWGSGFIpiQKYGEEFAKGTKGRKGRKpvrllysgsNHYDLL 158
OTU_plant_OTU3_4-like cd22746
OTU (ovarian tumor) domain of deubiquitinating enzymes OTU3 and OTU4 from plants, and similar ...
 85-154 2.74e-03

OTU (ovarian tumor) domain of deubiquitinating enzymes OTU3 and OTU4 from plants, and similar proteins; Deubiquitinating enzyme OTU3 (also called OTU domain-containing protein 3) and deubiquitinating enzyme OTU4 (also called OTU domain-containing protein 4) are deubiquitinases (DUBs) or ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. OTU3 and OTU4 may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438583 [Multi-domain]  Cd Length: 141  Bit Score: 36.48  E-value: 2.74e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
6DX3_A       85 DLNGYLARIMKPNEWGSSLEVNFFSQ--KAKVTVYIWHEDAS--KHcdyVVRYGED-PMLESINIM-HRRNHYDYL 154
Cdd:cd22746  68 DFDAYCQRMSHPDTWGGEPELLMLADvlQRPIAVYLPTPGKGglRK---IQEYGEEyLGGEPIRLLyNGGNHYDLL 140
OTU_plant_OTU4-like cd22760
OTU (ovarian tumor) domain of deubiquitinating enzyme OTU4 from plants and similar proteins; ...
 29-154 4.86e-03

OTU (ovarian tumor) domain of deubiquitinating enzyme OTU4 from plants and similar proteins; Deubiquitinating enzyme OTU4, also called OTU domain-containing protein 4, is a deubiquitinase (DUB) or ubiquitin thiolesterase (EC 3.4.19.12) that catalyzes the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. OTU4 may play an important regulatory role at the level of protein turnover by preventing degradation. OTU4 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad.


Pssm-ID: 438597 [Multi-domain]  Cd Length: 138  Bit Score: 35.43  E-value: 4.86e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6DX3_A       29 FEIVNQPMDGNCLYHSLACGM------------IEEQQPDSY--KLIKEQVREAAGLFWdtteetkTTGEDLNGYLARIM 94
Cdd:cd22760   2 YRVHGIAGDGRCLFRAVAHGEclargkaapdeeRERELADELrtRAADELVKRREETEW-------FIEGDFDEYVARMR 74

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....
6DX3_A       95 KPNEWGSSLEVNFFSQ--KAKVTVYIwHEDASKHCDYVVRYGED-PMLESINIM-HRRNHYDYL 154
Cdd:cd22760  75 RPGVWGGEPELLMLSHvlQRPITVYM-ADEGEGGLISIAEYGQEyGKGNPIRVLfHGFGHYEAL 137
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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