ID POLR_TYMV Reviewed; 1844 AA. AC P10358; DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot. DT 01-AUG-1992, sequence version 2. DT 13-SEP-2023, entry version 121. DE RecName: Full=RNA replicase polyprotein; DE AltName: Full=206 kDa polyprotein; DE AltName: Full=206K; DE Contains: DE RecName: Full=Methyltransferase/Protease/Ubiquitinyl hydrolase; DE EC=2.1.1.-; DE EC=3.4.19.12 {ECO:0000269|PubMed:22117220, ECO:0000269|PubMed:23345508, ECO:0000269|PubMed:23966860}; DE EC=3.4.22.-; DE AltName: Full=98 kDa protein; DE AltName: Full=MET/PRO; DE Contains: DE RecName: Full=Putative helicase; DE EC=3.6.4.-; DE AltName: Full=42 kDa protein; DE AltName: Full=HEL; DE Contains: DE RecName: Full=RNA-directed RNA polymerase; DE EC=2.7.7.48; DE AltName: Full=66 kDa protein; DE AltName: Full=POL; OS Turnip yellow mosaic virus. OC Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Alsuviricetes; OC Tymovirales; Tymoviridae; Tymovirus; Tymovirus brassicae. OX NCBI_TaxID=12154; OH NCBI_TaxID=3705; Brassica. OH NCBI_TaxID=51351; Brassica rapa subsp. pekinensis (Chinese cabbage) (Brassica pekinensis). OH NCBI_TaxID=82359; Cardamine lilacina. RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC RNA]. RX PubMed=3399388; DOI=10.1093/nar/16.13.6157; RA Morch M.D., Boyer J.C., Haenni A.L.; RT "Overlapping open reading frames revealed by complete nucleotide sequencing RT of turnip yellow mosaic virus genomic RNA."; RL Nucleic Acids Res. 16:6157-6173(1988). RN [2] RP SUBCELLULAR LOCATION (RNA-DIRECTED RNA POLYMERASE). RX PubMed=11222099; DOI=10.1006/viro.2000.0769; RA Prod'homme D., Le Panse S., Drugeon G., Jupin I.; RT "Detection and subcellular localization of the turnip yellow mosaic virus RT 66K replication protein in infected cells."; RL Virology 281:88-101(2001). RN [3] RP PROTEOLYTIC CLEAVAGE (RNA REPLICASE POLYPROTEIN), AND SUBCELLULAR LOCATION. RX PubMed=17686855; DOI=10.1128/jvi.01428-07; RA Jakubiec A., Drugeon G., Camborde L., Jupin I.; RT "Proteolytic processing of turnip yellow mosaic virus replication proteins RT and functional impact on infectivity."; RL J. Virol. 81:11402-11412(2007). RN [4] RP FUNCTION (METHYLTRANSFERASE/PROTEASE/UBIQUITINYL HYDROLASE), AND CATALYTIC RP ACTIVITY (METHYLTRANSFERASE/PROTEASE/UBIQUITINYL HYDROLASE). RX PubMed=22117220; DOI=10.1038/emboj.2011.424; RA Chenon M., Camborde L., Cheminant S., Jupin I.; RT "A viral deubiquitylating enzyme targets viral RNA-dependent RNA polymerase RT and affects viral infectivity."; RL EMBO J. 31:741-753(2012). RN [5] RP CATALYTIC ACTIVITY (METHYLTRANSFERASE/PROTEASE/UBIQUITINYL HYDROLASE), RP FUNCTION (METHYLTRANSFERASE/PROTEASE/UBIQUITINYL HYDROLASE), RP BIOPHYSICOCHEMICAL PROPERTIES (METHYLTRANSFERASE/PROTEASE/UBIQUITINYL RP HYDROLASE), AND MUTAGENESIS OF GLU-10; SER-101 AND THR-128. RX PubMed=23345508; DOI=10.1128/jvi.03252-12; RA Capodagli G.C., Deaton M.K., Baker E.A., Lumpkin R.J., Pegan S.D.; RT "Diversity of ubiquitin and ISG15 specificity among nairoviruses' viral RT ovarian tumor domain proteases."; RL J. Virol. 87:3815-3827(2013). RN [6] {ECO:0007744|PDB:4A5U} RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 728-879, FUNCTION RP (METHYLTRANSFERASE/PROTEASE/UBIQUITINYL HYDROLASE), ACTIVE SITE RP (METHYLTRANSFERASE/PROTEASE/UBIQUITINYL HYDROLASE), AND CATALYTIC ACTIVITY RP (METHYLTRANSFERASE/PROTEASE/UBIQUITINYL HYDROLASE). RX PubMed=23966860; DOI=10.1371/journal.ppat.1003560; RA Lombardi C., Ayach M., Beaurepaire L., Chenon M., Andreani J., Guerois R., RA Jupin I., Bressanelli S.; RT "A compact viral processing proteinase/ubiquitin hydrolase from the OTU RT family."; RL PLoS Pathog. 9:e1003560-e1003560(2013). RN [7] {ECO:0007744|PDB:5LW5, ECO:0007744|PDB:5LWA} RP X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF 728-874, ACTIVE SITE RP (METHYLTRANSFERASE/PROTEASE/UBIQUITINYL HYDROLASE), MUTAGENESIS OF ASP-843; RP ILE-847; GLY-865 AND 866-PRO-PRO-867, DOMAIN RP (METHYLTRANSFERASE/PROTEASE/UBIQUITINYL HYDROLASE), AND FUNCTION RP (METHYLTRANSFERASE/PROTEASE/UBIQUITINYL HYDROLASE). RX PubMed=29117247; DOI=10.1371/journal.ppat.1006714; RA Jupin I., Ayach M., Jomat L., Fieulaine S., Bressanelli S.; RT "A mobile loop near the active site acts as a switch between the dual RT activities of a viral protease/deubiquitinase."; RL PLoS Pathog. 13:e1006714-e1006714(2017). RN [8] {ECO:0007744|PDB:6YPT} RP X-RAY CRYSTALLOGRAPHY (3.66 ANGSTROMS) OF 728-879 IN COMPLEX WITH RP UBIQUITIN, AND FUNCTION (METHYLTRANSFERASE/PROTEASE/UBIQUITINYL HYDROLASE). RX PubMed=32732284; DOI=10.1074/jbc.ra120.014628; RA Fieulaine S., Witte M.D., Theile C.S., Ayach M., Ploegh H.L., Jupin I., RA Bressanelli S.; RT "Turnip yellow mosaic virus protease binds ubiquitin suboptimally to fine- RT tune its deubiquitinase activity."; RL J. Biol. Chem. 295:13769-13783(2020). CC -!- FUNCTION: Acts as a cysteine protease, methyltransferase and CC deubiquitinase (PubMed:22117220, PubMed:23966860, PubMed:29117247, CC PubMed:32732284) (Probable). The cysteine protease activity cleaves the CC polyprotein giving rise to mature proteins (PubMed:23966860). The CC methyltransferase domain is probably involved in viral RNA capping CC (Probable). The deubiquitylating activity counteracts the degradation CC of the viral polymerase mediated by the host ubiquitin-proteasome CC system (PubMed:22117220). The polymerase is thus stabilized and CC infectivity is increased (PubMed:22117220). Favors K63 poly-Ub linkage CC (PubMed:23345508). {ECO:0000269|PubMed:22117220, CC ECO:0000269|PubMed:23345508, ECO:0000269|PubMed:23966860, CC ECO:0000269|PubMed:29117247, ECO:0000269|PubMed:32732284, ECO:0000305, CC ECO:0000305|PubMed:23345508}. CC -!- FUNCTION: RNA-directed RNA polymerase is responsible for the CC replication and transcription of the genome. {ECO:0000255|PROSITE- CC ProRule:PRU00539, ECO:0000269|PubMed:22117220}. CC -!- CATALYTIC ACTIVITY: CC Reaction=Thiol-dependent hydrolysis of ester, thioester, amide, peptide CC and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76- CC residue protein attached to proteins as an intracellular targeting CC signal).; EC=3.4.19.12; Evidence={ECO:0000269|PubMed:22117220, CC ECO:0000269|PubMed:23345508}; CC -!- CATALYTIC ACTIVITY: CC Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + CC RNA(n+1); Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:14527, Rhea:RHEA- CC COMP:17342, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557, ChEBI:CHEBI:140395; CC EC=2.7.7.48; Evidence={ECO:0000255|PROSITE-ProRule:PRU00539}; CC -!- BIOPHYSICOCHEMICAL PROPERTIES: CC Kinetic parameters: CC KM=70.2 uM for Ub-AMC {ECO:0000269|PubMed:23345508}; CC -!- SUBUNIT: Interacts with host ubiquitin. {ECO:0000269|PubMed:32732284}. CC -!- SUBCELLULAR LOCATION: [Methyltransferase/Protease/Ubiquitinyl CC hydrolase]: Host chloroplast envelope. CC -!- SUBCELLULAR LOCATION: [Putative helicase]: Host chloroplast envelope. CC -!- SUBCELLULAR LOCATION: [RNA-directed RNA polymerase]: Host chloroplast CC envelope {ECO:0000269|PubMed:11222099}. CC -!- DOMAIN: [Methyltransferase/Protease/Ubiquitinyl hydrolase]: The viral CC OTU domain (vOTU) is responsible for the deubiquitination activity CC (PubMed:23345508). Both protease (PRO) and deubiquitination (DUB) CC activities rely on the single catalytic site of the cysteine proteinase CC (PubMed:29117247). The switch in the PRO/DUB activities is due to the CC mobility of a GPP flap (PubMed:29117247). {ECO:0000269|PubMed:23345508, CC ECO:0000269|PubMed:29117247}. CC -!- MISCELLANEOUS: The deubiquitinase activity is low compared to that of CC Bunyaviruses or coronaviruses. {ECO:0000269|PubMed:22117220, CC ECO:0000269|PubMed:23345508, ECO:0000269|PubMed:23966860}. CC -!- SIMILARITY: Belongs to the tymovirus NS35 RNA replicase polyprotein CC family. {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; X07441; CAA30322.1; ALT_SEQ; Genomic_RNA. DR PIR; S01956; S01956. DR RefSeq; NP_663297.1; NC_004063.1. DR PDB; 4A5U; X-ray; 2.00 A; A=728-879. DR PDB; 5LW5; X-ray; 1.65 A; A/B=728-874. DR PDB; 5LWA; X-ray; 1.65 A; A/B=728-879. DR PDB; 6YPT; X-ray; 3.66 A; A/C=728-879. DR PDBsum; 4A5U; -. DR PDBsum; 5LW5; -. DR PDBsum; 5LWA; -. DR PDBsum; 6YPT; -. DR SMR; P10358; -. DR MEROPS; C21.001; -. DR GeneID; 951158; -. DR KEGG; vg:951158; -. DR Proteomes; UP000000401; Genome. DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW. DR GO; GO:0004197; F:cysteine-type endopeptidase activity; IEA:InterPro. DR GO; GO:0008174; F:mRNA methyltransferase activity; IEA:InterPro. DR GO; GO:0003723; F:RNA binding; IEA:InterPro. DR GO; GO:0003968; F:RNA-dependent RNA polymerase activity; IEA:UniProtKB-KW. DR GO; GO:0006351; P:DNA-templated transcription; IEA:InterPro. DR GO; GO:0039648; P:modulation by symbiont of host protein ubiquitination; IEA:UniProtKB-KW. DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW. DR GO; GO:0006396; P:RNA processing; IEA:InterPro. DR GO; GO:0039694; P:viral RNA genome replication; IEA:InterPro. DR CDD; cd23247; Tymoviridae_RdRp; 1. DR Gene3D; 3.90.70.100; -; 1. DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1. DR InterPro; IPR027351; (+)RNA_virus_helicase_core_dom. DR InterPro; IPR002588; Alphavirus-like_MT_dom. DR InterPro; IPR043502; DNA/RNA_pol_sf. DR InterPro; IPR027417; P-loop_NTPase. DR InterPro; IPR008043; Peptidase_C21. DR InterPro; IPR001788; RNA-dep_RNA_pol_alsuvir. DR InterPro; IPR007094; RNA-dir_pol_PSvirus. DR InterPro; IPR043629; Salyut_dom. DR InterPro; IPR043181; TYMV_endopept_dom. DR Pfam; PF05381; Peptidase_C21; 1. DR Pfam; PF00978; RdRP_2; 1. DR Pfam; PF19227; Salyut; 1. DR Pfam; PF01443; Viral_helicase1; 1. DR Pfam; PF01660; Vmethyltransf; 1. DR SUPFAM; SSF56672; DNA/RNA polymerases; 1. DR PROSITE; PS51743; ALPHAVIRUS_MT; 1. DR PROSITE; PS51738; PEPTIDASE_C21; 1. DR PROSITE; PS51657; PSRV_HELICASE; 1. DR PROSITE; PS50507; RDRP_SSRNA_POS; 1. PE 1: Evidence at protein level; KW 3D-structure; ATP-binding; Host-virus interaction; Hydrolase; KW Methyltransferase; KW Modulation of host ubiquitin pathway by viral deubiquitinase; KW Modulation of host ubiquitin pathway by virus; Multifunctional enzyme; KW Nucleotide-binding; Nucleotidyltransferase; Protease; Reference proteome; KW RNA-directed RNA polymerase; Thiol protease; Transferase; KW Viral RNA replication. FT CHAIN 1..1844 FT /note="RNA replicase polyprotein" FT /id="PRO_0000222938" FT CHAIN 1..879 FT /note="Methyltransferase/Protease/Ubiquitinyl hydrolase" FT /id="PRO_0000418048" FT CHAIN 880..1259 FT /note="Putative helicase" FT /id="PRO_0000418049" FT CHAIN 1260..1844 FT /note="RNA-directed RNA polymerase" FT /id="PRO_0000418050" FT DOMAIN 58..219 FT /note="Alphavirus-like MT" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01079" FT DOMAIN 728..879 FT /note="OTU" FT /evidence="ECO:0000269|PubMed:23345508" FT DOMAIN 730..884 FT /note="Peptidase C21" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01074" FT DOMAIN 946..1103 FT /note="(+)RNA virus helicase ATP-binding" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00990" FT DOMAIN 1104..1236 FT /note="(+)RNA virus helicase C-terminal" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00990" FT DOMAIN 1572..1678 FT /note="RdRp catalytic" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00539" FT REGION 571..739 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 859..887 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT MOTIF 865..867 FT /note="GPP flap" FT /evidence="ECO:0000269|PubMed:29117247" FT COMPBIAS 571..587 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 598..623 FT /note="Pro residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 624..644 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 673..698 FT /note="Pro residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT ACT_SITE 783 FT /note="For protease activity" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01074, FT ECO:0000269|PubMed:23966860, ECO:0000269|PubMed:29117247" FT ACT_SITE 869 FT /note="For protease activity" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01074, FT ECO:0000269|PubMed:23966860, ECO:0000269|PubMed:29117247" FT BINDING 976..983 FT /ligand="ATP" FT /ligand_id="ChEBI:CHEBI:30616" FT /evidence="ECO:0000250" FT SITE 879..880 FT /note="Cleavage; by viral protease" FT /evidence="ECO:0000269|PubMed:17686855" FT SITE 1259..1260 FT /note="Cleavage; by viral protease" FT /evidence="ECO:0000269|PubMed:17686855" FT MUTAGEN 843 FT /note="D->A: 70% loss of deubiquitinase activity." FT /evidence="ECO:0000269|PubMed:29117247" FT MUTAGEN 847 FT /note="I->A: 80% loss of deubiquitinase activity." FT /evidence="ECO:0000269|PubMed:29117247" FT MUTAGEN 847 FT /note="I->D: Almost complete loss of deubiquitinase FT activity." FT /evidence="ECO:0000269|PubMed:29117247" FT MUTAGEN 865 FT /note="G->A: 70% loss of deubiquitinase activity." FT /evidence="ECO:0000269|PubMed:29117247" FT MUTAGEN 866..867 FT /note="PP->GG: Almost complete loss of deubiquitinase FT activity." FT /evidence="ECO:0000269|PubMed:29117247" FT HELIX 734..737 FT /evidence="ECO:0007829|PDB:5LW5" FT STRAND 742..748 FT /evidence="ECO:0007829|PDB:5LW5" FT HELIX 749..752 FT /evidence="ECO:0007829|PDB:5LW5" FT STRAND 765..769 FT /evidence="ECO:0007829|PDB:5LW5" FT HELIX 783..792 FT /evidence="ECO:0007829|PDB:5LW5" FT HELIX 796..804 FT /evidence="ECO:0007829|PDB:5LW5" FT HELIX 809..811 FT /evidence="ECO:0007829|PDB:5LW5" FT HELIX 815..820 FT /evidence="ECO:0007829|PDB:5LW5" FT HELIX 824..833 FT /evidence="ECO:0007829|PDB:5LW5" FT STRAND 836..842 FT /evidence="ECO:0007829|PDB:5LW5" FT STRAND 845..850 FT /evidence="ECO:0007829|PDB:5LW5" FT STRAND 855..863 FT /evidence="ECO:0007829|PDB:5LW5" FT STRAND 865..867 FT /evidence="ECO:0007829|PDB:5LW5" FT STRAND 869..872 FT /evidence="ECO:0007829|PDB:5LW5" SQ SEQUENCE 1844 AA; 206641 MW; A016D758C83D128C CRC64; MAFQLALDAL APTTHRDPSL HPILESTVDS IRSSIQTYPW SIPKELLPLL NSYGIPTSGL GTSHHPHAAH KTIETFLLCT HWSFQATTPS SVMFMKPSKF NKLAQVNSNF RELKNYRLHP NDSTRYPFTS PDLPVFPTIF MHDALMYYHP SQIMDLFLRK PNLERLYASL VVPPEAHLSD QSFYPKLYTY TTTRHTLHYV PEGHEAGSYN QPSDAHSWLR INSIRLGNHH LSVTILESWG PVHSLLIQRG TPPPDPSLQA PPTLMTSDLF RSYQEPRLDV VSFRIPDAIE LPQATFLQQP LRDRLVPRAV YNALFTYTRA VRTLRTSDPA AFVRMHSSKP DHDWVTSNAW DNLQTFALLN VPLRPNVVYH VLQSPIASLS LYLRQHWRRL TATAVPILSF LTLLQRFLPL PIPLAEVKSI TAFRRELYRK KEPHHPLDVF HLQHRVRNYH SAISAVRPAS PPHQKLPHAL QKAALLLLRP ISPLLTATPF FRSEQKSMLP NAELSWTLKR FALPWQASLV LLALSESSIL LHKLFSPPTL QAQHDTYHRH LHPGSYSLQW ERTPLSIPRT TAFLPFTPTT STAPPDRSEA SLPPAFASTF VPRPPPAASS PGAQPPTTTA APPTPIEPTQ RTHQNSDLAL ESSTSTEPPP PPIRSPDMTP SAPVLFPEIN SPRRFPPQLP ATPDLEPAHT PPPLSIPHQD PTDSADPLMG SHLLHHSLPA PPTHPLPSSQ LLPAPLTNDP TAIGPVLPFE ELHPRRYPEN TATFLTRLRS LPSNHLPQPT LNCLLSAVSD QTKVSEEHLW ESLQTILPDS QLSNEETNTL GLSTEHLTAL AHLYNFQATV YSDRGPILFG PSDTIKRIDI THTTGPPSHF SPGKRLLGSQ PSAKGHPSDP LIRAMKSFKV SGNYLPFSEA HNHPTSISHA KNLISNMKNG FDGVLSLLDV STGQRTGPTP KERIIQIDHY LDTNPGKTTP VVHFAGFAGC GKTYPIQQLL KTKLFKDFRV SCPTTELRTE WKTAMELHGS QSWRFNTWES SILKSSRILV IDEIYKMPRG YLDLSILADP ALELVIILGD PLQGEYHSQS KDSSNHRLPS ETLRLLPYID MYCWWSYRIP QCIARLFQIH SFNAWQGVIG SVSTPHDQSP VLTNSHASSL TFNSLGYRSC TISSSQGLTF CDPAIIVLDN YTKWLSSANG LVALTRSRSG VQFMGPSSYV GGTNGSSAMF SDAFNNSLII MDRYFPSLFP QLKLITSPLT TRGPKLNGAT PSASPTHRSP NFHLPPHIPL SYDRDFVTVN PTLPDQGPET RLDTHFLPPS RLPLHFDLPP AITPPPVSTS VDPPQAKASP VYPGEFFDSL AAFFLPAHDP STREILHKDQ SSNQFPWFDR PFSLSCQPSS LISAKHAPNH DPTLLPASIN KRLRFRPSDS PHQITADDVV LGLQLFHSLC RAYSRQPNST VPFNPELFAE CISLNEYAQL SSKTQSTIVA NASRSDPDWR HTTVKIFAKA QHKVNDGSIF GSWKACQTLA LMHDYVILVL GPVKKYQRIF DNADRPPNIY SHCGKTPNQL RDWCQEHLTH STPKIANDYT AFDQSQHGES VVLEALKMKR LNIPSHLIQL HVHLKTNVST QFGPLTCMRL TGEPGTYDDN TDYNLAVIYS QYDVGSCPIM VSGDDSLIDH PLPTRHDWPS VLKRLHLRFK LELTSHPLFC GYYVGPAGCI RNPLALFCKL MIAVDDDALD DRRLSYLTEF TTGHLLGESL WHLLPETHVQ YQSACFDFFC RRCPRHEKML LDDSTPALSL LERITSSPRW LTKNAMYLLP AKLRLAITSL SQTQSFPESI EVSHAESELL HYVQ //