POLR_TYMV
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 03-AUG-2022, entry version 116.
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.
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}.
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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-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0039648; P:modulation by virus 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:0006351; P:transcription, DNA-templated; IEA:InterPro.
DR GO; GO:0039694; P:viral RNA genome replication; IEA:InterPro.
DR Gene3D; 3.40.50.300; -; 1.
DR Gene3D; 3.90.70.100; -; 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; IPR007094; RNA-dir_pol_PSvirus.
DR InterPro; IPR043629; Salyut_dom.
DR InterPro; IPR001788; Tymovirus_RNA-dep_RNA_pol.
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; SSF56672; 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
