POL1_TORVR
ID POL1_TORVR Reviewed; 2197 AA.
AC P29150; Q88875; Q88876;
DT 01-DEC-1992, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2004, sequence version 2.
DT 03-AUG-2022, entry version 115.
DE RecName: Full=RNA1 polyprotein;
DE AltName: Full=P1;
DE Contains:
DE RecName: Full=Protein X1;
DE Contains:
DE RecName: Full=Protein X2;
DE Contains:
DE RecName: Full=Putative ATP-dependent helicase;
DE EC=3.6.4.-;
DE AltName: Full=Membrane-binding protein;
DE AltName: Full=NTP-binding protein;
DE Short=NTB;
DE Contains:
DE RecName: Full=Viral genome-linked protein;
DE AltName: Full=VPg;
DE Contains:
DE RecName: Full=Picornain 3C-like protease;
DE Short=3C-like protease;
DE Short=PRO;
DE EC=3.4.22.-;
DE Contains:
DE RecName: Full=RNA-directed RNA polymerase;
DE Short=POL;
DE EC=2.7.7.48;
OS Tomato ringspot virus (isolate raspberry) (ToRSV).
OC Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
OC Picornavirales; Secoviridae; Comovirinae; Nepovirus.
OX NCBI_TaxID=12281;
OH NCBI_TaxID=4097; Nicotiana tabacum (Common tobacco).
OH NCBI_TaxID=4030; Pelargonium.
OH NCBI_TaxID=3754; Prunus.
OH NCBI_TaxID=23216; Rubus (bramble).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX PubMed=7844569; DOI=10.1099/0022-1317-76-2-465;
RA Rott M.E., Gilchrist A., Lee L., Rochon D.M.;
RT "Nucleotide sequence of tomato ringspot virus RNA1.";
RL J. Gen. Virol. 76:465-473(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 1-354.
RX PubMed=1926788; DOI=10.1016/0042-6822(91)90801-h;
RA Rott M.E., Tremaine J.H., Rochon D.M.;
RT "Comparison of the 5' and 3' termini of tomato ringspot virus RNA1 and
RT RNA2: evidence for RNA recombination.";
RL Virology 185:468-472(1991).
RN [3]
RP PROTEIN SEQUENCE OF 1213-1247 AND 1487-1502, PROTEOLYTIC PROCESSING OF
RP POLYPROTEIN, AND MUTAGENESIS OF GLN-1465 AND GLN-1486.
RX PubMed=10092022; DOI=10.1099/0022-1317-80-3-799;
RA Wang A., Carrier K., Chisholm J., Wieczorek A., Huguenot C., Sanfacon H.;
RT "Proteolytic processing of tomato ringspot nepovirus Picornain 3C-like
RT protease precursors: definition of the domains for the VPg, protease and
RT putative RNA-dependent RNA polymerase.";
RL J. Gen. Virol. 80:799-809(1999).
RN [4]
RP CHARACTERIZATION OF PROTEASE, AND MUTAGENESIS OF HIS-1283 AND HIS-1451.
RX PubMed=9049338; DOI=10.1099/0022-1317-76-4-917;
RA Hans F., Sanfacon H.;
RT "Tomato ringspot nepovirus protease: characterization and cleavage site
RT specificity.";
RL J. Gen. Virol. 76:917-927(1995).
RN [5]
RP PROTEOLYTIC PROCESSING OF POLYPROTEIN, AND MUTAGENESIS OF GLN-423; GLN-620;
RP GLN-1212 AND HIS-1283.
RX PubMed=11038391; DOI=10.1099/0022-1317-81-11-2771;
RA Wang A., Sanfacon H.;
RT "Proteolytic processing at a novel cleavage site in the N-terminal region
RT of the tomato ringspot nepovirus RNA-1-encoded polyprotein in vitro.";
RL J. Gen. Virol. 81:2771-2781(2000).
RN [6]
RP SUBCELLULAR LOCATION OF THE NTB-VPG POLYPROTEIN.
RX PubMed=12477857; DOI=10.1128/jvi.77.1.523-534.2003;
RA Han S., Sanfacon H.;
RT "Tomato ringspot virus proteins containing the nucleoside triphosphate
RT binding domain are transmembrane proteins that associate with the
RT endoplasmic reticulum and cofractionate with replication complexes.";
RL J. Virol. 77:523-534(2003).
RN [7]
RP TOPOLOGY OF THE NTB-VPG POLYPROTEIN, GLYCOSYLATION, AND MUTAGENESIS OF
RP THR-1230.
RX PubMed=14769910; DOI=10.1099/vir.0.19612-0;
RA Wang A., Han S., Sanfacon H.;
RT "Topogenesis in membranes of the NTB-VPg protein of Tomato ringspot
RT nepovirus: definition of the C-terminal transmembrane domain.";
RL J. Gen. Virol. 85:535-545(2004).
CC -!- FUNCTION: Picornain 3C-like protease is a thiol protease that cleaves
CC at Gln-|-Gly or Gln-|-Ser sites in the P1 and P2 polyproteins.
CC -!- FUNCTION: The VPg-NTB polyprotein may act as a membrane-anchor for the
CC replication complex.
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 -!- SUBCELLULAR LOCATION: [Viral genome-linked protein]: Host endoplasmic
CC reticulum lumen {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: [Putative ATP-dependent helicase]: Host
CC endoplasmic reticulum membrane; Single-pass membrane protein. Note=The
CC NTB-VPg polyprotein is associated with endoplasmic-derived membranes
CC that are active in viral replication.
CC -!- PTM: Specific enzymatic cleavages by picornain 3C-like protease in vivo
CC yield mature proteins. Picornain 3C-like protease is autocatalytically
CC processed. NTB exists as NTB-VPg polyprotein as well as NTB mature
CC protein. {ECO:0000269|PubMed:10092022, ECO:0000269|PubMed:11038391}.
CC -!- PTM: VPg is uridylylated by the polymerase and is covalently linked to
CC the 5'-end of genomic RNA. This uridylylated form acts as a nucleotide-
CC peptide primer for the polymerase (By similarity). {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the nepoviruses RNA1 polyprotein family.
CC {ECO:0000305}.
CC -!- CAUTION: It is uncertain whether Met-1 or Met-122 is the initiator.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA47942.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; L19655; AAA78254.1; -; Genomic_RNA.
DR EMBL; M73822; AAA47941.1; -; Genomic_RNA.
DR EMBL; M73822; AAA47942.1; ALT_INIT; Genomic_RNA.
DR PIR; A40787; GNVVSR.
DR RefSeq; NP_620765.1; NC_003840.1.
DR SMR; P29150; -.
DR MEROPS; C03.012; -.
DR iPTMnet; P29150; -.
DR PRIDE; P29150; -.
DR GeneID; 956647; -.
DR KEGG; vg:956647; -.
DR Proteomes; UP000000410; Genome.
DR GO; GO:0044166; C:host cell endoplasmic reticulum lumen; IEA:UniProtKB-SubCell.
DR GO; GO:0044167; C:host cell endoplasmic reticulum membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004197; F:cysteine-type endopeptidase activity; IEA:InterPro.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003724; F:RNA helicase activity; IEA:InterPro.
DR GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:0018144; P:RNA-protein covalent cross-linking; IEA:UniProtKB-KW.
DR GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
DR GO; GO:0039694; P:viral RNA genome replication; IEA:InterPro.
DR Gene3D; 3.30.70.270; -; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR000605; Helicase_SF3_ssDNA/RNA_vir.
DR InterPro; IPR014759; Helicase_SF3_ssRNA_vir.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR044067; PCV_3C_PRO.
DR InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR InterPro; IPR001205; RNA-dir_pol_C.
DR InterPro; IPR007094; RNA-dir_pol_PSvirus.
DR Pfam; PF00680; RdRP_1; 1.
DR Pfam; PF00910; RNA_helicase; 1.
DR SUPFAM; SSF56672; SSF56672; 1.
DR PROSITE; PS51874; PCV_3C_PRO; 1.
DR PROSITE; PS50507; RDRP_SSRNA_POS; 1.
DR PROSITE; PS51218; SF3_HELICASE_2; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Covalent protein-RNA linkage; Direct protein sequencing;
KW Glycoprotein; Helicase; Host endoplasmic reticulum; Host membrane;
KW Hydrolase; Membrane; Nucleotide-binding; Nucleotidyltransferase; Protease;
KW Reference proteome; RNA-binding; RNA-directed RNA polymerase;
KW Thiol protease; Transferase; Transmembrane; Transmembrane helix;
KW Viral RNA replication.
FT CHAIN 1..423
FT /note="Protein X1"
FT /id="PRO_0000037086"
FT CHAIN 424..620
FT /note="Protein X2"
FT /id="PRO_0000037087"
FT CHAIN 621..1212
FT /note="Putative ATP-dependent helicase"
FT /id="PRO_0000037088"
FT CHAIN 1213..1239
FT /note="Viral genome-linked protein"
FT /id="PRO_0000037089"
FT CHAIN 1240..1486
FT /note="Picornain 3C-like protease"
FT /id="PRO_0000037090"
FT CHAIN 1487..2197
FT /note="RNA-directed RNA polymerase"
FT /id="PRO_0000037091"
FT TOPO_DOM 621..1167
FT /note="Cytoplasmic"
FT /evidence="ECO:0000269|PubMed:14769910"
FT TRANSMEM 1168..1188
FT /note="Helical"
FT /evidence="ECO:0000305"
FT TOPO_DOM 1189..1212
FT /note="Lumenal"
FT /evidence="ECO:0000269|PubMed:14769910"
FT DOMAIN 766..933
FT /note="SF3 helicase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00551"
FT DOMAIN 1243..1475
FT /note="Peptidase C3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01222"
FT DOMAIN 1765..1888
FT /note="RdRp catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT ACT_SITE 1283
FT /note="For picornain 3C-like protease activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01222"
FT ACT_SITE 1331
FT /note="For picornain 3C-like protease activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01222"
FT ACT_SITE 1433
FT /note="For picornain 3C-like protease activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01222"
FT BINDING 796..803
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00551"
FT SITE 1451
FT /note="Involved in the cleavage site specificity"
FT CARBOHYD 1228
FT /note="N-linked (GlcNAc...) asparagine; by host"
FT /evidence="ECO:0000269|PubMed:14769910"
FT MUTAGEN 423
FT /note="Missing: No cleavage between X1 and X2."
FT /evidence="ECO:0000269|PubMed:11038391"
FT MUTAGEN 620
FT /note="Missing: No cleavage between X2 and NTB."
FT /evidence="ECO:0000269|PubMed:11038391"
FT MUTAGEN 1212
FT /note="Missing: No cleavage between NTB and VPg."
FT /evidence="ECO:0000269|PubMed:11038391"
FT MUTAGEN 1230
FT /note="T->A: Complete loss of N-linked glycosylation."
FT /evidence="ECO:0000269|PubMed:14769910"
FT MUTAGEN 1283
FT /note="H->D: Complete loss of protease activity."
FT /evidence="ECO:0000269|PubMed:11038391,
FT ECO:0000269|PubMed:9049338"
FT MUTAGEN 1451
FT /note="H->L: Complete loss of protease activity."
FT /evidence="ECO:0000269|PubMed:9049338"
FT MUTAGEN 1465
FT /note="Q->A: No effect."
FT /evidence="ECO:0000269|PubMed:10092022"
FT MUTAGEN 1486
FT /note="Q->A: No cleavage between 3C-like protease and RNA-
FT directed RNA polymerase."
FT /evidence="ECO:0000269|PubMed:10092022"
FT CONFLICT 1230
FT /note="T -> A (in Ref. 3; AA sequence)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 2197 AA; 244130 MW; 2D8EF928E58DBC89 CRC64;
MSSICFAGGN HARLPSKAAY YRAISDRELD REGRFPCGCL AQYTVQAPPP AKTQEKAVGR
SADLQKGNVA PLKKQRCDVV VAVSGPPPLE LVYPARVGQH RLDQPSKGPL AVPSAKQTST
AMEVVLSVGE AALTAPWLLC SYKSGVSSPP PPMTQRQQFA AIKRRLVQKG QQIIRELIRA
RKAAKYAAFA ARKKAAAVAA QKARAEAPRL AAQKAAIAKI LRDRQLVSLP PPPPPSAARL
AAEAELASKS ASLQRLKAFH RANRVRPVLN NSFPSPPLAC KPDPALLERL RLATPSRCTV
ATKRQRDFVV APLATQIRVA KCASHQEAYD SCRSILIEEW PESRYLFGPL SFVGDWEHVP
GMLMQYRLCV LFSMVRDVMP ALSLVADTLH ALRSGTAPNI VFKNAMSTAN QILECSHSSH
AAQGFGNFLS RGKSAAINLA SGLSSFVGEK VVSGANHVVN KASEVIVDKL FVPFVKLLRE
HFDDTIGKWI PKLLGATQKI EELWRWSLEW AQNMSKKLDV SLRVLRGSAL VGVGLLLVSG
ILYFAEQLLR SFGLLIVAGS FISMFVGGCL LAYAGSMAGI FDEQMMRVRG ILCEIPMLLY
LKAQPDPFFP KKSGGRAPTQ GLTDVFGVPL SIMNAIGDGL VHHSLDTLTL MGKFGAAMDN
VRKGITCMRS FVSWLMEHLA LALDKITGKR TSFFRELATL INFDVEKWVR DSQQYLLAAE
IYVDGDTVVM DTCRHLLDKG LKLQRMMVSA KSGCSFNYGR LVGDLVKRLS DLHKRYCASG
RRVHYRLAPF WVYLYGGPRC GKSLFAQSFM NAAVDFMGTT VDNCYFKNAR DDFWSGYRQE
AICCVDDLSS CETQPSIESE FIQLITTMRY GLNMAGVEEK GASFDSKMVI TTSNFFTAPT
TAKIASKAAY NDRRHACILV QRKEGVAYNP SDPAAAAEAM FVDSTTQHPL SEWMSMQELS
AELLLRYQQH REAQHAEYSY WKSTSRTSHD VFDILQKCVN GDTQWLSLPV DVIPPSIRQK
HKGNRVFAID GRIFMFDYMT LEYDEIKEKE NLDARHLEAR ILEKYGDTRL LLEKWGANGV
VAQFIEQLLE GPSNVASLEV LSKDSLESHK EFFSTLGLIE RATLRAVQKK IDAAREDLMH
LSGLKPGRSL TELFVEAYDW VYANGGKLLL VLAAVILILF FGSACIKLMQ AIFCGAAGGT
VSMAAVGKMT VQSTIPSGSY ADVYNARNMT RVFRPQSVQG SSLAEAQFNE SHAVNMLVRI
DLPDGNIISA CRFRGKSLAL TKHQALTIPP GAKIHIVYTD NNGNTKAPLT HFFQPTGPNG
EHFLRFFNGT EVCIYSHPQL SALPGAPQNY FLKDVEKISG DIAIKGCGIK LGRTSVGECV
GVKDNEPVLN HWRAVAKVRT TKITIDNYSE GGDYSNDLPT SIISEYVNSP EDCGALLVAH
LEGGYKIIGM HVAGSSYPVE VDGVQMPRYI SHASFFPDYS SFAPCQSSVI KSLIQEAGVE
ERGVSKVGHI KDPAETPHVG GKTKLELVDE AFLVPSPVEV KIPSILSKDD PRIPEAYKGY
DPLGDAMEKF YEPMLDLDED VLESVMADMY DEFYDCQTTL RIMSDDEVIN GSDFGFNIEA
VVKGTSEGYP FVLSRRPGEK GKARFLEELE PQPGDTKPKY KLVVGTEVHS AMVAMEQQAR
TEVPLLIGMD VPKDERLKPS KVLEKPKTRT FVVLPMHYNL LLRKYVGILC SSMQVNRHRL
ACAVGTNPYS RDWTDIYQRL AEKNSVALNC DYSRFDGLLN YQAYVHIVNF INKLYNDEHS
IVRGNLLMAM YGRWSVCGQR VFEVRAGMPS GCALTVIINS LFNEMLIRYV YRITVPRPLV
NNFKQEVCLI VYGDDNLISI KPDTMKYFNG EQIKTILAKY KVTITDGSDK NSPVLRAKPL
KQLDFLKRGF RVESDGRVLA PLDLQAIYSS LYYINPQGNI LKSLFLNAQV ALRELYLHGD
VEQFTAVRNF YVNQIGGNFL SLPQWRHCAS FHDEQYSQWK PWSPVKFLEV DVPDAKFLQH
KAPATALSIV ADRLAVAGPG WRNKDPDRYL LVSLTSLKAN EGGLYFPVDY GEGTGQQATE
ASIRAYRRLK DHRVRHMRDS WNEGKTIVFR CEGPFVSGWA AAISFGTSVG MNAQDLLINY
GIQGGAHKEY LGRYFVGARF KELERYDRPF QSRIIAS
