ID   POL1_TOTV               Reviewed;        2158 AA.
AC   A1XIP9;
DT   11-JAN-2011, integrated into UniProtKB/Swiss-Prot.
DT   06-FEB-2007, sequence version 1.
DT   03-AUG-2022, entry version 73.
DE   RecName: Full=RNA1 polyprotein;
DE   Contains:
DE     RecName: Full=Protease-cofactor;
DE   Contains:
DE     RecName: Full=Putative helicase;
DE              EC=3.6.4.-;
DE   Contains:
DE     RecName: Full=Picornain 3C-like protease;
DE              Short=3C-like protease;
DE              EC=3.4.22.-;
DE   Contains:
DE     RecName: Full=RNA-directed RNA polymerase;
DE              EC=2.7.7.48;
OS   Tomato torrado virus (isolate Solanum lycopersicum/Spain/PRIToTV0301/-)
OS   (ToTV).
OC   Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
OC   Picornavirales; Secoviridae; Torradovirus.
OX   NCBI_TaxID=686948;
OH   NCBI_TaxID=4072; Capsicum annuum (Capsicum pepper).
OH   NCBI_TaxID=4097; Nicotiana tabacum (Common tobacco).
OH   NCBI_TaxID=4081; Solanum lycopersicum (Tomato) (Lycopersicon esculentum).
OH   NCBI_TaxID=4111; Solanum melongena (Eggplant) (Aubergine).
OH   NCBI_TaxID=4113; Solanum tuberosum (Potato).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX   PubMed=17226066; DOI=10.1007/s00705-006-0917-6;
RA   Verbeek M., Dullemans A.M., van den Heuvel J.F., Maris P.C.,
RA   van der Vlugt R.A.;
RT   "Identification and characterisation of tomato torrado virus, a new plant
RT   picorna-like virus from tomato.";
RL   Arch. Virol. 152:881-890(2007).
CC   -!- FUNCTION: Picornain 3C-like protease is a thiol protease that probably
CC       cleaves the polyprotein. {ECO:0000250}.
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: [Putative helicase]: Host membrane {ECO:0000305};
CC       Single-pass membrane protein {ECO:0000305}.
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DR   EMBL; DQ388879; ABD38934.1; -; Genomic_RNA.
DR   RefSeq; YP_001039627.1; NC_009013.1.
DR   PRIDE; A1XIP9; -.
DR   GeneID; 5130563; -.
DR   KEGG; vg:5130563; -.
DR   Proteomes; UP000000825; Genome.
DR   GO; GO:0033644; C:host cell 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:InterPro.
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:0006260; P:DNA replication; 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; 2.40.10.10; -; 1.
DR   Gene3D; 3.30.70.270; -; 1.
DR   InterPro; IPR043502; DNA/RNA_pol_sf.
DR   InterPro; IPR004004; Helic/Pol/Pept_Calicivir-typ.
DR   InterPro; IPR000605; Helicase_SF3_ssDNA/RNA_vir.
DR   InterPro; IPR014759; Helicase_SF3_ssRNA_vir.
DR   InterPro; IPR044067; PCV_3C_PRO.
DR   InterPro; IPR009003; Peptidase_S1_PA.
DR   InterPro; IPR043504; Peptidase_S1_PA_chymotrypsin.
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   PRINTS; PR00918; CALICVIRUSNS.
DR   SUPFAM; SSF50494; SSF50494; 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   3: Inferred from homology;
KW   ATP-binding; Covalent protein-RNA linkage; DNA replication; Helicase;
KW   Host membrane; Hydrolase; Membrane; Nucleotide-binding;
KW   Nucleotidyltransferase; Phosphoprotein; Protease; Reference proteome;
KW   RNA-directed RNA polymerase; Thiol protease; Transferase; Transmembrane;
KW   Transmembrane helix; Viral RNA replication.
FT   PROPEP          1..105
FT                   /note="Removed in mature form"
FT                   /evidence="ECO:0000305"
FT                   /id="PRO_0000441104"
FT   CHAIN           106..?338
FT                   /note="Protease-cofactor"
FT                   /evidence="ECO:0000255"
FT                   /id="PRO_5000214031"
FT   CHAIN           ?339..?860
FT                   /note="Putative helicase"
FT                   /evidence="ECO:0000255"
FT                   /id="PRO_5000214032"
FT   CHAIN           ?861..?1103
FT                   /note="Picornain 3C-like protease"
FT                   /evidence="ECO:0000255"
FT                   /id="PRO_5000214033"
FT   CHAIN           ?1104..2158
FT                   /note="RNA-directed RNA polymerase"
FT                   /evidence="ECO:0000255"
FT                   /id="PRO_5000214034"
FT   TRANSMEM        801..821
FT                   /note="Helical"
FT                   /evidence="ECO:0000255"
FT   DOMAIN          367..534
FT                   /note="SF3 helicase"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00551"
FT   DOMAIN          870..1083
FT                   /note="Peptidase C3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01222"
FT   DOMAIN          1376..1511
FT                   /note="RdRp catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT   ACT_SITE        910
FT                   /note="For picornain 3C-like protease activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01222"
FT   ACT_SITE        946
FT                   /note="For picornain 3C-like protease activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01222"
FT   ACT_SITE        1041
FT                   /note="For picornain 3C-like protease activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01222"
FT   BINDING         393..400
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00551"
FT   SITE            338..339
FT                   /note="Cleavage"
FT                   /evidence="ECO:0000255"
FT   SITE            860..861
FT                   /note="Cleavage"
FT                   /evidence="ECO:0000255"
FT   SITE            1103..1104
FT                   /note="Cleavage"
FT                   /evidence="ECO:0000255"
FT   MOD_RES         844
FT                   /note="O-(5'-phospho-RNA)-serine"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   2158 AA;  241087 MW;  859B9689A6784615 CRC64;
     MSFSKMFPGF NSVTEKCATS SSGSFFSELT ASISNFSRTL SNVTKVSSQI SSHIEDLKPS
     VTDAASSFTS TCNSVTKLLD KIMTLIEPFI KAYSFVASMY KSICDMVAKI VASIKDKFTL
     GFNWVLDKSE DVDVLVIAFL IFAISMLIIV FICPSSVLDG VVQMTHIVFN TVGNFFSALY
     KLDWLPTWSQ KFSMMAQANV LPGESMSHSP LSQVVASLIA FGISTLVFVA VPGRPNGLSN
     PLSKILYSAG SGAQQCNQLF TLFRNMKDCT SQAFSWVLEI IVDIFGFKNP VLSAISATLS
     TDLFTWMEEV DAVCDPAHRL ENFANPAFTI KLQHLREQAL KISAYIATHP VAAFMSHRVT
     AAIXHLDKIY GENCQHTGVG QYRAEPFMVQ WYGASGCGKS TSMRLFINDV LDRMEEPKLN
     RLYAVSKRDA YWSNYAHQTA ILMDDMGALR DGAGQCQDIK DLIDIKSTQP APLPMAAVED
     KGRHFTSRYI FATSNLISAP AQCGLTYPDA FERRRDVLVE CRKVGEFNTD APTSHLEFDV
     VESKRPHAIT HRGLSYDDLL EYVVAKCKVH AEISGKLYGA TSGKVAQVDV SPEEIIASMD
     MLNIQDTKQD AKLPVVVVSE EDRVAYSQEL TVEALKYAYQ GSLNPAAYFP HDMHKQAIFD
     VLSESAKETF TRWVNDMLYQ GCCNENYRWL IKNIPADYIM HFKSFIYAST INERSFDVQK
     QLPDGMAHRA IDADVDTLIC VEQMPAHVQF LYTAFVRYWC RRKMEQPRQS WVVVCYHSIV
     DYIKNAWYDL PYILRVLIKA GLILIALNGA FGAVTAFCAC WQSNTFPSAE GRGGITNESN
     SISSRKNKGK SIFARSLLAQ AKGDMLEKWA SDDGFINEGL KKNLVVLRLG EGVYFRGTYV
     CSGWVMTVAH AFSSLRDGTT FSIIHAQSIS KVQYNAKTAR FLKEQDIVLL NVGNPDGPKP
     DIRKHFPVRD GVCFSKGTQG VCVRAVASKD ASQGNLEYLR FNVMMSKGYL EKVTYQMDSS
     SFKLESQASY EYHMNGENGD CGTLLLLPNV QDKQPCIVGI HCASYDEEAA HKGFVASNAT
     AIFRDQLEDL PTGPVKVAMV RCQLLKDLRA RDAALFEEKQ VAFVGTLPAE QAATVPHKTT
     LRRSGLFEAF GPAETAPSII SASDKRGEGF DPYVAGIQKY NETAQNFDED IARLAYEGLR
     QAILPVLHSQ RVPFGKPVTQ NEDVVLNGVD GFDYFDGMEL STSCGYPYNK LGMGTSKREF
     VEPSGDGDRV QLKRTTPIFD DWEALDVEIR KGNFVELVTT QCAKDERLPL EKVFGKRKTR
     LFEILPFHYN MLVRKYFLDF SASLMASHNA LPCKVGINPG GIEWTLLANG FRAVSDTGFS
     ADYSSFDGRA PIFAFQWFCD LVDDYYGSPP GSPDSNARHV LLMMASCHYT ICENKVFRLV
     GGMPSGFALT VIFNSLLNEF YMRYAFISLL RRPHIAAQAI GCKPSDFNKL FVAVYGDDNL
     VAVPMELHWY TLPAIAQELE MVNVIIKNGI DKNMDVSSSK MLDLSELTFL SRGFKRHRLG
     YVQAPLKWVS IIEPMYWIRP SVGCPDALAM LENIDTGVRE AFHHGPQVFE KLVTDVQNAL
     KERCFPATTF PTYFELEQDW LVEVTGNPAI GLIKELHIAA SAFVPLPPGN TVLNFSDGVH
     TFADRVSFCS SRTAAAQQWD TTTVLVNCTG AKRPTWVRGP TTWRDFEGLI WPYTMAAIKD
     HICSIVTKGV TKPHVVFVCG NGYAIGPVCA ALYCLSTGQY SSQDVVVRLR TIADVTDLSQ
     YPGGCAKYLL KCADTREEEL ADTCKIAQAK GETPAYIPQG GFSLGNFRIV QGRIDLQLAQ
     RLPFTVGPYG GWGQHTTREL KLLLKDMEKI YQILVQRESF ITLYFDYLSS EQVMLLVDFL
     RLQGFFPRQN DVDYLLKAFK LSKQRHNKEN CHTVYFRKPF LSRKMTMGSK EILSATAAES
     LFGMDVSANV LKSRLLHLQK PIKCSSMELA FKIYCVIQGH LSKEVVTHFQ RMYQQDLTEG
     IIEKVILWLT ATLSESFPVD LVDVPLGLDN IEIQDKGFSL NPNNINMNAC DAILFQLTEC
     YNRSTKKHVF CRYTTASSLV VAYVLAHRHQ TIDELPSFYA THPDVLLLTP ILTGYKAP