ID POL1_RCMV Reviewed; 1864 AA.
AC P35930; Q66182;
DT 01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1994, sequence version 1.
DT 08-NOV-2023, entry version 122.
DE RecName: Full=RNA1 polyprotein;
DE AltName: Full=Genome polyprotein B;
DE AltName: Full=P1;
DE Contains:
DE RecName: Full=Protease cofactor;
DE AltName: Full=32 kDa protein;
DE Contains:
DE RecName: Full=Putative helicase;
DE EC=3.6.4.-;
DE AltName: Full=58 kDa protein;
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 EC=3.4.22.- {ECO:0000250|UniProtKB:P03600};
DE AltName: Full=24 kDa protein;
DE Contains:
DE RecName: Full=RNA-directed RNA polymerase {ECO:0000255|PROSITE-ProRule:PRU00539};
DE EC=2.7.7.48 {ECO:0000255|PROSITE-ProRule:PRU00539};
DE AltName: Full=87 kDa protein;
OS Red clover mottle virus (RCMV).
OC Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
OC Picornavirales; Secoviridae; Comovirinae; Comovirus; Comovirus trifolii.
OX NCBI_TaxID=12262;
OH NCBI_TaxID=57577; Trifolium pratense (Red clover).
RN [1]
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=S;
RX PubMed=1402822; DOI=10.1099/0022-1317-73-9-2473;
RA Shanks M., Lomonossoff G.P.;
RT "The nucleotide sequence of red clover mottle virus bottom component RNA.";
RL J. Gen. Virol. 73:2473-2477(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE OF 912-1167.
RX PubMed=2179468; DOI=10.1099/0022-1317-71-3-735;
RA Shanks M., Lomonossoff G.P.;
RT "The primary structure of the 24K protease from red clover mottle virus:
RT implications for the mode of action of comovirus proteases.";
RL J. Gen. Virol. 71:735-738(1990).
CC -!- FUNCTION: [Picornain 3C-like protease]: Thiol protease that cleaves the
CC RNA1 and RNA2 polyproteins. {ECO:0000250|UniProtKB:P03600}.
CC -!- FUNCTION: [Viral genome-linked protein]: Plays a role in RNA
CC replication. It is covalently linked to the 5'terminus of both viral
CC single-stranded RNA1 and RNA2 molecules.
CC {ECO:0000250|UniProtKB:P03600}.
CC -!- FUNCTION: [Protease cofactor]: Down-regulates the RNA1 polyprotein
CC processing and enhances trans-cleavage of RNA2 polyproteins. The
CC protease cofactor and the putative helicase seem to target the
CC replication complexes to ER membranes. Their physical association
CC causes the membrane rearrangement of host ER that may result in
CC formation of the small membranous vesicles that are the site of viral
CC RNA synthesis. {ECO:0000250|UniProtKB:P03600}.
CC -!- FUNCTION: [Putative helicase]: The protease cofactor and the putative
CC helicase seem to target the replication complexes to ER membranes.
CC Their physical association causes the membrane rearrangement of host ER
CC that may result in formation of the small membranous vesicles that are
CC the site of viral RNA synthesis. {ECO:0000250|UniProtKB:P03600}.
CC -!- FUNCTION: [RNA-directed RNA polymerase]: Replicates the viral genome.
CC {ECO:0000250|UniProtKB:P03600}.
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
CC {ECO:0000250|UniProtKB:P03600}; Single-pass membrane protein
CC {ECO:0000250|UniProtKB:P03600}. Host cytoplasm, host perinuclear region
CC {ECO:0000250|UniProtKB:P03600}.
CC -!- SUBCELLULAR LOCATION: [RNA-directed RNA polymerase]: Host endoplasmic
CC reticulum {ECO:0000250|UniProtKB:P03600}.
CC -!- SUBCELLULAR LOCATION: [Protease cofactor]: Host cytoplasm, host
CC perinuclear region {ECO:0000250|UniProtKB:P03600}.
CC -!- PTM: [RNA1 polyprotein]: Specific enzymatic cleavages by picornain 3C-
CC like protease in vivo yield mature proteins. Picornain 3C-like protease
CC is autocatalytically processed. {ECO:0000250|UniProtKB:P03600}.
CC -!- PTM: [Viral genome-linked protein]: Uridylylated by the polymerase and
CC is covalently linked to the 5'-end of genomic RNA. This uridylylated
CC form acts as a nucleotide-peptide primer for the polymerase.
CC {ECO:0000250|UniProtKB:P03600}.
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; X64886; CAA46104.1; -; Unassigned_RNA.
DR EMBL; D00657; BAA00547.1; -; Genomic_RNA.
DR PIR; JQ1657; JQ1657.
DR RefSeq; NP_620468.1; NC_003741.1.
DR SMR; P35930; -.
DR MEROPS; C03.003; -.
DR GeneID; 1502336; -.
DR KEGG; vg:1502336; -.
DR Proteomes; UP000006361; Genome.
DR GO; GO:0044165; C:host cell endoplasmic reticulum; IEA:UniProtKB-SubCell.
DR GO; GO:0033644; C:host cell membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0044220; C:host cell perinuclear region of cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0016020; C: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-dependent RNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0006351; P:DNA-templated transcription; IEA:InterPro.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:0039694; P:viral RNA genome replication; IEA:InterPro.
DR Gene3D; 3.30.70.270; -; 1.
DR Gene3D; 2.40.10.10; Trypsin-like serine proteases; 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; IPR044067; PCV_3C_PRO.
DR InterPro; IPR000199; Peptidase_C3A/C3B_picornavir.
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; PF00548; Peptidase_C3; 1.
DR Pfam; PF00680; RdRP_1; 1.
DR Pfam; PF00910; RNA_helicase; 1.
DR SUPFAM; SSF56672; DNA/RNA polymerases; 1.
DR SUPFAM; SSF50494; Trypsin-like serine proteases; 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; Helicase; Host cytoplasm;
KW Host endoplasmic reticulum; Host membrane; Hydrolase; Membrane;
KW Nucleotide-binding; Nucleotidyltransferase; Phosphoprotein; Protease;
KW RNA-directed RNA polymerase; Thiol protease; Transferase; Transmembrane;
KW Transmembrane helix; Viral RNA replication.
FT CHAIN 1..1864
FT /note="RNA1 polyprotein"
FT /id="PRO_0000445836"
FT CHAIN 1..315
FT /note="Protease cofactor"
FT /id="PRO_0000037016"
FT CHAIN 316..915
FT /note="Putative helicase"
FT /id="PRO_0000037017"
FT CHAIN 916..943
FT /note="Viral genome-linked protein"
FT /id="PRO_0000037018"
FT CHAIN 944..1151
FT /note="Picornain 3C-like protease"
FT /id="PRO_0000037019"
FT CHAIN 1152..1864
FT /note="RNA-directed RNA polymerase"
FT /id="PRO_0000037020"
FT TRANSMEM 892..912
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 457..622
FT /note="SF3 helicase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00551"
FT DOMAIN 943..1146
FT /note="Peptidase C3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01222"
FT DOMAIN 1426..1556
FT /note="RdRp catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT ACT_SITE 983
FT /note="For picornain 3C-like protease activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01222"
FT ACT_SITE 1019
FT /note="For picornain 3C-like protease activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01222"
FT ACT_SITE 1109
FT /note="For picornain 3C-like protease activity"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01222"
FT BINDING 483..490
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00551"
FT SITE 315..316
FT /note="Cleavage; by viral protease"
FT /evidence="ECO:0000250|UniProtKB:P03600"
FT SITE 915..916
FT /note="Cleavage; by viral protease"
FT /evidence="ECO:0000250|UniProtKB:P03600"
FT SITE 943..944
FT /note="Cleavage; by viral protease"
FT /evidence="ECO:0000250|UniProtKB:P03600"
FT SITE 1151..1152
FT /note="Cleavage; by viral protease"
FT /evidence="ECO:0000250|UniProtKB:P03600"
FT MOD_RES 916
FT /note="O-(5'-phospho-RNA)-serine"
FT /evidence="ECO:0000250|UniProtKB:P03600"
SQ SEQUENCE 1864 AA; 210256 MW; 8DDD9D6C17C2B154 CRC64;
MYMLTFEPGL CVAGIIRQVR SNPFMHVVQA YARTTETYRE DIEMTKSMLK LKADEPLLVM
SIVAAAMDFQ TMVMAPIEME ASEFLYGFYA ERMSYIVTNR GMSELHEYIQ LQCQRHLLVK
VEIDGQYLVQ EHEYEAQGFN IKRVKELITD VATWVPKKVK GMIGWSVDAV LDSFQEYFYK
VITERIPMAM KVCSWVATVW DQIKTWIEDA MTAMSSFLQG CNELLTWGLA TLAACCALNV
LERILIFMEF LDESIDIAGI FLRTGVVAAA CYHFSSTAKG FTEMMSVLSV ATTAVAAVVC
ANYFGGSKTK KVNAQGNPVD LLERIAAGLS SISQDSLVSL GKSCSAINSI ATSYGHLRNF
AGRVLTMLRD FAWKILGLET RFLADAALVF GEDVDGWLQR ISALREAYVS KAYSSQDEVF
EMNVLLERGY KMRHLMATGS RVSPAIGNML MQGLADLERL HRNAAVQGVK GVRKIPFTVF
AHGNSRCGKS LLIGKLISDF QEHKGLGEDT VYSRNTTETH WSGYRRQPIV VIDDFAAVES
DISAEAQLIN LVSSTPYSVV MAAIEEKGMT FDSQFIFAST NFLEVSPNGK IRCDDAFRNR
RHVLIDVKLK PEVEYQSDDF TANQSYNILE HSHGRYNVVA TFDNYEELLA YCLTKHEQHE
AEQEANLAKL RRTNKFESHF KKFEQVLQLS TYFSSSIERI KREALATTDG ADDYHLLYVV
PRNGSYLHVA ANKDFQIQQW YGPVEEVAEE DILRASERML LGAYEFLLLS TELNVVVKNH
LPELICTDNY DHNLEFCGVV GDPVYHQQLL KNIRALKPWH RAVLFGIGTL MGAKNPTPWY
KRMWEGIKDV LYKAYSTEIS QWPVPLKITC GIVLVGIVGA GFWKTVSVLT NAGNGAGLVG
AAVNSFSVVS TAEAQSRKPN RFEVQQYRYK NVPLTRRSWG NAQMSLDQST VSILNKCHAK
FIIASQHAQI VLVPGRRFIG YSHFFCNLKH PLMVQIETAD RTYFHRYQPE NMEYIEDSEL
CVYHSSCLED ISHSCWDLFC WDPDKELPKK FSADFVSCKY NTWTKSVEPT WANVDAEVIK
EDFTICDGEY RNTVSTSIRY EAPTVMSDCG SMIITNVGGK TKIVGIHVAG RDNKIGMASL
LPPLLPCAQA QGAEKYFNFY PIEYDAAEGI ARVGELKPKL YIPLPKKTSL VKTPEEWHLG
TPCDKVPSIL VKGDPRLADT VHADYDPCLS GLTKYSTPMS PLDSVLLGET CQEILDEWFD
CLPEGFELGE VTINEALNGV DGVDYMDRIP LATSEGFPHV MSREQGEKGK QRFVQGDGHI
VSLIPGTSVH EAYETLSRTI ATEVPTLVGI ECPKDEKLPF RKVFTKPKTR NFTILPMEYN
ILVRQYFLNF VRFIMKKRDV LPCQVGINPY SMEWSIVASR LKSQGNDILC CDYSSFDGLL
SKQIMEMMAD MINRFCGGGT LICAKRKNLL MACCSRLAIS RDSVWRIECG IPSGFPLTVI
CNSIFNEILV RYHYKLLLQE HNAPNMYVQS FKNLISMVTY GDDNLISVNA VVKPYFDGTK
LKQAMARNGI IITDGKDKTS ATLEFRRLED CDFLKRGFLK RSSVLWDAPE EKASLWAQLH
YVNVNNCEMQ VAYMTNLVNV LRELYMHDPT EMVEFRRLAL KSIPWLNTTD LPTLYQVKEF
YAEQRLRNIP DHNDSLDMLT SVDLLGPAIL GEGVPQEALV LSELLEVRDL RYHTVPDNDN
GKEVWILFNT MYPQKLLPSN CHSFTWNCGQ GRGGLPTQHW LATNVTRTDS KLNKLIRTAV
AANKKIVLAT KDNILPINVI AVLLAARNKV MPSLATNALL TYVIGAAKKL NFLTSECQFA
FFNV
//
