ID   R1AB_LIYV9              Reviewed;        2379 AA.
AC   Q83045;
DT   30-NOV-2010, integrated into UniProtKB/Swiss-Prot.
DT   30-NOV-2010, sequence version 2.
DT   03-AUG-2022, entry version 88.
DE   RecName: Full=Replicase polyprotein 1ab;
DE   Contains:
DE     RecName: Full=Leader protease;
DE              Short=L-PRO;
DE              EC=3.4.22.-;
DE   Contains:
DE     RecName: Full=Methyltransferase/helicase/RNA-directed RNA polymerase;
DE              EC=2.1.1.-;
DE              EC=2.7.7.48;
DE              EC=3.6.4.13;
OS   Lettuce infectious yellows virus (isolate United States/92) (LIYV).
OC   Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Alsuviricetes;
OC   Martellivirales; Closteroviridae; Crinivirus.
OX   NCBI_TaxID=651355;
OH   NCBI_TaxID=161934; Beta vulgaris (Sugar beet).
OH   NCBI_TaxID=3654; Citrullus lanatus (Watermelon) (Citrullus vulgaris).
OH   NCBI_TaxID=3656; Cucumis melo (Muskmelon).
OH   NCBI_TaxID=3661; Cucurbita maxima (Pumpkin) (Winter squash).
OH   NCBI_TaxID=3662; Cucurbita moschata (Winter crookneck squash) (Cucurbita pepo var. moschata).
OH   NCBI_TaxID=3663; Cucurbita pepo (Vegetable marrow) (Summer squash).
OH   NCBI_TaxID=4039; Daucus carota (Wild carrot).
OH   NCBI_TaxID=4236; Lactuca sativa (Garden lettuce).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX   PubMed=11831736; DOI=10.1006/viro.1995.1133;
RA   Klaassen V.A., Boeshore M.L., Koonin E.V., Tian T., Falk B.W.;
RT   "Genome structure and phylogenetic analysis of lettuce infectious yellows
RT   virus, a whitefly-transmitted, bipartite closterovirus.";
RL   Virology 208:99-110(1995).
CC   -!- FUNCTION: RNA-dependent RNA polymerase replicates the viral genome
CC       composed of 2 RNA segments, RNA1 and RNA2. {ECO:0000305}.
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   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC         ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC         ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Ribosomal frameshifting; Named isoforms=2;
CC         Comment=The replicase 1a is produced from conventional translation of
CC         the 1a ORF. The replicase 1ab is generated probably by a +1 ribosomal
CC         frameshifting mechanism occurring at the 1a-1b genes boundary.;
CC       Name=Replicase 1ab;
CC         IsoId=Q83045-1; Sequence=Displayed;
CC       Name=Replicase 1a;
CC         IsoId=Q83044-1; Sequence=External;
CC   -!- DOMAIN: The C-terminal domain is required for autoproteolysis.
CC       {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the ssRNA positive-strand viruses RNA-directed
CC       RNA polymerase family. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAA61798.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; U15440; AAA61798.1; ALT_SEQ; Genomic_RNA.
DR   PRIDE; Q83045; -.
DR   Proteomes; UP000001099; Genome.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR   GO; GO:0008234; F:cysteine-type peptidase activity; IEA:UniProtKB-KW.
DR   GO; GO:0008174; F:mRNA methyltransferase activity; IEA:InterPro.
DR   GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR   GO; GO:0003724; F:RNA helicase activity; IEA:UniProtKB-EC.
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: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; -; 2.
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; IPR007094; RNA-dir_pol_PSvirus.
DR   InterPro; IPR001788; Tymovirus_RNA-dep_RNA_pol.
DR   Pfam; PF00978; RdRP_2; 1.
DR   Pfam; PF01443; Viral_helicase1; 1.
DR   Pfam; PF01660; Vmethyltransf; 1.
DR   SUPFAM; SSF52540; SSF52540; 1.
DR   SUPFAM; SSF56672; SSF56672; 1.
DR   PROSITE; PS51743; ALPHAVIRUS_MT; 1.
DR   PROSITE; PS51657; PSRV_HELICASE; 1.
DR   PROSITE; PS50507; RDRP_SSRNA_POS; 1.
PE   3: Inferred from homology;
KW   ATP-binding; Helicase; Hydrolase; Methyltransferase; Nucleotide-binding;
KW   Nucleotidyltransferase; Protease; Reference proteome;
KW   Ribosomal frameshifting; RNA-directed RNA polymerase; Thiol protease;
KW   Transferase; Viral RNA replication.
FT   CHAIN           1..2379
FT                   /note="Replicase polyprotein 1ab"
FT                   /id="PRO_0000402510"
FT   CHAIN           1..413
FT                   /note="Leader protease"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000402511"
FT   CHAIN           414..2379
FT                   /note="Methyltransferase/helicase/RNA-directed RNA
FT                   polymerase"
FT                   /evidence="ECO:0000250"
FT                   /id="PRO_0000402512"
FT   DOMAIN          495..674
FT                   /note="Alphavirus-like MT"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01079"
FT   DOMAIN          1538..1705
FT                   /note="(+)RNA virus helicase ATP-binding"
FT   DOMAIN          1706..1874
FT                   /note="(+)RNA virus helicase C-terminal"
FT   DOMAIN          2138..2251
FT                   /note="RdRp catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT   REGION          1356..1381
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        344
FT                   /note="For leader protease activity"
FT                   /evidence="ECO:0000250"
FT   ACT_SITE        393
FT                   /note="For leader protease activity"
FT                   /evidence="ECO:0000250"
FT   SITE            413..414
FT                   /note="Cleavage; by the leader protease"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   2379 AA;  276048 MW;  4EFB720D826A26F6 CRC64;
     MALEVESAFS LSYLLKENKQ TSNNLFSLIQ VPYTKMTHAK GKKTHLLRCI LGSPFETLTK
     SSIRRSLKNL REVCNLPYCN FKKIPKNISY KYQNPFLKLY EINNNFINCK VGATGNTNST
     YDWRNLSTIG NGWSVTSYHN DSVSRLHVSM VNNIPNSNTK KLSWWVTRVR SKNPWKRPYK
     VIYQRDFRDD GIKPYVSEFI LYAPKNRADL EMQSILLSSV ECFQDIKYAL NYWTNLKFKE
     ICNSALKRFT QTNIIITPVK PRVVSVNKAR EVSSSVEVKL QRYEREGEVF VVSKAGKEDT
     RVLNDDNAIR NLFNATLNGG KYKLHPEAKS ATGKRFKYYK DGFCWLDVFA DANRRIPEWV
     KPHCLLTGSV LMSCGLWDFA KRKMVSVSHG LLHYDRKLER SSARAGVRDF VGASNEAVQR
     EDFRDLDLRV EEFAERVLET ANLRSDNRLI DNILTRASDY INKKSKESKE LDINVCLSMD
     EKKMITNLFP DIQMSFNQKS YSNHGVFNAM RACENFYFSR KFKNSDYIDA GGDVVSTLRS
     KNHNVHICSP RLDLKDAARH IQRATVIDGL KGYGETISFC TNKTEDCAVN RDIIIAVEVY
     DMTLRDMAKA MLSHGSRKFE FSCIIPPEIF TKECNVELYE GRLKVTRIGD NVEYYYGSNG
     ETFSHSCQTL KDILSVQVFQ FGGRVFKKTL EHSRGQLHFF SICICEKIEP GSVKLKTYYQ
     RSELDKVTLR IPVKDSFGVV THYIIKEDRE FVSSMIEYVA NTGIKIDDKM VEWTYSQYRA
     KKTVTIKSGK VTQKETRIRK ELIPGFIAII MSEGIRAREK THYLAKMLYT SHYKPSIVNI
     IFRLIMHFLG GTKRFIYESL VDCLKFLTNS DYIDTIVNTE SRIEDLDKWF VFEQNVTITT
     DAEDQPSILE QSVKTFLSKY SEDVYERGDR SEFELEEFSS EQDLVDQLLN SGGGSKEDEW
     FYSYIFSIVR TKCTLSLAWR WTNRIFNFIT SCRAKGKDFV KYIYEIIKII INKPWEALCH
     YLVQGYKTVL KIPMTCVDSV NYLKRKSLEK ILSYFSHERA DDEYIFPGYD SDFSEESGDY
     GDENTELDSR SRCTVIKSKV EMLFRNIKGH IEKFLQRCGI IDQYNKIYHW FKSILTDVDC
     FNSVLNFITH TGCDALLAVL TGHFSIASCA LKFMTDVVIE KNLSEKHHTT TKLIAGNLTQ
     CIYKLDFIHP IWIPIRWGVK EISKIHIKKK LLNWRSTKEV TNESICKDLV HKSYIKYFDI
     KKAVWLLWFS LLIIFLHPTL GFFILFSIYP AIEIKRYYNN VVCFNNIKMS YPHVIDRLGG
     TYNFAKLKKA VREKFSENKS QGVKISEIPA EKDEDVMPPL EEVETPKRSV GRPSSKQDDI
     EDECNIKEDP TESLNFSNIE ATSNRYDTLR VGNSKLCKFL RFYPKSKCYA NIQTGDLIRD
     SIEEFYHLER SKLDIEISKM QRVVEIMNDT GRMLDNVRRM IDDRSMYVTL DGVSWYRLGC
     KDKNPAKEDF KAIFDHNFNI MEGNAKVKEF AVSSDEWRGM YSNERCRAIE QLFNDNNEMV
     RRPDVNGLKF YNKPPGAGKT TTIAKLMSKD LKNKVKCLAL SYTKVGRLEL IDKLKKDGIE
     KPEKYVKTYD SFLMNNDNIL EIVNLYCDEV FMMHAGHFLT LLTKIAYQNG YCYGDVNQIP
     FINRDPYTPA YLSREFFRKQ DLNYDTYTYR CPLDTCYLLS NLKDEMGNII YAGGVKNVNE
     VYPTIRSLNL FGINVVGEVP VEYNAKYLTF TQDEKLNLQR HIDSQGGCRN AVSTVNEAQG
     CTFSEVNLVR LVQFDNPVMS DINQFVVAIS RHTTTFKYFT PHSRLNDRVS NAISSLQSVS
     DFVLKTIILD SAFDVYTLNL THRDFKLPLC RPPAARYESI IDLMDIISPG VAFYNYLHRT
     LIFEYSDYYL PPCEDLRITL SKSKPYHPGA YVVSKILGKG ERNRPNTWKQ VIQSLSHRNF
     NAPIINHKLD VKRSAQILYD SVVKSLRQDR LTEWYEPILP DLFKIGKWLD DRDGSKYRML
     NRRLDFASLA DKFKTLNLMV KGETKPKMDL STYDSYNAPA NIVYYQQIVN LYFSPIFLEC
     FARLTYCLSD KIVLYSGMNT DVLAELIESK LPLGLNAYHT LEIDFSKFDK SQGTCFKLYE
     EMMYKMFGFS PELYDRDFKY TEYFCRAKAT CGVDLELGTQ RRTGSPNTWL SNTLVTLGMM
     LSSYDIDDID LLLVSGDDSL IFSRKHLPNK TQEINKNFGM EAKYIEKSSP YFCSKFIVEL
     NGKLKVIPDP IRFFEKLSIP IRQEDFVNGS VVKERFISFK DLMKEYDNDV AVIRIDEAVC
     YRYSIPVGCS YAALCYIHCC MSNFVSFRRI YDNCEIVWI