ID   RDRP_SHVX               Reviewed;        1718 AA.
AC   Q04575;
DT   01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-1994, sequence version 1.
DT   03-AUG-2022, entry version 104.
DE   RecName: Full=RNA replication protein;
DE   AltName: Full=194 kDa protein;
DE   Includes:
DE     RecName: Full=RNA-directed RNA polymerase;
DE              EC=2.7.7.48;
DE   Includes:
DE     RecName: Full=Helicase;
DE              EC=3.6.4.13;
GN   ORFNames=ORF1;
OS   Shallot virus X (ShVX).
OC   Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Alsuviricetes;
OC   Tymovirales; Alphaflexiviridae; Allexivirus; Acarallexivirus.
OX   NCBI_TaxID=31770;
OH   NCBI_TaxID=28911; Allium cepa var. aggregatum (Shallot) (Allium ascalonicum).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX   PubMed=1339468; DOI=10.1099/0022-1317-73-10-2553;
RA   Kanyuka K.V., Vishnichenko V.K., Levay K.E., Kondrikov D.Y., Ryabov E.V.,
RA   Zavriev S.K.;
RT   "Nucleotide sequence of shallot virus X RNA reveals a 5'-proximal cistron
RT   closely related to those of potexviruses and a unique arrangement of the
RT   3'-proximal cistrons.";
RL   J. Gen. Virol. 73:2553-2560(1992).
CC   -!- FUNCTION: RNA replication. The central part of this protein possibly
CC       functions as an ATP-binding helicase (Probable). {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   -!- SIMILARITY: Belongs to the potexvirus/carlavirus RNA replication
CC       protein family. {ECO:0000305}.
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DR   EMBL; M97264; AAA47787.1; -; Genomic_RNA.
DR   PIR; JQ1734; JQ1734.
DR   RefSeq; NP_620648.1; NC_003795.1.
DR   GeneID; 944368; -.
DR   KEGG; vg:944368; -.
DR   Proteomes; UP000001663; Genome.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
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: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; 2.60.120.590; -; 1.
DR   Gene3D; 3.40.50.300; -; 1.
DR   InterPro; IPR027351; (+)RNA_virus_helicase_core_dom.
DR   InterPro; IPR027450; AlkB-like.
DR   InterPro; IPR037151; AlkB-like_sf.
DR   InterPro; IPR002588; Alphavirus-like_MT_dom.
DR   InterPro; IPR043502; DNA/RNA_pol_sf.
DR   InterPro; IPR005123; Oxoglu/Fe-dep_dioxygenase.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   InterPro; IPR007094; RNA-dir_pol_PSvirus.
DR   InterPro; IPR001788; Tymovirus_RNA-dep_RNA_pol.
DR   Pfam; PF13532; 2OG-FeII_Oxy_2; 1.
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; PS51471; FE2OG_OXY; 1.
DR   PROSITE; PS51657; PSRV_HELICASE; 1.
DR   PROSITE; PS50507; RDRP_SSRNA_POS; 1.
PE   3: Inferred from homology;
KW   ATP-binding; Helicase; Hydrolase; Multifunctional enzyme;
KW   Nucleotide-binding; Nucleotidyltransferase; Reference proteome;
KW   RNA-directed RNA polymerase; Transferase; Viral RNA replication.
FT   CHAIN           1..1718
FT                   /note="RNA replication protein"
FT                   /id="PRO_0000222564"
FT   DOMAIN          59..223
FT                   /note="Alphavirus-like MT"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01079"
FT   DOMAIN          653..743
FT                   /note="Fe2OG dioxygenase"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00805"
FT   DOMAIN          889..1042
FT                   /note="(+)RNA virus helicase ATP-binding"
FT   DOMAIN          1043..1176
FT                   /note="(+)RNA virus helicase C-terminal"
FT   DOMAIN          1413..1520
FT                   /note="RdRp catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT   REGION          466..513
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          548..578
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          746..796
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        466..512
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        558..575
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        746..772
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         915..922
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255"
SQ   SEQUENCE   1718 AA;  194531 MW;  820FEAE1EB62415C CRC64;
     MTAVQKLFDQ ISDPNTKAGY SNACFEAAQR RPKKAMAIAP FSVTTPEALT LERFGITTSP
     FATTSHTHAA DKIIENDCLT IIGHYLPKRE AVTLIQLKRS KIHLLGRQPS QDNFQNYCHE
     PKDVLRYGIT HPNSCPVVNT EYAVLADTLH FMSPRQLYHL FSRNPKLERL FATLVLPIEA
     QHRLPSLFPD VYRLEYYKDH FAYMPGGHGG GAYVHSYGTL KWLDTAQVGP VDYTKSSITN
     PWPITDYLSI EKIETKAAHH IMFIQRTRAQ VDWPLPPIWV YHASEYVKLP LIFYPPEANV
     QKTYPHTLIK RMQLYCFSVK AVSLRDIFAK LRQVIETQEL VRYSMADLIR LANYFLFITG
     MNQVSDYESP LLENLFGKMC ASIRMRLRTF FQNLLGKTSY AALLTVTDVI PVHFTTQPKR
     REAVGELWFQ EPKWSVSTMT QPRKEHHRLQ MTWTLLAWFH QLESSGSMSE PCNNSESTPQ
     RTATSQQKAA KLTTSQKHNR RTDQTTMNPQ YPPLMLTIAP MMPRHSLMKK TIATPCRTLE
     EISDLDLDDF DDLPNEASNE PPSANEQSPD NHAETTTRGV FPCECGTEIT VNSFGRAIEV
     AGVNLTDHMK GRLAAFYSRD GQGYSYTGYS HKSQGWLEGL DKLIEACGEK PTTYNQCLVQ
     KYEQGSRIGF HSDEQAIYPK GNKILTVNAA GSGTFGIKCA KGETTLNLED GDYFQMPSGF
     QETHKHNVVA VTPRLSFTFR STVVNSQKKP AEPEKLNQNN ACPKPSDPSN ASGKQHKKTH
     PAKGNEKSSS PNLEPLDAPT VEILKLHGFT ALTPQHDGTC QIRPVYFNKD IHLRRKAVKT
     DMSPPARPFF DLATSLHRGI YTHKIDNRRA TAYMSDVKNN LTGLVLPKLD RDLLSSWVAL
     AETTTREVAV LAIHGAGGAG KSRALQELLR SSPELADSIN IVVPTINLAN DWKAKLPQMD
     PRRVMTFQKA CERECKSVTI FDDYGKLPAG FVDAYLAIKV NVELAILTGD QRQSTHHQER
     ESQISSLQSN IAQFSKYADY YLNATHRQPR RLANPIKVHA ERQLGGAVLK ANIVPDLAMV
     LVPAFRSQSL LTDLGRHAMT YAGCQGLTLN HLTIILDKDT PLCSDEVLYT AFSRASESIT
     FVNTHSDNPA FLAKLDATPY LKTLISWVRE DEEAGADCPA TEPLVKDVPT KTHIPVANDK
     VQLEGKIEAM EDKDTRELWS GEEKTNLMQT QDPVVQLFPH QQAKDEALFK ITIGERIRMA
     TPEQNAKQLR HTLNAGDLLF EAYAQFMKVP KETQPFDKRL WTHCRQLALR TYLSKPTSNL
     QQGARQDPDF PDNAIALFNK SQWVKKLEKV GARFKAGQTI SAFKQEVVLL TTTMALYLRK
     KREQHQPDNV FIMCERTPEQ FNAFVMTKWD FDRPNYTSDY TQYDQSQDAA FLNFEIRKAR
     HLGVPEDVLS FYKFIKTHAK TFLGNLAIMR LSAEGPTFDA NTECNIAYDA LRFRLGDDVR
     ASYAGDDLVR DKACEERAGW VYSESLFSLK AKPLVTNKPD FCGWRLTRHG IVKSPIQLYQ
     SLQLALRLGK IDEVKRSYAI DYLFAYRLGD KIYDIFDEDE LEKHQLVTRT LIKKGMQPPE
     SGNHLPIFHI TSDRLIRDPD AVKVQSYECD RILLKQPHII DDYIPAGTQP RNTEHPASAD
     RRDMTRACNL SAEKLAFGGN TINHLFRTSW EGRSPLSN