ID   RDRP_PAV                Reviewed;         973 AA.
AC   Q9J7Z2;
DT   16-APR-2002, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2000, sequence version 1.
DT   13-SEP-2023, entry version 75.
DE   RecName: Full=RNA-directed RNA polymerase {ECO:0000255|PROSITE-ProRule:PRU00539};
DE            Short=RdRp;
DE            EC=2.7.7.48 {ECO:0000255|PROSITE-ProRule:PRU00539};
DE   AltName: Full=RNA replicase;
DE            Short=Protein A;
OS   Pariacoto virus (PaV).
OC   Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Magsaviricetes;
OC   Nodamuvirales; Nodaviridae; Alphanodavirus.
OX   NCBI_TaxID=103782;
OH   NCBI_TaxID=37547; Spodoptera eridania (Southern armyworm).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX   PubMed=10799587; DOI=10.1128/jvi.74.11.5123-5132.2000;
RA   Johnson K.N., Zeddam J.-L., Ball L.A.;
RT   "Characterization and construction of functional cDNA clones of Pariacoto
RT   virus, the first Alphanodavirus isolated outside Australasia.";
RL   J. Virol. 74:5123-5132(2000).
CC   -!- FUNCTION: RNA-dependent RNA polymerase, which replicates the viral
CC       genome composed of 2 RNA segments, RNA1 and RNA2. Does not need an
CC       exogenous primer. Also possesses a terminal nucleotidyl transferase
CC       (TNTase) activity. The TNTase catalyzes the addition of nucleotide to
CC       the 3'-end of plus- and minus-stranded RNAs, probably to repair the 3'-
CC       end nucleotide loss. Forms the open necked connection to the cytosol of
CC       the virus-induced replication vesicles. Mediates viral RNA1
CC       recruitment. {ECO:0000250|UniProtKB:Q66929}.
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       PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:21249;
CC         Evidence={ECO:0000250|UniProtKB:Q66929};
CC   -!- COFACTOR:
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000250|UniProtKB:Q66929};
CC       Note=For RdRP activity. {ECO:0000250|UniProtKB:Q66929};
CC   -!- SUBUNIT: Homododecamer. Forms 2 stacked rings of 35-nm in diameter,
CC       arranged in a crown-like structure at the opening of virus-induced
CC       replication vesicles. Interacts with protein B2.
CC       {ECO:0000250|UniProtKB:Q66929}.
CC   -!- SUBCELLULAR LOCATION: Host mitochondrion outer membrane
CC       {ECO:0000250|UniProtKB:Q66929}. Note=Part of the 30- to 90-nm
CC       invaginations of the host mitochondrial outer membrane that form the
CC       viral replication complexes vesicules. {ECO:0000250|UniProtKB:Q66929}.
CC   -!- DOMAIN: The N-terminus is important for both membrane association and
CC       mitochondrial localization. It may also contain a RNA methyltransferase
CC       (MTase-GTase) capping domain. The C-terminus contains the RNA-dependent
CC       RNA polymerase domain and a structurally disordered region at the very
CC       end. {ECO:0000250|UniProtKB:Q66929}.
CC   -!- MISCELLANEOUS: The viral bipartite genome is composed of RNA1 and RNA2.
CC       {ECO:0000250|UniProtKB:Q66929}.
CC   -!- SIMILARITY: Belongs to the nodaviridae RNA polymerase family.
CC       {ECO:0000305}.
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DR   EMBL; AF171942; AAF71691.1; -; Genomic_RNA.
DR   RefSeq; NP_620109.1; NC_003691.1.
DR   SMR; Q9J7Z2; -.
DR   GeneID; 956347; -.
DR   KEGG; vg:956347; -.
DR   OrthoDB; 155at10239; -.
DR   Proteomes; UP000204174; Genome.
DR   GO; GO:0044193; C:host cell mitochondrial outer membrane; IEA:UniProtKB-SubCell.
DR   GO; GO:0016020; C:membrane; IEA:UniProtKB-KW.
DR   GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR   GO; GO:0003723; F:RNA binding; 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:0039694; P:viral RNA genome replication; IEA:InterPro.
DR   CDD; cd23173; ps-ssRNAv_Nodaviridae_RdRp; 1.
DR   InterPro; IPR043502; DNA/RNA_pol_sf.
DR   InterPro; IPR043647; Noda_Vmethyltr_dom.
DR   InterPro; IPR001205; RNA-dir_pol_C.
DR   InterPro; IPR007094; RNA-dir_pol_PSvirus.
DR   Pfam; PF19222; Noda_Vmethyltr; 1.
DR   Pfam; PF00680; RdRP_1; 1.
DR   SUPFAM; SSF56672; DNA/RNA polymerases; 1.
DR   PROSITE; PS50507; RDRP_SSRNA_POS; 1.
PE   3: Inferred from homology;
KW   Host membrane; Host mitochondrion; Host mitochondrion outer membrane;
KW   Membrane; Nucleotide-binding; Nucleotidyltransferase;
KW   RNA-directed RNA polymerase; Transferase; Viral RNA replication.
FT   CHAIN           1..973
FT                   /note="RNA-directed RNA polymerase"
FT                   /id="PRO_0000222449"
FT   DOMAIN          558..683
FT                   /note="RdRp catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT   REGION          96..264
FT                   /note="Capping"
FT                   /evidence="ECO:0000250|UniProtKB:Q66929"
FT   REGION          853..973
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        880..894
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        952..973
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        669
FT                   /note="For RdRp/TNTase activity"
FT                   /evidence="ECO:0000250|UniProtKB:Q66929"
SQ   SEQUENCE   973 AA;  108099 MW;  C08835451D46EA1E CRC64;
     MEEHIPLPSQ YESPKALPPR VPSSRWLRSL RPRLANSCLA LKIRAHESLV KIRLCKPYDA
     QSRSKIIEKV IERRETRKTL AHQLKDLKLV PVARDHTHGR AAKFRTSANI WMNEAMRAAG
     YEPYNVSMSN HDIERGNRYF YFAKDLTIPY RNDPVSDNTG FVFCDVDYYA DMEKWMQHFK
     PMLLYTLVPE SLSYHCDDHS FHVNDDRVFF DVRGGASYSH QLWDYTGDTI CVRGKNKELL
     VFTIEQKCIQ GDPHRRIIFL EPAARVAWPF YKPMKVEVGL KRKCMTAGQV NVLYEPIDDK
     ISLSASGSRH TVETTGRTLA AITARMKNKT SPPMVADVER ILRDAGDKEA CVNAPILFEL
     IPEAKFRVNV VKTTATPTHF QPLGPLRTED GETCGHAVTT TLATAPALLP MRGVNSDVAT
     VNGRVKKPAN TVIPFKEYKE YASEFVEFLV PEPGVGHPWD TAAVREVQDN RQQKARINMV
     AATVSTHSSN RLKAFIKAEA YAATNDPRNI TTMAPELTLM MSCFTYAFKE KILYEQPWYG
     PGKTPKQVGR RLQSIAKHGT LESDYSRFDG SISEWLQKNV VKAAYMRFFK EHQRTEFQSW
     FSKVFMQMGT TTAGVRYEAG WGTRSGSPIT TDGNTMLNAF VVYCCYRKLC HTPAEAWRKL
     SQGALLTGDD AVLAHENGLE PALLDVVKNL GLKVEAKVNG PDDPVSFCGR IYPRLSDCIT
     SFQDPLRTIP KLHLTTNKGV SPEQAAANRA HGYLATDKAT PIIGTWARRV IELTGDLKVK
     GATREEQYKL SNAHQQLDPS LIETAMANIL GIDVGELKAL DKAVSEAKAL DQMPVVLGNC
     YKHKIEAVVG GEVVGPGPRV ETVEPNHEQS SGTPEVVPEM AGHSERRDKS SNPRPGGKAE
     GLSSKAGKPR VPTRPAADRK AAAGSGNRRG PTNGRRPIRD RAPRGGGRPN PGTTPPVSNS
     ETTTTTAVVH ASA
//