ID RDRP_NODAM Reviewed; 1043 AA.
AC Q9IMM4;
DT 16-APR-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 08-NOV-2023, entry version 70.
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 Nodamura virus (strain Mag115) (NoV).
OC Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Magsaviricetes;
OC Nodamuvirales; Nodaviridae; Alphanodavirus; Nodamura virus.
OX NCBI_TaxID=914672;
OH NCBI_TaxID=7158; Aedes.
OH NCBI_TaxID=7088; Lepidoptera (butterflies and moths).
OH NCBI_TaxID=9823; Sus scrofa (Pig).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX PubMed=11457991; DOI=10.1099/0022-1317-82-8-1855;
RA Johnson K.N., Johnson K.L., Dasgupta R., Gratsch T., Ball L.A.;
RT "Comparisons among the larger genome segments of six nodaviruses and their
RT encoded RNA replicases.";
RL J. Gen. Virol. 82:1855-1866(2001).
RN [2]
RP PROTEIN SEQUENCE OF 917-942; 947-955; 960-978 AND 994-1001, AND ALTERNATIVE
RP INITIATION.
RX PubMed=12573589; DOI=10.1006/viro.2002.1769;
RA Johnson K.L., Price B.D., Ball L.A.;
RT "Recovery of infectivity from cDNA clones of nodamura virus and
RT identification of small nonstructural proteins.";
RL Virology 305:436-451(2003).
RN [3]
RP SUBCELLULAR LOCATION.
RX PubMed=24696464; DOI=10.1128/jvi.03032-13;
RA Gant V.U. Jr., Moreno S., Varela-Ramirez A., Johnson K.L.;
RT "Two membrane-associated regions within the Nodamura virus RNA-dependent
RT RNA polymerase are critical for both mitochondrial localization and RNA
RT replication.";
RL J. Virol. 88:5912-5926(2014).
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}; Single-pass membrane protein
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. Has a N-terminal membrane-
CC spanning mitochondrial anchor. {ECO:0000250|UniProtKB:Q66929}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative initiation; Named isoforms=2;
CC Name=RNA-directed RNA polymerase;
CC IsoId=Q9IMM4-1; Sequence=Displayed;
CC Name=B1;
CC IsoId=Q9IMM4-2; Sequence=VSP_040283;
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; AF174533; AAF97860.1; -; Genomic_RNA.
DR RefSeq; NP_077730.1; NC_002690.1.
DR SMR; Q9IMM4; -.
DR KEGG; vg:962117; -.
DR Proteomes; UP000166289; 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 1: Evidence at protein level;
KW Alternative initiation; Direct protein sequencing; Host membrane;
KW Host mitochondrion; Host mitochondrion outer membrane; Membrane;
KW Nucleotide-binding; Nucleotidyltransferase; Reference proteome;
KW RNA-directed RNA polymerase; Transferase; Transmembrane;
KW Transmembrane helix; Viral RNA replication.
FT CHAIN 1..1043
FT /note="RNA-directed RNA polymerase"
FT /id="PRO_0000222448"
FT TRANSMEM 26..42
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 588..713
FT /note="RdRp catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT REGION 43..1043
FT /note="Cytoplasmic"
FT /evidence="ECO:0000250|UniProtKB:Q66929"
FT REGION 105..291
FT /note="Capping"
FT /evidence="ECO:0000250|UniProtKB:Q66929"
FT REGION 879..902
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 918..1043
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 885..902
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 918..952
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 968..982
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 699
FT /note="For RdRp/TNTase activity"
FT /evidence="ECO:0000250|UniProtKB:Q66929"
FT VAR_SEQ 1..912
FT /note="Missing (in isoform B1)"
FT /evidence="ECO:0000305"
FT /id="VSP_040283"
SQ SEQUENCE 1043 AA; 115774 MW; 0DF0CBDB5DBF3EBB CRC64;
MLNYETIING ASSALNIVSR ALGYRVPLAK SLALVAGSCV VYKIIVHRRT LVAFLVIGPY
ATVVQHRLPM ALQRAIIEYT REDREISLFP QNSIVSAEHA RKADNGHPIS GGTRDVARET
ISLAIRAAGF RHYEISPARQ SPAEAASHQH YAAADLVRAA TEDKIQDGDV VVAIDIDYYL
RDIDRYLGRG VPFMAYTFNP VEVAGRDGDS FFRITNNQVT FDVSGGGSWS HEVWDWCAFG
EFIETRDASW LAWFARAVGL TKSQIHKVHY CRPWPQSPHR ALVWCLPVAS YWRFTFIPTD
LHTRTLRRVR YQDTSRPGWN SIVSTGSEGL NISLGREGAD HCVTIPKVHY DMLMGLSSAQ
SLSSRMIGLK YTDPSVLATV AQYYQGKNVE VADADRIGRA INPKVHWPAH VEVDEAEVSA
RVYASPLVSD ENMMPMIKRW ETLSLSLDRR VTFQRNPKVP GKRLRAYAIE FVDLVVPERG
VGVPYSLEDT AAMLDKPSQT LAIQQVWETV DMPPRRLIEA FVKNEPTMKA GRIISSFADM
RFLLRFSSYT LAFRDQVLHA EHNRHWFCPG LTPEQIATKV VDYVSGVEEP SEGDFSNFDG
TVSEWLQRHV MNAVYLRYFN HRAQRDLRSY TDMLVSCPAR AKRFGFAYDA GVGVKSGSPT
TCDLNTVCNG FLQYCSIRMT HPELTPIDAF RLIGLAFGDD SLFERRFAKN YAKVSAEVGM
VLKIERFDPA QGITFLARVY PDPYTSTTSF QDPLRTWRKL HLTTRDPTIP LATAAIDRVE
GYLVTDGLSP LTGAYCRMVK RVYEAGGAED AAKRRSRKSH SREKPYWLTV GGAWPQDVKD
VDLMFQCAAA RTGVDLETLR SLDQRLGEIT DVWADITINR DNEPNPYKDT LDLEGPADGR
VDDRVFQNDK HVMRLRANQV TSSQAGAAGS GDASNDPNAH DRGSQRQQGS ASVLRVPDRA
APAGVSSDEQ PAHQTASRSS ASRGGAGPGR GGRRRPGPPA KTTAGGARDG NQARAPTSGP
SKRQAEGRSR SSRGPAGSRG RGK
//
