L_RSVT
ID L_RSVT Reviewed; 2919 AA.
AC Q85431;
DT 11-JAN-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 87.
DE RecName: Full=RNA-directed RNA polymerase L;
DE Short=Protein L;
DE EC=2.7.7.48 {ECO:0000250|UniProtKB:I0DF35};
DE AltName: Full=Large structural protein;
DE AltName: Full=Replicase;
DE AltName: Full=Transcriptase;
DE Includes:
DE RecName: Full=cap-snatching endonuclease;
DE EC=3.1.-.- {ECO:0000269|PubMed:30439393};
GN ORFNames=pc1;
OS Rice stripe virus (isolate T) (RSV).
OC Viruses; Riboviria; Orthornavirae; Negarnaviricota; Polyploviricotina;
OC Ellioviricetes; Bunyavirales; Phenuiviridae; Tenuivirus.
OX NCBI_TaxID=36394;
OH NCBI_TaxID=4498; Avena sativa (Oat).
OH NCBI_TaxID=66017; Digitaria.
OH NCBI_TaxID=38413; Eragrostis.
OH NCBI_TaxID=4513; Hordeum vulgare (Barley).
OH NCBI_TaxID=4530; Oryza sativa (Rice).
OH NCBI_TaxID=4555; Setaria italica (Foxtail millet) (Panicum italicum).
OH NCBI_TaxID=4556; Setaria viridis (Green bristlegrass) (Setaria italica subsp. viridis).
OH NCBI_TaxID=4565; Triticum aestivum (Wheat).
OH NCBI_TaxID=4577; Zea mays (Maize).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX PubMed=7996149; DOI=10.1099/0022-1317-75-12-3569;
RA Toriyama S., Takahashi M., Sano Y., Shimizu T.;
RT "Nucleotide sequence of RNA 1, the largest genomic segment of rice stripe
RT virus, the prototype of the tenuiviruses.";
RL J. Gen. Virol. 75:3569-3579(1994).
RN [2]
RP REVIEW.
RX PubMed=28418734; DOI=10.1080/1040841x.2017.1307805;
RA Amroun A., Priet S., de Lamballerie X., Querat G.;
RT "Bunyaviridae RdRps: structure, motifs, and RNA synthesis machinery.";
RL Crit. Rev. Microbiol. 43:753-778(2017).
RN [3]
RP FUNCTION, DOMAIN, MUTAGENESIS OF HIS-535; ASP-547; ASP-567; GLU-585;
RP THR-587 AND LYS-604, AND CATALYTIC ACTIVITY.
RX PubMed=30439393; DOI=10.1016/j.virusres.2018.11.006;
RA Zhao S., Xu G., He G., Peng Y., Liang C.;
RT "Characterization of an endonuclease in rice stripe tenuivirus Pc1 in
RT vitro.";
RL Virus Res. 260:33-37(2019).
RN [4]
RP REVIEW.
RX PubMed=31948728; DOI=10.1016/j.tim.2019.12.006;
RA Olschewski S., Cusack S., Rosenthal M.;
RT "The Cap-Snatching Mechanism of Bunyaviruses.";
RL Trends Microbiol. 28:293-303(2020).
CC -!- FUNCTION: RNA-dependent RNA polymerase, which is responsible for the
CC replication and transcription of the viral RNA genome using antigenomic
CC RNA as an intermediate (By similarity). During transcription,
CC synthesizes subgenomic RNAs and assures their capping by a cap-
CC snatching mechanism, which involves the endonuclease activity cleaving
CC the host capped pre-mRNAs (By similarity). These short capped RNAs are
CC then used as primers for viral transcription. The 3'-end of subgenomic
CC mRNAs molecules are not polyadenylated. During replication, the
CC polymerase binds the 5' and 3' vRNA extremities at distinct sites (By
CC similarity). In turn, significant conformational changes occur in the
CC polymerase and in vRNA to initiate active RNA synthesis. As a
CC consequence of the use of the same enzyme for both transcription and
CC replication, these mechanisms need to be well coordinated (By
CC similarity). {ECO:0000250|UniProtKB:A5HC98,
CC ECO:0000250|UniProtKB:I0DF35, ECO:0000250|UniProtKB:J3TRD1,
CC ECO:0000250|UniProtKB:P27316}.
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 -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:30439393};
CC Note=For endonuclease activity. Binds 2 Mn(2+) ions in the active site
CC (By similarity). The divalent metal ions are crucial for catalytic
CC activity (PubMed:30439393). {ECO:0000250|UniProtKB:P27316,
CC ECO:0000269|PubMed:30439393};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P27316};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000250|UniProtKB:P27316};
CC Note=For polymerase activity. Initiation activity is stronger in the
CC presence of Mn(2+) than in the presence of Mg(2+).
CC {ECO:0000250|UniProtKB:P27316};
CC -!- SUBUNIT: Homomultimer. Interacts with glycoprotein N; this interaction
CC allows efficient polymerase packaging into virus particles. Interacts
CC with nucleoprotein N. {ECO:0000250|UniProtKB:P27316}.
CC -!- SUBCELLULAR LOCATION: Host Golgi apparatus
CC {ECO:0000250|UniProtKB:I0DF35}. Host endoplasmic reticulum
CC {ECO:0000250|UniProtKB:I0DF35}. Host endoplasmic reticulum-Golgi
CC intermediate compartment {ECO:0000250|UniProtKB:I0DF35}. Virion
CC {ECO:0000250|UniProtKB:P20470}.
CC -!- DOMAIN: The N-terminus contains the endonuclease activity (endoN)
CC (PubMed:30439393). The central region contains the RdRp activity (By
CC similarity). The C-terminus contains the cap-binding region (By
CC similarity). {ECO:0000250|UniProtKB:A2SZS3,
CC ECO:0000250|UniProtKB:I0DF35, ECO:0000269|PubMed:30439393}.
CC -!- MISCELLANEOUS: Classified as His(+) endonuclease since it has a
CC histidine upstream of the active site that coordinates the first
CC cation. {ECO:0000303|PubMed:31948728}.
CC -!- SIMILARITY: Belongs to the Bunyavirales RNA polymerase family.
CC {ECO:0000305}.
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DR EMBL; D31879; BAA06677.1; -; Genomic_RNA.
DR RefSeq; NP_620522.1; NC_003755.1.
DR SMR; Q85431; -.
DR PRIDE; Q85431; -.
DR GeneID; 962685; -.
DR KEGG; vg:962685; -.
DR Proteomes; UP000006677; Genome.
DR GO; GO:0030430; C:host cell cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0006351; P:transcription, DNA-templated; IEA:InterPro.
DR GO; GO:0039694; P:viral RNA genome replication; IEA:InterPro.
DR InterPro; IPR022531; DUF3770.
DR InterPro; IPR029124; L_protein_N.
DR InterPro; IPR003323; OTU_dom.
DR InterPro; IPR007099; RNA-dir_pol_NSvirus.
DR InterPro; IPR015842; RNA-dir_pol_tenuivirus.
DR InterPro; IPR007322; RNA_pol_bunyavir.
DR Pfam; PF04196; Bunya_RdRp; 1.
DR Pfam; PF12603; DUF3770; 1.
DR Pfam; PF15518; L_protein_N; 1.
DR PIRSF; PIRSF036873; L_TenuV; 1.
DR PROSITE; PS50802; OTU; 1.
DR PROSITE; PS50525; RDRP_SSRNA_NEG_SEG; 1.
PE 1: Evidence at protein level;
KW Host endoplasmic reticulum; Host Golgi apparatus; Hydrolase; Magnesium;
KW Manganese; Metal-binding; Nucleotide-binding; Nucleotidyltransferase;
KW Reference proteome; RNA-directed RNA polymerase; Transferase;
KW Viral RNA replication; Virion.
FT CHAIN 1..2919
FT /note="RNA-directed RNA polymerase L"
FT /id="PRO_0000403929"
FT DOMAIN 1472..1671
FT /note="RdRp catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00539"
FT REGION 86..675
FT /note="Endonuclease"
FT /evidence="ECO:0000250|UniProtKB:A5HC98"
FT REGION 2494..2632
FT /note="Cap-binding"
FT /evidence="ECO:0000250|UniProtKB:A5HC98"
FT ACT_SITE 604
FT /note="For endonuclease activity"
FT /evidence="ECO:0000250|UniProtKB:I0DF35"
FT BINDING 535
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:A5HC98"
FT BINDING 567
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:A5HC98"
FT BINDING 567
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:A5HC98"
FT BINDING 585
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:A5HC98"
FT BINDING 1636
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic; for RdRp activity"
FT /evidence="ECO:0000250|UniProtKB:I0DF35"
FT MUTAGEN 535
FT /note="H->A: Reduced endonuclease activity."
FT /evidence="ECO:0000269|PubMed:30439393"
FT MUTAGEN 547
FT /note="D->A: Complete loss of endonuclease activity."
FT /evidence="ECO:0000269|PubMed:30439393"
FT MUTAGEN 567
FT /note="D->A: Complete loss of endonuclease activity."
FT /evidence="ECO:0000269|PubMed:30439393"
FT MUTAGEN 585
FT /note="E->A: Complete loss of endonuclease activity."
FT /evidence="ECO:0000269|PubMed:30439393"
FT MUTAGEN 587
FT /note="T->A: No effect on endonuclease activity."
FT /evidence="ECO:0000269|PubMed:30439393"
FT MUTAGEN 604
FT /note="K->A: Complete loss of endonuclease activity."
FT /evidence="ECO:0000269|PubMed:30439393"
SQ SEQUENCE 2919 AA; 336877 MW; 16FB7BC57FB12FC0 CRC64;
MTTPPLVIPL HVHGRSYELL AGYHEVDWQE IEELEETDVR GDGFCLYHSI LYSMGLSKEN
SRTTEFMIKL RSNPAICQLD QEMQLSLMKQ LDPNDSSAWG EDIAIGFIAI ILRIKIIAYQ
TVDGKLFKTI YGAEFESTIR IRNYGNYHFK SLETDFDHKV KLRSKIEEFL RMPVEDCESI
SLWHASVYKP IVSDSLSGHK SFSNVDELIG SIISSMYKIM DNGDQCFLWS AMRMVARPSE
KLYALAVFLG FNLKFYHVRK RAEKLTAKLE SDHTNLGVKL IEVYEVSEPT RSTWVLKPGG
SRITETRNFV IEEIIDNRRS LESLFVSSSE YPAELCSQKL SAIKDRIALM FGFINRTPEN
SGRELYINTY YLKRILQVER NVIRDSLRSQ PAVGMIQIIR LPTAFGTYNP EVGTLLLAQT
GLIYRLGTTT RVQMEVRRSP SVISRSHKIT SFPETQKHNN NLYDYAPRTQ ETFYHPNAEI
YEAVDVKTPS VITEIVDNHI VIKLNTDDKG WSVSDSIKQD FVYRKRLMDA KNIVHDFVFD
ILSTETDKSF KGADLSIGGI SDNWSPDVII SRESDPQYED IVVYEFTTRS TESIESLLRS
VEVKSLRYKE AIQERAITLK KRISYYTICV SLDAVATNLL SLPADVCREL IIRLRVANQV
KIQLADNDIN LDSATLLAPD IYRIKEMFRE SFPNNKFIHP ITKEMYEHFV NPMISGEKDY
VANLKSIIDK ETRDEQRKNL ESLKVVDGKK YTERKAETAL NEMSQAEEHY RSYFENDNFR
STLKAPVQLP LIIPDVSSQD NQFSNKELSD RIRKKPIDHP IYNIWDQAVN KRNCSIALGH
LDELEISMLE GQVAKKVEES YKKDRSQYNR TTLLTNMKED IYLAERGINA KKRLEEPDVK
FYRDQSKRPF HPFVSETRDI EQFTQKECLE LNEESGHCSL INVEDLVLSA LELHEVGDLE
HLWNNIKAHS KTKFALYAKF ISDLATELAI SLSQNCKEDT YVVKKLRDFS CYVLIKPVNL
KSNVFFSLYI PSNIYKSHNT TFKTLIGSPE SGYMTDFVSA NVSKLVNWVR CEAMMLAQRG
FWREFYAVAP SIEEQDGMAE PDSVCQMMSW TLLILLNDKH QLEEMITVSR FVHMEGFVTF
PAWPKPYKMF DKLSVTPRSR LECLVIKRLI MLMKHYSENP IKFMIEDEKK KWFGFKNMFL
LDCNGKLADL SDQDQMLNLF YLGYLKNKDE EVEDNGMGQL LTKILGFESA MPKTRDFLGM
KDPEYGTIKK HEFSISYVKD LCDKFLDRLK KTHGIKDPIT YLGDKIAKFL STQFIETMAS
LKASSNFSED YYLYTPSRRL KNQEQSRSKH VIDAGGNISA SVKGKLYHRS KVIEKLTTLI
KDETPGKELK IVVDLLPKAM EVLNKNECMH ICIFKKNQHG GLREIYVLNI FERIMQKTVE
DFSRAILECC PSETMTSPKN KFRIPELHNM EARKTLKNEY MTISTSDDAS KWNQGHYVSK
FMCMLLRLTP TYYHGFLVQA LQLWHHKKIF LGDQLLQLFN QNAMLNTMDT TLMKVFQAYK
GEIQVPWMKA GRSYIETETG MMQGILHYTS SLFHAIFLDQ LAEECRRDIN RAIKTINNKE
NEKVSCIVNN MESSDDSSFI ISIPNFKENE AAQLYLLCVV NSWFRKKEKL GTYLGIYKSP
KSTTQTLFVM EFNSEFFFSG DVHRPTFRWV NAAVLIGEQE TLSGIQEELS NTLKDVIEGG
GTYALTFIVQ VAQAMIHYRM LGSSASSVWP AYETLLKNSY DPALGFFLMD NPKCAGLLGF
NYNVWIACTT TPLGEKYHEM IQEEMKAESQ SLKSVTEDTI NTGLVSRTTM VGFGNKKRWM
KLMTTLNLSA DVYEKIEEEP RVYFFHAATA EQIIQKIAIK MKSPGVIQSL SKGNMLARKI
ASSVFFISRH IVFTMSAYYD ADPETRKTSL LKELINSSKI PQRHDYLQEP HTLKPTKVEV
DEDSWEFKSA KEECVRVLKQ RIKIHTGREE RSISLLFENM AKSMIGRCTD QYDVRENVSI
LACALKMNYS IFKKDAAPNR YLLDEKNLVY PLIGKEVSVY VKSDKVHIEI SEKKERLSTK
LFNIDKMKDI EETLSLLFPS YGDYLSLKET IDQVTFQSAI HKVNERRRVR ADVHLTGTEG
FSKLPMYTAA VWAWFDVKTI PAHDSIYRTI WKVYKEQYSW LSDTLKETVE KGPFKTVQGV
VNFISRAGVR SRVVHLVGSF GKNVRGSINL VTAIKDNFSN GLVFKGNIFD IKAKKTRESL
DNYLSICTTL SQAPITKHDK NQILRSLFVS GPRIQYVSSQ FGSRRNRMSI LQEVVADDPT
LHWPDQDTSQ KQLEDKFREL AHKELPFLTE KVFHDYLEKI EQLMKENTHL GGRDVDASKT
PYVLARANDI EIHCYELWRE YDEDEDEAYQ AYCSEVEAAM DQEKLNALIE RYHVDPKANW
IQMLMNGEIE TVEELNKLDK GFESHRLALV ERIRVGKLGI LGSYTKCQQR IEELDGEGNK
THRYTGEGIW RGSFDDSDVC IVVQDLKKTR ESYLKCVVFS KVSDYKVLMG HLKTWCREHH
ISNDEFPTCT QKELLSYGVT KSSVLLYKMN GMKMLRNMEK GIPLYWNPSL STRSQTYINW
LAVDITDHSL RLRNRTVENG RVVNQTIMVV PLYKTDVQIF KTSPVDLEQD VQNDRLKLLS
VTKAGELRWL QDWIMWRSSA VDDLNILNQV RRNKAARDHF NAKPEFKKWI KELWDYALDT
TLINKKVFIT TQGSESQSTV SSGDSDSAVA PLTDEAVDEI HDLLDKELEK GTLKQIIHDA
TIDAQLDIPA IESFLAEEME VFKSSLAKSH PLLLNYVRYM IQEIGVTNFR SLIDSFNQKD
PLKSVSLSIL DLKEVFKFVY QDINDAYFVK QEEDHKFDF
