ID   L_ALLVP                 Reviewed;        2201 AA.
AC   Q6XQI9;
DT   20-JAN-2009, integrated into UniProtKB/Swiss-Prot.
DT   26-FEB-2008, sequence version 2.
DT   03-AUG-2022, entry version 71.
DE   RecName: Full=RNA-directed RNA polymerase L {ECO:0000255|HAMAP-Rule:MF_04086};
DE            Short=Protein L {ECO:0000255|HAMAP-Rule:MF_04086};
DE            EC=2.7.7.48 {ECO:0000255|HAMAP-Rule:MF_04086};
DE   AltName: Full=Large structural protein {ECO:0000255|HAMAP-Rule:MF_04086};
DE   AltName: Full=Replicase {ECO:0000255|HAMAP-Rule:MF_04086};
DE   AltName: Full=Transcriptase {ECO:0000255|HAMAP-Rule:MF_04086};
DE   Includes:
DE     RecName: Full=cap-snatching endonuclease {ECO:0000255|HAMAP-Rule:MF_04086};
DE              EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_04086};
GN   Name=L {ECO:0000255|HAMAP-Rule:MF_04086};
OS   Allpahuayo mammarenavirus (isolate Rat/Peru/CLHP-2472/1997) (ALLV).
OC   Viruses; Riboviria; Orthornavirae; Negarnaviricota; Polyploviricotina;
OC   Ellioviricetes; Bunyavirales; Arenaviridae; Mammarenavirus.
OX   NCBI_TaxID=144752;
OH   NCBI_TaxID=48011; Oecomys bicolor (Bicolored arboreal rice rat).
OH   NCBI_TaxID=48012; Oecomys roberti (Robert's arboreal rice rat).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RX   PubMed=14698659; DOI=10.1016/j.virol.2003.08.016;
RA   Charrel R.N., Lemasson J.J., Garbutt M., Khelifa R., De Micco P.,
RA   Feldmann H., de Lamballerie X.;
RT   "New insights into the evolutionary relationships between arenaviruses
RT   provided by comparative analysis of small and large segment sequences.";
RL   Virology 317:191-196(2003).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC RNA].
RA   Emonet S., de Lamballerie X., de Micco P., Charrel R.N.;
RT   "Complete sequence determination and analysis of the large RNA segment of
RT   arenaviruses.";
RL   Submitted (MAY-2004) to the EMBL/GenBank/DDBJ databases.
RN   [3]
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   [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. During transcription, synthesizes subgenomic
CC       RNAs and assures their capping by a cap-snatching mechanism, which
CC       involves the endonuclease activity cleaving the host capped pre-mRNAs.
CC       These short capped RNAs are then used as primers for viral
CC       transcription. The 3'-end of subgenomic mRNAs molecules are
CC       heterogeneous and not polyadenylated. The replicase function is to
CC       direct synthesis of antigenomic and genomic RNA which are encapsidated
CC       and non capped. As a consequence of the use of the same enzyme for both
CC       transcription and replication, these mechanisms need to be well
CC       coordinated. These processes may be regulated by proteins N and Z in a
CC       dose-dependent manner. {ECO:0000255|HAMAP-Rule:MF_04086}.
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|HAMAP-Rule:MF_04086};
CC   -!- COFACTOR:
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_04086};
CC       Note=For endonuclease activity. Binds 2 Mn(2+) ions in the active site.
CC       The divalent metal ions are crucial for catalytic activity.
CC       {ECO:0000255|HAMAP-Rule:MF_04086};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_04086};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_04086};
CC       Note=For polymerase activity. {ECO:0000255|HAMAP-Rule:MF_04086};
CC   -!- SUBUNIT: Homomultimer; the oligomeric structure is essential for the
CC       polymerase activity. Interacts with nucleoprotein N. Interacts with
CC       protein Z; this interaction inhibits viral transcription and
CC       replication. {ECO:0000255|HAMAP-Rule:MF_04086}.
CC   -!- SUBCELLULAR LOCATION: Virion {ECO:0000255|HAMAP-Rule:MF_04086}. Host
CC       cytoplasm {ECO:0000255|HAMAP-Rule:MF_04086}.
CC   -!- DOMAIN: The N-terminus contains the endonuclease activity (endoN). The
CC       central region contains the RdRp activity. {ECO:0000255|HAMAP-
CC       Rule:MF_04086}.
CC   -!- MISCELLANEOUS: Classified as His(-) endonuclease since it does not have
CC       a histidine upstream of the active site that coordinates the first
CC       cation. His(-) endonucleases display very low activity in vitro,
CC       although they are clearly active in vivo. {ECO:0000255|HAMAP-
CC       Rule:MF_04086}.
CC   -!- SIMILARITY: Belongs to the Bunyavirales RNA polymerase family.
CC       {ECO:0000255|HAMAP-Rule:MF_04086}.
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DR   EMBL; AY216502; AAP44538.2; -; Genomic_RNA.
DR   RefSeq; YP_001649212.1; NC_010249.1.
DR   SMR; Q6XQI9; -.
DR   PRIDE; Q6XQI9; -.
DR   GeneID; 5848365; -.
DR   KEGG; vg:5848365; -.
DR   Proteomes; UP000009258; Genome.
DR   GO; GO:0030430; C:host cell cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0044423; C:virion component; IEA:UniProtKB-UniRule.
DR   GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR   GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0003968; F:RNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0075526; P:cap snatching; IEA:UniProtKB-UniRule.
DR   GO; GO:0039689; P:negative stranded viral RNA replication; ISS:UniProtKB.
DR   GO; GO:0039696; P:RNA-templated viral transcription; ISS:UniProtKB.
DR   HAMAP; MF_04086; ARENA_L; 1.
DR   InterPro; IPR026382; CapSnatchArena.
DR   InterPro; IPR007099; RNA-dir_pol_NSvirus.
DR   InterPro; IPR010453; RNA_pol_arenavir.
DR   Pfam; PF06317; Arena_RNA_pol; 1.
DR   Pfam; PF17296; ArenaCapSnatch; 1.
DR   PIRSF; PIRSF000836; L_ArenaV; 1.
DR   PROSITE; PS50525; RDRP_SSRNA_NEG_SEG; 1.
PE   3: Inferred from homology;
KW   Cap snatching; Host cytoplasm; Hydrolase; Magnesium; Manganese;
KW   Metal-binding; Nucleotide-binding; Nucleotidyltransferase;
KW   RNA-directed RNA polymerase; Transferase; Viral RNA replication; Virion.
FT   CHAIN           1..2201
FT                   /note="RNA-directed RNA polymerase L"
FT                   /id="PRO_0000361632"
FT   DOMAIN          1156..1352
FT                   /note="RdRp catalytic"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_04086"
FT   REGION          26..285
FT                   /note="Endonuclease"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_04086"
FT   ACT_SITE        114
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_04086"
FT   BINDING         51
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_04086"
FT   BINDING         88
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_04086"
FT   BINDING         88
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_04086"
FT   BINDING         101
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_04086"
FT   BINDING         1312
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_note="catalytic; for RdRp activity"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_04086"
SQ   SEQUENCE   2201 AA;  252792 MW;  BBD00195D874F7D3 CRC64;
     MDVHLIELRD LVRKWVPDDL ELSEQKNIML AQTQIRATVV ESLKLLSTIV EVDSCKKHSC
     VHNTSKTVNA ILREHKIIGP TLPDVTPDGY CVIGDVLILL EVFVRTNQES FEKKFNQDFE
     KLMQMSADLK KCGVTLVPTI DGRSTYYVDF IPDWVVERLR WLISRLMSSL REDGQEIEEL
     EYERLISSLS SLENQSLGLE SLLAMREKGL SYKETLDKLF LEGMENKLTV DESRTRIMKM
     FQIFRTLLES GYLERKYQTT DREDMLKRLR DHEFIVCSKS VEYTFDCPNC SVHLYKVLNL
     LLNQGSRGAP HQCLGEYMKT LSICNKIKSM KILNTRRNTL LILDTIMLNK FLDLEKVFGH
     VVVERVMIMQ SLMTVNDRLL SIDVLMEMLE KKMTRNPLWF LKVNEKLRKL CPPEVYQSIE
     EYVHEVDRDH WFELKLTLHQ TWPAKPLIDY KGKMRCTCVE KDSNNKNQLS DLTEEKFQLL
     LKKLSSFCLG ITNSLKTSAV AKLRVNQPDD YYGKVTCSEV FFQSLDKEHS AVLLYQKTGE
     KSRAYGLAFN NVVTGQYTTE ASFYCDPKRF FLPIMSDVVL FRMCNEMLSW LDYLSDDVML
     EVRTCLYRLV LSILCTPSKR VQVYIQGLRY FIMAFVNEFH CTGLLDKLKV TALTESERYC
     MKLCDDLVVK VLNSVEDENM AKAFKFVLNT SYLCHLITKE TPDRLTDQIK CFEKFLEPKL
     DFGSVIVNPD SSCELTAGQE EQFYQGLEKL FTDKKLESSY ANKPGVCKEV LNVCMSLFNS
     GALEVKPLLN HDPITPSFTS TALDLSSNKS VVVPKLDELG EVLTEYDYSK LVSSVVVDLV
     EHFKTKGKYV VSPRSLQYKI YKRLSNLVQQ RAGKGNKESE LTEEEFLEQV TAEQLEVINK
     VETKVSRTLS GIKLSSDTEN AKHDDDYHLK KLWSKDIMVR IKAETSLHEV KDFNVDTLPF
     DLYRELVDAI YNDPAANSHY FSERIFNPCP LELLIKNLTL KAYKEEDFFE CFKYILISSN
     FDNKVGKYDH KNRSRLGLSS AALLVKDEAR ISMRESNSES IAKRLDKSFF TNSSLRNLCF
     YSDESPTERT SVSSNVGKLK FGLSYKEQVG GNRELYVGDL NTKLTTRLVE DYAESLTSDM
     KYTCLNNENE FERALLDMKS VVRQSGLAVS MDHSKWGPHM SPALFSLMLR GLDFRLKDGT
     LIDKEAVVNI LSWHIHKMVE VPFNVVEAYL KGFIKRGLGL MDRGGATRVE EFMFGYFDQG
     IVPSHISSVI DMGQGILHNL SDLYGLITEQ FIVYALDLCY SSSFMAYTSS DDEILLSISN
     SFKRNDGSMD MDLAIEALEF HYFLSDRLNK FVSPKTVAGT FASEFKSRFF IWSQEVPLLT
     KFVAASLHNV KAKAPSQLAE TIDTILDQSV ANGVSIEIIG AIAPRTNALI TYSGHPFNLF
     LCLEETDVRD WVDGSRGYRL QRSIENAFPD DVLPEIIRSA CRKIFYRIQS GTLEEDYIVT
     TLQQSPDDCL KQMLTSCDVE KEAIDDICNY RWLNLRAHGD LRLVLRTKIM TSTRTLQKEE
     VPSLIKSVQS KLSKNFVRGA KKILADAINK SAFQSCISSG FVGVCKSMGS KCVRDGKGGF
     KYIKDILKEI KHHEKPDCHF CKELKGIYCS ELLENISEFS RPLFWDYFSL VLSNACELGN
     WVFCKIEIPK SVYHLNNPNH FWPIKPSSHA ELEEKVGMNH VLYSIRRNFP VLFDEHISPY
     LSDLNMLKLN WVQKIRFLDI CVAIDMTSEC LGIISHIIRR KREELYIVKQ SELSMSHTRV
     SLPLERGFNI EPDEVCHNFL LQILFESMIH PVLLTTSQFK RYFWYSEVEL LPKEALHDLG
     QFTQFIIDCK VLNSSRAMCL DDLDVGYVSS KVKRTDTYLN LSTFMTNLDW ENRHEYSSFE
     DLILSSPSEV FLFEITFTFS HIRRSHKFRY DRSTNYILKT KLVIEKSELV NGEDGVYCVT
     PHSIEYYVSQ SSGNHISLDG VSLLVLDPLI SGRELVNMDE LLQNQDVTFS APSQILSKIK
     LDFKPFTKEI KNKFSYKLIG PDVDMSPLHL DKGAIKEGDR IVSQIEIQVS FKSVITAIEL
     LDEDQRKIFV GNLFVYLTSL KSVNRALSMS ESDLRLLVEN YPSVIEYMLS GCDGWLNCGS
     FSLIKSKTLQ CIMLADERGP YRIKGQNCRR LFPTEEAIEI E