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HAMAP rule MF_04086

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General rule information [?]

Accession MF_04086
Dates 8-FEB-2018 (Created)
19-NOV-2022 (Last updated, Version 10)
Scope(s) Viruses
Template(s) P14240 (L_LYCVA); [ Recover all ]
Triggered by HAMAP; MF_04086 (Get profile general information and statistics)

Propagated annotation [?]

Identifier, protein and gene names [?]

Identifier L
RecName: Full=RNA-directed RNA polymerase L;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Short=Protein L;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;EC=<a href="https://enzyme.expasy.org/EC/"></a>;<br /> AltName: Full=Large structural protein;<br /> AltName: Full=Replicase;<br /> AltName: Full=Transcriptase;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Includes:<br /> RecName: Full=cap-snatching endonuclease;<br /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;EC=<a href="https://enzyme.expasy.org/EC/3.1.-.-">3.1.-.-</a>;
Gene name Name=L;

Comments [?]

FUNCTIONRNA-dependent RNA polymerase, which is responsible for the replication and transcription of the viral RNA genome using antigenomic RNA as an intermediate. During transcription, synthesizes subgenomic RNAs and assures their capping by a cap-snatching mechanism, which involves the endonuclease activity cleaving the host capped pre-mRNAs. These short capped RNAs are then used as primers for viral transcription. The 3'-end of subgenomic mRNAs molecules are heterogeneous and not polyadenylated. The replicase function is to direct synthesis of antigenomic and genomic RNA which are encapsidated and non capped. As a consequence of the use of the same enzyme for both transcription and replication, these mechanisms need to be well coordinated. These processes may be regulated by proteins N and Z in a dose-dependent manner.
CATALYTIC ACTIVITY Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1); Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:14527, Rhea:RHEA- COMP:17342, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557, ChEBI:CHEBI:140395; EC=;
COFACTOR Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Note=For endonuclease activity. Binds 2 Mn(2+) ions in the active site. The divalent metal ions are crucial for catalytic activity;
COFACTOR Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Note=For polymerase activity;
SUBUNITHomomultimer; the oligomeric structure is essential for the polymerase activity. Interacts with nucleoprotein N. Interacts with protein Z; this interaction inhibits viral transcription and replication.
SUBCELLULAR LOCATIONVirion. Host cytoplasm.
DOMAINThe N-terminus contains the endonuclease activity (endoN). The central region contains the RdRp activity.
SIMILARITYBelongs to the Bunyavirales RNA polymerase family.
MISCELLANEOUSClassified as His(-) endonuclease since it does not have a histidine upstream of the active site that coordinates the first cation. His(-) endonucleases display very low activity in vitro, although they are clearly active in vivo.

Keywords [?]

Gene Ontology [?]

GO:0030430; Cellular component:host cell cytoplasm
GO:0000166; Molecular function:nucleotide binding
GO:0003968; Molecular function:RNA-dependent RNA polymerase activity
GO:0075526; Biological process:cap snatching
GO:0039689; Biological process:negative stranded viral RNA replication
GO:0039696; Biological process:RNA-templated viral transcription

Cross-references [?]

Pfam PF06317; Arena_RNA_pol; 1;
Pfam PF17296; ArenaCapSnatch; 1;
PIRSF PIRSF000836; L_ArenaV; 1;

Features [?]

From: L_LYCVA (P14240)
Key From To Description Tag Condition FTGroup
DOMAIN 1166 1360 /note="RdRp catalytic"
REGION 26 287 /note="Endonuclease"
ACT_SITE 115 115
BINDING 51 51 /ligand="Mn(2+)"
BINDING 89 89 /ligand="Mn(2+)"
BINDING 89 89 /ligand="Mn(2+)"
BINDING 102 102 /ligand="Mn(2+)"
BINDING 1322 1322 /ligand="Mg(2+)"
/ligand_note="catalytic; for RdRp activity"

Additional information [?]

Size range 2198-2238 amino acids
Related rules None
Fusion Nter: None Cter: None

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