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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)
Viruses; Arenaviridae
Template P14240 (L_LYCVA)

Propagated annotation [?]

Identifier, protein and gene names [?]

Protein name
RecName: Full=RNA-directed RNA polymerase L;
Short=Protein L;
AltName: Full=Large structural protein;
AltName: Full=Replicase;
AltName: Full=Transcriptase;
RecName: Full=cap-snatching endonuclease;
EC 3.1.-.-;
Gene name

Comments [?]

Function RNA-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 RHEA:21248: a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1)
Cofactor Mn(2+)
Note: For endonuclease activity. Binds 2 Mn(2+) ions in the active site. The divalent metal ions are crucial for catalytic activity;
Note: For polymerase activity;
Subunit Homomultimer; 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 location Virion. Host cytoplasm.
Domain The N-terminus contains the endonuclease activity (endoN). The central region contains the RdRp activity.
Similarity Belongs to the Bunyavirales RNA polymerase family.
Miscellaneous Classified 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;
PF17296; ArenaCapSnatch; 1;
PIRSF PIRSF000836; L_ArenaV; 1;

Features [?]

From: L_LYCVA (P14240)
Key     From     To       Description   Tag   Condition   FTGroup
DOMAIN     1166     1360       RdRp catalytic        
REGION     26     287       Endonuclease        
ACT_SITE     115     115                
BINDING     51     51       /ligand="Mn(2+)" /ligand_id="ChEBI:CHEBI:29035" /ligand_label="1        
BINDING     89     89       /ligand="Mn(2+)" /ligand_id="ChEBI:CHEBI:29035" /ligand_label="1        
BINDING     89     89       /ligand="Mn(2+)" /ligand_id="ChEBI:CHEBI:29035" /ligand_label="2        
BINDING     102     102       /ligand="Mn(2+)" /ligand_id="ChEBI:CHEBI:29035" /ligand_label="1        
BINDING     1322     1322       /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_note="catalytic; for RdRp activity        

Additional information [?]

Size range 2198-2238 amino acids
Related rules None
Fusion None