HAMAP rule MF_04086

General rule information [?]

Accession	MF_04086
Dates	8-FEB-2018 (Created) 19-NOV-2022 (Last updated, Version 10)

Name

ARENA_L

Scope

Viruses; Arenaviridae

Template

P14240 (L_LYCVA)

Triggered by

HAMAP; MF_04086 (Get profile general information and statistics)

Propagated annotation [?]

Identifier, protein and gene names [?]

Identifier

Protein name

RecName:		Full=RNA-directed RNA polymerase L;
		Short=Protein L;
		EC 2.7.7.48;
AltName:		Full=Large structural protein;
AltName:		Full=Replicase;
AltName:		Full=Transcriptase;
Includes:
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) EC 2.7.7.48
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;
	Mg(2+) Mn(2+) 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 [?]

Cap snatching
Host cytoplasm
Hydrolase
Nucleotide-binding
Nucleotidyltransferase
RNA-directed RNA polymerase
Transferase
Viral RNA replication
Virion
Metal-binding
Magnesium
Manganese

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 [?]

PROSITE	PS50525; RDRP_SSRNA_NEG_SEG; 1;
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

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