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(s) |
Viruses Arenaviridae |
| 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 /> Short=Protein L;<br /> EC=<a href="https://enzyme.expasy.org/EC/2.7.7.48">2.7.7.48</a>;<br /> AltName: Full=Large structural protein;<br /> AltName: Full=Replicase;<br /> AltName: Full=Transcriptase;<br /> Includes:<br /> RecName: Full=cap-snatching endonuclease;<br /> EC=<a href="https://enzyme.expasy.org/EC/3.1.-.-">3.1.-.-</a>; | |
| Gene name | Name=L; |
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 | 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=2.7.7.48; |
| 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; |
| 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; |
| 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+)" /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 | Nter: None Cter: None |