HAMAP logo

HAMAP rule MF_04150

Send feedback

General rule information [?]

Accession MF_04150
Dates 6-MAR-2020 (Created)
1-JUN-2023 (Last updated, Version 7)
Scope(s) Viruses
Template(s) P32277 (RLIG2_BPT4); [ Recover all ]
Triggered by HAMAP; MF_04150 (Get profile general information and statistics)

Propagated annotation [?]

Identifier, protein and gene names [?]

case <FTGroup:1>
Protein name RecName: Full=RNA ligase 2;
AltName: Full=Rnl2;
Protein name RecName: Full=RNA ligase;
end case

Comments [?]

FUNCTIONRepairs 3'-OH/5'-PO4 nicks in duplex RNA or RNA:DNA hybrid in which the broken 3'-OH strand is RNA. The nick ligation reaction entails three nucleotidyl transfer steps. In the first step, the RNA ligase reacts with ATP in the absence of nucleic acid to form a covalent ligase-AMP intermediate and release pyrophosphate. In step 2, the ligase-AMP binds to the nicked duplex nucleic acid and transfers the adenylate to the 5'-PO4 terminus to form an adenylylated nicked intermediate. In step 3, the RNA ligase directs the attack of the nick 3'-OH on the 5'-phosphoanhydride linkage, resulting in a repaired 3' - 5' phosphodiester and release of AMP.
case <FTGroup:1>
CATALYTIC ACTIVITY Reaction=ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho- (ribonucleotide)m = (ribonucleotide)n+m + AMP + diphosphate.; EC=;
COFACTOR Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Note=Binds 2 magnesium ions that may perform the catalytic activity via a two-metal mechanism;
end case
DOMAINThe adenylyltransferase domain in the N-terminus performs step 1 and step 3 reactions. The C-terminus domain is required for step 2 of the ligation pathway.
SIMILARITYBelongs to the RNA ligase 2 family.

Keywords [?]

Gene Ontology [?]

GO:0005524; Molecular function:ATP binding
GO:0046872; Molecular function:metal ion binding
GO:0003972; Molecular function:RNA ligase (ATP) activity
GO:0042245; Biological process:RNA repair

Cross-references [?]

Pfam PF09414; RNA_ligase; 1;
Pfam PF18043; T4_Rnl2_C; 1;
NCBIfam TIGR02307; RNA_lig_RNL2; 1;

Features [?]

From: RLIG2_BPT4 (P32277)
Key From To Description Tag Condition FTGroup
REGION 1 234 /note="Adenylyltransferase"
ACT_SITE 35 35 /note="N6-AMP-lysine intermediate" K 1
BINDING 204 204 /ligand="Mg(2+)"
E 1
case <OC:Tequatrovirus>
BINDING 162 162 /ligand="Mg(2+)"
BINDING 164 164 /ligand="Mg(2+)"
BINDING 166 166 /ligand="Mg(2+)"
BINDING 206 206 /ligand="Mg(2+)"
SITE 218 218 /note="Interaction with RNA" N
SITE 314 314 /note="Interaction with RNA" K
end case
BINDING 34 34 /ligand="AMP"
BINDING 36 36 /ligand="AMP"
BINDING 40 40 /ligand="AMP"
BINDING 55 55 /ligand="AMP"
BINDING 99 99 /ligand="AMP"
BINDING 225 225 /ligand="AMP"
BINDING 227 227 /ligand="AMP"

Additional information [?]

Size range 270-360 amino acids
Related rules None
Fusion Nter: None Cter: None

View rule in raw text format (no links)