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Annotation rule MF_04150
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General rule information [?]

Accession MF_04150
Dates 6-MAR-2020 (Created)
7-APR-2020 (Last updated, Version 2)
Name RNALIG2_T4
Scope
Viruses
Template P32277 (RLIG2_BPT4)
Triggered by

Propagated annotation [?]


Identifier, protein and gene names [?]

case <FTGroup:1>
Protein name
RecName: Full=RNA ligase 2;
EC 6.5.1.3;
AltName: Full=Rnl2;
else
Protein name
RecName: Full=RNA ligase;
EC 6.5.1.-;
end case

Comments [?]

Function Repairs 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=6.5.1.3;
Cofactor Mg(2+)
Mn(2+)
Note: Binds 2 magnesium ions that may perform the catalytic activity via a two-metal mechanism;
end case
Domain The 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.
Similarity Belongs to the RNA ligase 2 family.

Keywords [?]

ATP-binding
Ligase
case <FTGroup:1>
Magnesium
Metal-binding
end case
Nucleotide-binding
RNA repair

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;
PF18043; T4_Rnl2_C; 1;
TIGRFAMs TIGR02307; RNA_lig_RNL2; 1;

Features [?]

From: RLIG2_BPT4 (P32277)
Key     From     To       Description   Tag   Condition   FTGroup
REGION     1     234       Adenylyltransferase        
ACT_SITE     35     35       N6-AMP-lysine intermediate     K   1
METAL     204     204       Magnesium     E   1
case <OC:Tequatrovirus>
METAL     162     162       Magnesium 2; via carbonyl oxygen     I  
METAL     164     164       Magnesium 2; via carbonyl oxygen     L  
METAL     166     166       Magnesium 2     N  
METAL     206     206       Magnesium 2     Y  
SITE     218     218       Interaction with RNA     N  
SITE     314     314       Interaction with RNA     K  
end case
BINDING     34     34       AMP     E  
BINDING     36     36       AMP     [IL]  
BINDING     40     40       AMP     N  
BINDING     55     55       AMP     R  
BINDING     99     99       AMP     E  
BINDING     225     225       AMP     K  
BINDING     227     227       AMP     K  

Additional information [?]

Size range 270-360 amino acids
Related rules None
Fusion None


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