AC   MF_04150;
DC   Protein; auto
TR   HAMAP; MF_04150; -; 1; level=0
XX
Names: RNALIG2_T4
XX
case <FTGroup:1>
DE   RecName: Full=RNA ligase 2;
DE            EC=6.5.1.3;
DE   AltName: Full=Rnl2;
else
DE   RecName: Full=RNA ligase;
DE            EC=6.5.1.-;
end case
XX
CC   -!- FUNCTION: Repairs 3'-OH/5'-PO4 nicks in duplex RNA or RNA:DNA hybrid in
CC       which the broken 3'-OH strand is RNA. The nick ligation reaction
CC       entails three nucleotidyl transfer steps. In the first step, the RNA
CC       ligase reacts with ATP in the absence of nucleic acid to form a
CC       covalent ligase-AMP intermediate and release pyrophosphate. In step 2,
CC       the ligase-AMP binds to the nicked duplex nucleic acid and transfers
CC       the adenylate to the 5'-PO4 terminus to form an adenylylated nicked
CC       intermediate. In step 3, the RNA ligase directs the attack of the nick
CC       3'-OH on the 5'-phosphoanhydride linkage, resulting in a repaired 3'
CC       - 5' phosphodiester and release of AMP.
case <FTGroup:1>
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC         (ribonucleotide)m = (ribonucleotide)n+m + AMP + diphosphate.;
CC         EC=6.5.1.3;
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC       Note=Binds 2 magnesium ions that may perform the catalytic activity via
CC       a two-metal mechanism;
end case
CC   -!- DOMAIN: The adenylyltransferase domain in the N-terminus performs step
CC       1 and step 3 reactions. The C-terminus domain is required for step 2 of
CC       the ligation pathway.
CC   -!- SIMILARITY: Belongs to the RNA ligase 2 family.
XX
DR   Pfam; PF09414; RNA_ligase; 1; trigger=no
DR   Pfam; PF18043; T4_Rnl2_C; 1; trigger=no
DR   NCBIfam; TIGR02307; RNA_lig_RNL2; 1; trigger=no
XX
KW   ATP-binding
KW   Ligase
case <FTGroup:1>
KW   Magnesium
KW   Metal-binding
end case
KW   Nucleotide-binding
KW   RNA repair
XX
GO   GO:0005524; F:ATP binding
GO   GO:0046872; F:metal ion binding
GO   GO:0003972; F:RNA ligase (ATP) activity
GO   GO:0042245; P:RNA repair
XX
FT   From: RLIG2_BPT4 (P32277)
FT   REGION          1..234
FT                   /note="Adenylyltransferase"
FT   ACT_SITE        35
FT                   /note="N6-AMP-lysine intermediate"
FT   Group: 1; Condition: K
FT   BINDING         204
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT   Group: 1; Condition: E
case <OC:Tequatrovirus>
FT   BINDING         162
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT   Condition: I
FT   BINDING         164
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT   Condition: L
FT   BINDING         166
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT   Condition: N
FT   BINDING         206
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT   Condition: Y
FT   SITE            218
FT                   /note="Interaction with RNA"
FT   Condition: N
FT   SITE            314
FT                   /note="Interaction with RNA"
FT   Condition: K
end case
FT   BINDING         34
FT                   /ligand="AMP"
FT                   /ligand_id="ChEBI:CHEBI:456215"
FT   Condition: E
FT   BINDING         36
FT                   /ligand="AMP"
FT                   /ligand_id="ChEBI:CHEBI:456215"
FT   Condition: [IL]
FT   BINDING         40
FT                   /ligand="AMP"
FT                   /ligand_id="ChEBI:CHEBI:456215"
FT   Condition: N
FT   BINDING         55
FT                   /ligand="AMP"
FT                   /ligand_id="ChEBI:CHEBI:456215"
FT   Condition: R
FT   BINDING         99
FT                   /ligand="AMP"
FT                   /ligand_id="ChEBI:CHEBI:456215"
FT   Condition: E
FT   BINDING         225
FT                   /ligand="AMP"
FT                   /ligand_id="ChEBI:CHEBI:456215"
FT   Condition: K
FT   BINDING         227
FT                   /ligand="AMP"
FT                   /ligand_id="ChEBI:CHEBI:456215"
FT   Condition: K
XX
Size: 270-360;
Related: None;
Template: P32277;
Scope:
 Viruses
Fusion:
 Nter: None
 Cter: None
Duplicate: None
Plasmid: None
Comments: None
XX
# Revision 1.7 2023/06/01
//