AC   MF_04149;
DC   Protein; auto
TR   HAMAP; MF_04149; -; 1; level=0
XX
Names: RNALIG_T4
XX
ID   RLIG
case <FTGroup:1>
DE   RecName: Full=RNA ligase 1;
DE            EC=6.5.1.3;
DE   AltName: Full=Rnl1;
else
DE   RecName: Full=RNA ligase;
DE            EC=6.5.1.-;
end case
XX
case <OS:Enterobacteria phage T4>
CC   -!- FUNCTION: Involved in countering a host defense mechanism which,
CC       following viral infection, activates the host anticodon nuclease and
CC       shuts off viral translation. Repairs 5'-PO4 and 3'-OH groups in the
CC       cleaved host tRNA(Lys). The nick ligation reaction entails three
CC       nucleotidyl transfer steps. In the first step, the RNA ligase reacts
CC       with ATP in the absence of nucleic acid to form a covalent ligase-AMP
CC       intermediate and release pyrophosphate. In step 2, the ligase-AMP binds
CC       to the nicked duplex nucleic acid and transfers the adenylate to the
CC       5'-PO4 terminus to form an adenylylated nicked intermediate. In step 3,
CC       the RNA ligase directs the attack of the nick 3'-OH on the 5'-
CC       phosphoanhydride linkage, resulting in a repaired 3'-5' phosphodiester
CC       and release of AMP.
CC   -!- DOMAIN: The N-terminus contains the nucleotidyltransferase domain. The
CC       C-terminus probably confers the tRNA specificity.
else
CC   -!- FUNCTION: Involved in countering a host defense mechanism which,
CC       following viral infection, activates the host anticodon nuclease and
CC       shuts off viral translation. Repairs 5'-PO4 and 3'-OH groups in the
CC       cleaved host tRNA.
end case
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       Note=Binds 2 magnesium ions that perform the catalytic activity via a
CC       two-metal mechanism. One of the catalytic Mg(2+), which is coordinated
CC       by 5 water molecules, engages the lysine nucleophile and the ATP alpha
CC       phosphate while the Mg(2+) orients the PPi leaving group;
end case
CC   -!- SIMILARITY: Belongs to the Tequatrovirus RNA ligase 1 family.
XX
DR   Pfam; PF09511; RNA_lig_T4_1; 1; trigger=no
DR   NCBIfam; TIGR02308; RNA_lig_T4_1; 1; trigger=no
XX
KW   ATP-binding
KW   Evasion of bacteria-mediated translation shutoff by virus
KW   Host-virus interaction
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: RLIG_BPT4 (P00971)
FT   ACT_SITE        99
FT                   /note="N6-AMP-lysine intermediate"
FT   Group: 1; Condition: K
FT   BINDING         272
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_note="catalytic"
FT   Group: 1; Condition: D
FT   BINDING         37
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT   Condition: Y
FT   BINDING         54
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT   Condition: R
FT   BINDING         75
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT   Condition: K
FT   BINDING         159
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT   Condition: E
FT   BINDING         240
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT   Condition: K
FT   BINDING         242
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT   Condition: K
FT   SITE            159
FT                   /note="Essential for RNA ligase activity"
FT   Group: 1; Condition: E
FT   SITE            246
FT                   /note="Essential for RNA ligase activity"
FT   Group: 1; Condition: Y
XX
Size: 300-400;
Related: None;
Template: P00971;
Scope:
 Viruses
Fusion:
 Nter: None
 Cter: None
Duplicate: None
Plasmid: None
Comments: None
XX
# Revision 1.9 2023/06/01
//