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Annotation rule MF_04149
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General rule information [?]

Accession MF_04149
Dates 28-FEB-2020 (Created)
7-APR-2020 (Last updated, Version 4)
Name RNALIG_T4
Scope
Viruses
Template P00971 (RLIG_BPT4)
Triggered by

Propagated annotation [?]


Identifier, protein and gene names [?]

Identifier
RLIG
case <FTGroup:1>
Protein name
RecName: Full=RNA ligase 1;
EC 6.5.1.3;
AltName: Full=Rnl1;
else
Protein name
RecName: Full=RNA ligase;
EC 6.5.1.-;
end case

Comments [?]

case <OS:Enterobacteria phage T4>
Function Involved in countering a host defense mechanism which, following viral infection, activates the host anticodon nuclease and shuts off viral translation. Repairs 5'-PO4 and 3'-OH groups in the cleaved host tRNA(Lys). 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.
Domain The N-terminus contains the nucleotidyltransferase domain. The C-terminus probably confers the tRNA specificity.
else
Function Involved in countering a host defense mechanism which, following viral infection, activates the host anticodon nuclease and shuts off viral translation. Repairs 5'-PO4 and 3'-OH groups in the cleaved host tRNA. 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.
end case
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+)
Note: Binds 2 magnesium ions that perform the catalytic activity via a two-metal mechanism. One of the catalytic Mg(2+), which is coordinated by 5 water molecules, engages the lysine nucleophile and the ATP alpha phosphate while the Mg(2+) orients the PPi leaving group;
end case
Similarity Belongs to the Tequatrovirus RNA ligase 1 family.

Keywords [?]

ATP-binding
Evasion of bacteria-mediated translation shutoff by virus
Host-virus interaction
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 PF09511; RNA_lig_T4_1; 1;
TIGRFAMs TIGR02308; RNA_lig_T4_1; 1;

Features [?]

From: RLIG_BPT4 (P00971)
Key     From     To       Description   Tag   Condition   FTGroup
ACT_SITE     99     99       N6-AMP-lysine intermediate     K   1
METAL     272     272       Magnesium; catalytic     D   1
BINDING     37     37       ATP     Y  
BINDING     54     54       ATP     R  
BINDING     75     75       ATP     K  
BINDING     159     159       ATP     E  
BINDING     240     240       ATP     K  
BINDING     242     242       ATP     K  
SITE     159     159       Essential for RNA ligase activity     E   1
SITE     246     246       Essential for RNA ligase activity     Y   1

Additional information [?]

Size range 300-400 amino acids
Related rules None
Fusion None


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