HAMAP rule MF_04149

General rule information [?]

Accession	MF_04149
Dates	28-FEB-2020 (Created) 1-JUN-2023 (Last updated, Version 9)
Name	RNALIG_T4
Scope(s)	Viruses
Template(s)	P00971 (RLIG_BPT4); [ Recover all ]
Triggered by	HAMAP; MF_04149 (Get profile general information and statistics)

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.
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	Name=Mg(2+); Xref=ChEBI:CHEBI:18420; 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;
NCBIfam	TIGR02308; RNA_lig_T4_1; 1;

Features [?]

From: RLIG_BPT4 (P00971)

Key

From

Description

Tag

Condition

FTGroup

ACT_SITE

/note="N6-AMP-lysine intermediate"

BINDING

272

/ligand="Mg(2+)"
/ligand_id="ChEBI:CHEBI:18420"
/ligand_note="catalytic"

BINDING