HAMAP rule MF_04150
General rule information
[?]
| Accession | MF_04150 |
| Dates | 6-MAR-2020 (Created)
1-JUN-2023 (Last updated, Version 7) |
| Name | RNALIG2_T4 |
| Scope(s) |
Viruses |
| Template(s) | P32277 (RLIG2_BPT4); [ Recover all ] |
| Triggered by |
HAMAP; MF_04150 (Get profile general information and statistics) |
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 | Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035; 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
[?]
Features
[?]
| From: RLIG2_BPT4 (P32277) | ||||||||||||
| Key | From | To | Description | Tag | Condition | FTGroup | ||||||
| REGION | 1 | 234 | /note="Adenylyltransferase" | |||||||||
| ACT_SITE | 35 | 35 | /note="N6-AMP-lysine intermediate" | K | 1 | |||||||
| BINDING | 204 | 204 | /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="1" |
E | 1 | |||||||
| case <OC:Tequatrovirus> | ||||||||||||
| BINDING | 162 | 162 | /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="2" |
I | ||||||||
| BINDING | 164 | 164 | /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="2" |
L | ||||||||
| BINDING | 166 | 166 | /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="2" |
N | ||||||||
| BINDING | 206 | 206 | /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_label="2" |
Y | ||||||||
| SITE | 218 | 218 | /note="Interaction with RNA" | N | ||||||||
| SITE | 314 | 314 | /note="Interaction with RNA" | K | ||||||||
| end case | ||||||||||||
| BINDING | 34 | 34 | /ligand="AMP" /ligand_id="ChEBI:CHEBI:456215" |
E | ||||||||
| BINDING | 36 | 36 | /ligand="AMP" /ligand_id="ChEBI:CHEBI:456215" |
[IL] | ||||||||
| BINDING | 40 | 40 | /ligand="AMP" /ligand_id="ChEBI:CHEBI:456215" |
N | ||||||||
| BINDING | 55 | 55 | /ligand="AMP" /ligand_id="ChEBI:CHEBI:456215" |
R | ||||||||
| BINDING | 99 | 99 | /ligand="AMP" /ligand_id="ChEBI:CHEBI:456215" |
E | ||||||||
| BINDING | 225 | 225 | /ligand="AMP" /ligand_id="ChEBI:CHEBI:456215" |
K | ||||||||
| BINDING | 227 | 227 | /ligand="AMP" /ligand_id="ChEBI:CHEBI:456215" |
K | ||||||||
Additional information
[?]
| Size range | 270-360 amino acids |
| Related rules |
None |
| Fusion | Nter: None Cter: None |