A0A0A7HDJ4 · A0A0A7HDJ4_9CAUD
- ProteinRNA ligase 2
- GenernlB
- StatusUniProtKB unreviewed (TrEMBL)
- Organism
- Amino acids334 (go to sequence)
- Protein existenceInferred from homology
- Annotation score3/5
Function
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.
Catalytic activity
Cofactor
Mn2+ (UniProtKB | Rhea| CHEBI:29035 )
Note: Binds 2 magnesium ions that may perform the catalytic activity via a two-metal mechanism.
Features
Showing features for binding site, active site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 34 | AMP (UniProtKB | ChEBI) | ||||
Sequence: E | ||||||
Active site | 35 | N6-AMP-lysine intermediate | ||||
Sequence: K | ||||||
Binding site | 36 | AMP (UniProtKB | ChEBI) | ||||
Sequence: I | ||||||
Binding site | 40 | AMP (UniProtKB | ChEBI) | ||||
Sequence: N | ||||||
Binding site | 55 | AMP (UniProtKB | ChEBI) | ||||
Sequence: R | ||||||
Binding site | 99 | AMP (UniProtKB | ChEBI) | ||||
Sequence: E | ||||||
Binding site | 204 | Mg2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: E | ||||||
Binding site | 225 | AMP (UniProtKB | ChEBI) | ||||
Sequence: K | ||||||
Binding site | 227 | AMP (UniProtKB | ChEBI) | ||||
Sequence: K |
GO annotations
Aspect | Term | |
---|---|---|
Molecular Function | ATP binding | |
Molecular Function | metal ion binding | |
Molecular Function | RNA ligase (ATP) activity | |
Biological Process | RNA repair |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameRNA ligase 2
- EC number
- Alternative names
Gene names
Organism names
- Organism
- Taxonomic lineageViruses > Duplodnaviria > Heunggongvirae > Uroviricota > Caudoviricetes > Straboviridae > Tevenvirinae > Gaprivervirus > Gaprivervirus vr26
Accessions
- Primary accessionA0A0A7HDJ4
Proteomes
Structure
Family & Domains
Features
Showing features for region, domain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Region | 1-234 | Adenylyltransferase | ||||
Sequence: MFKKYNSLENHYNNKFIEKIRLQGFTSGEWVAREKIHGTNFSLIIEQDNVTCAKRTGPIPPAEDFYGYEIVLKNYADSIKTVQRLLQDINYQSYQIYGEFAGAGIQKNVDYGDKDFYVFDIRVTKEDGSESVLTDSLMEAFCIIHKFKVAPRLATGSFEDLIKLPNDLDSVVPDYNFTVDNAGLTTANTTDFDAKVEGKVFTAEGYVLKPDTPAWLPNGERVAIKCKNSKFSEK | ||||||
Domain | 29-226 | RNA ligase | ||||
Sequence: EWVAREKIHGTNFSLIIEQDNVTCAKRTGPIPPAEDFYGYEIVLKNYADSIKTVQRLLQDINYQSYQIYGEFAGAGIQKNVDYGDKDFYVFDIRVTKEDGSESVLTDSLMEAFCIIHKFKVAPRLATGSFEDLIKLPNDLDSVVPDYNFTVDNAGLTTANTTDFDAKVEGKVFTAEGYVLKPDTPAWLPNGERVAIKC | ||||||
Domain | 249-318 | RNA ligase 2 C-terminal | ||||
Sequence: QDDMDLLWQFTDYVTVNRINNVISKIGEVTPKDFGKVMGLTAQDILEEASREELELTDAENPVEVKKQLI |
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.
Sequence similarities
Belongs to the RNA ligase 2 family.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length334
- Mass (Da)37,811
- Last updated2015-03-04 v1
- Checksum48F1EE619889F33D
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
KP007362 EMBL· GenBank· DDBJ | AIZ02827.1 EMBL· GenBank· DDBJ | Genomic DNA |