A0A0B6VSS9 · A0A0B6VSS9_9CAUD
- ProteinRNA ligase 2
- GenernlB
- StatusUniProtKB unreviewed (TrEMBL)
- Organism
- Amino acids333 (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 | 35 | AMP (UniProtKB | ChEBI) | ||||
Sequence: E | ||||||
Active site | 36 | N6-AMP-lysine intermediate | ||||
Sequence: K | ||||||
Binding site | 37 | AMP (UniProtKB | ChEBI) | ||||
Sequence: I | ||||||
Binding site | 41 | AMP (UniProtKB | ChEBI) | ||||
Sequence: N | ||||||
Binding site | 56 | AMP (UniProtKB | ChEBI) | ||||
Sequence: R | ||||||
Binding site | 98 | AMP (UniProtKB | ChEBI) | ||||
Sequence: E | ||||||
Binding site | 202 | Mg2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: E | ||||||
Binding site | 223 | AMP (UniProtKB | ChEBI) | ||||
Sequence: K | ||||||
Binding site | 225 | 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 > Kanagawavirus > Kanagawavirus pei20
Accessions
- Primary accessionA0A0B6VSS9
Proteomes
Structure
Family & Domains
Features
Showing features for domain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Domain | 31-224 | RNA ligase | ||||
Sequence: WVAREKIHGTNFSIIIERDAVTCAKRTGPILPAEDFFGYSIILKKYNDSIKAVQHTIKEGSSMQIFGEFAGGGIQKGVDYGEKDFYVFDILVKTDQGTNQFVDDYMMETMCNTFGFKMAPLLGRGKFDVLAQLPNDFDVVVGSYNSLIEHVDLETANKHTFGIEPGTRNIAEGYVLKPCYPKFFPNGTRVAIKC | ||||||
Domain | 252-317 | RNA ligase 2 C-terminal | ||||
Sequence: TLSTLAAYATLNRVNNVISKIGEVGPKDFGKVMGLTVQDILEEAGREEIFITDADQPDVVKKELVT |
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
- Length333
- Mass (Da)37,030
- Last updated2015-04-01 v1
- Checksum4DBD713A5766C940
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
AP014714 EMBL· GenBank· DDBJ | BAQ22845.1 EMBL· GenBank· DDBJ | Genomic DNA |