A0A249XVT1 · A0A249XVT1_9CAUD

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

  • ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m = (ribonucleotide)n+m + AMP + diphosphate.
    EC:6.5.1.3 (UniProtKB | ENZYME | Rhea)

Cofactor

Mg2+ (UniProtKB | Rhea| CHEBI:18420 )

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, site.

TypeIDPosition(s)Description
Binding site34AMP (UniProtKB | ChEBI)
Active site35N6-AMP-lysine intermediate
Binding site36AMP (UniProtKB | ChEBI)
Binding site40AMP (UniProtKB | ChEBI)
Binding site55AMP (UniProtKB | ChEBI)
Binding site99AMP (UniProtKB | ChEBI)
Binding site162Mg2+ 2 (UniProtKB | ChEBI)
Binding site164Mg2+ 2 (UniProtKB | ChEBI)
Binding site166Mg2+ 2 (UniProtKB | ChEBI)
Binding site204Mg2+ 1 (UniProtKB | ChEBI)
Binding site206Mg2+ 2 (UniProtKB | ChEBI)
Site218Interaction with RNA
Binding site225AMP (UniProtKB | ChEBI)
Binding site227AMP (UniProtKB | ChEBI)
Site314Interaction with RNA

GO annotations

AspectTerm
Molecular FunctionATP binding
Molecular Functionmetal ion binding
Molecular FunctionRNA ligase (ATP) activity
Biological ProcessRNA repair

Keywords

Enzyme and pathway databases

Names & Taxonomy

Protein names

  • Recommended name
    RNA ligase 2
  • EC number
  • Alternative names
    • Rnl2

Organism names

  • Taxonomic identifier
  • Organism
  • Taxonomic lineage
    Viruses > Duplodnaviria > Heunggongvirae > Uroviricota > Caudoviricetes > Straboviridae > Tevenvirinae > Tequatrovirus > Tequatrovirus sgallinarium

Accessions

  • Primary accession
    A0A249XVT1

Proteomes

Family & Domains

Features

Showing features for region, domain.

TypeIDPosition(s)Description
Region1-234Adenylyltransferase
Domain29-226RNA ligase
Domain246-322RNA ligase 2 C-terminal

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.

Family and domain databases

Sequence

  • Sequence status
    Complete
  • Length
    334
  • Mass (Da)
    37,562
  • Last updated
    2017-11-22 v1
  • Checksum
    1889A3F72A345589
MFKKYSSLENHYNSKFIEKLYSLGLTGGEWVAREKIHGTNFSLIIERDKATCAKRTGPILPAEDFFGYEIILKNYADSIKAVQDIMETSAVVSYQVFGEFAGPGIQKNVDYGDKDFYVFDIIVTTESGDVTYVDDYMMESFCNTFKFKMAPLLGRGKFEELIKLPNDLDSVVQDYNFTVDHAGLVDANKCVWNAEAKGEVFTAEGYVLKPCYPSWLHNGNRVAIKCKNSKFSEKKKSDKPIKVKVELSEADNKLVGILACYVTLNRVNNVISKIGEIGPKDFGKVMGLTVQDILEETSREGITLTQADNPSLIKKELVKMVQDVLRPAWIELVS

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
MF001354
EMBL· GenBank· DDBJ
ASZ76090.1
EMBL· GenBank· DDBJ
Genomic DNA

Similar Proteins

Disclaimer

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