A0A0A7HDJ4 · A0A0A7HDJ4_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.

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 site204Mg2+ 1 (UniProtKB | ChEBI)
Binding site225AMP (UniProtKB | ChEBI)
Binding site227AMP (UniProtKB | ChEBI)

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

Gene names

    • Name
      rnlB
    • ORF names
      VR26_190

Organism names

  • Taxonomic identifier
  • Taxonomic lineage
    Viruses > Duplodnaviria > Heunggongvirae > Uroviricota > Caudoviricetes > Straboviridae > Tevenvirinae > Gaprivervirus > Gaprivervirus vr26

Accessions

  • Primary accession
    A0A0A7HDJ4

Proteomes

Family & Domains

Features

Showing features for region, domain.

TypeIDPosition(s)Description
Region1-234Adenylyltransferase
Domain29-226RNA ligase
Domain249-318RNA 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.

Phylogenomic databases

Family and domain databases

Sequence

  • Sequence status
    Complete
  • Length
    334
  • Mass (Da)
    37,811
  • Last updated
    2015-03-04 v1
  • Checksum
    48F1EE619889F33D
MFKKYNSLENHYNNKFIEKIRLQGFTSGEWVAREKIHGTNFSLIIEQDNVTCAKRTGPIPPAEDFYGYEIVLKNYADSIKTVQRLLQDINYQSYQIYGEFAGAGIQKNVDYGDKDFYVFDIRVTKEDGSESVLTDSLMEAFCIIHKFKVAPRLATGSFEDLIKLPNDLDSVVPDYNFTVDNAGLTTANTTDFDAKVEGKVFTAEGYVLKPDTPAWLPNGERVAIKCKNSKFSEKKKSDKPIKAAVVLSQDDMDLLWQFTDYVTVNRINNVISKIGEVTPKDFGKVMGLTAQDILEEASREELELTDAENPVEVKKQLIANVRDTLRHVWIALIS

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
KP007362
EMBL· GenBank· DDBJ
AIZ02827.1
EMBL· GenBank· DDBJ
Genomic DNA

Genome annotation databases

Similar Proteins

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care. Our staff consists of biologists and biochemists that are not trained to give medical advice.
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