P00971 · RLIG_BPT4

Function

function

Involved in countering a host defense mechanism which, following viral infection, activates the host anticodon nuclease and shuts off viral translation. Repairs 5'-PO4 and 3'-OH groups in the cleaved host tRNA (PubMed:16671895, PubMed:17068206, PubMed:2444436).
The nick ligation reaction entails three nucleotidyl transfer steps (PubMed:12766156).
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 (PubMed:12766156).
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 (PubMed:12766156).
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 (By similarity) (PubMed:12766156).

Caution

An interaction between the carbonyl oxygen of Gly-269 and the magnesium ion may occur.

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 )

Note: Binds 2 magnesium ions that perform the catalytic activity via a two-metal mechanism (PubMed:16263720, PubMed:28223499).
One of the catalytic Mg2+, which is coordinated by 5 water molecules, engages the lysine nucleophile and the ATP alpha phosphate while the Mg2+ orients the PPi leaving group (PubMed:28223499).

pH Dependence

Optimum pH is 8.0.

Features

Showing features for binding site, active site, site.

TypeIDPosition(s)Description
Binding site37ATP (UniProtKB | ChEBI)
Binding site54ATP (UniProtKB | ChEBI)
Binding site75ATP (UniProtKB | ChEBI)
Active site99N6-AMP-lysine intermediate
Binding site159ATP (UniProtKB | ChEBI)
Site159Essential for RNA ligase activity
Binding site240ATP (UniProtKB | ChEBI)
Binding site242ATP (UniProtKB | ChEBI)
Site246Essential for RNA ligase activity
Binding site272Mg2+ (UniProtKB | ChEBI); catalytic

GO annotations

AspectTerm
Molecular FunctionATP binding
Molecular Functionmetal ion binding
Molecular FunctionRNA ligase (ATP) activity
Biological ProcessRNA repair
Biological Processvirus tail fiber assembly

Keywords

Enzyme and pathway databases

Names & Taxonomy

Protein names

  • Recommended name
    RNA ligase 1
  • EC number
  • Alternative names
    • Gene product 63 (gp63)
    • Rnl1

Gene names

    • Name
      63

Organism names

Accessions

  • Primary accession
    P00971

Proteomes

Phenotypes & Variants

Features

Showing features for mutagenesis.

TypeIDPosition(s)Description
Mutagenesis37No effect on the ligation of 5'-PO4 and 3'-OH termini of the RNA strand and on tRNA repair.
Mutagenesis45Partial loss of the ligation of 5'-PO4 and 3'-OH termini of the RNA strand and on tRNA repair.
Mutagenesis5465% loss of adenylyltransferase activity. 70% loss of ligase activity.
Mutagenesis7595% loss of adenylyltransferase activity. Impaired ligase activity.
Mutagenesis7790% loss of adenylyltransferase activity. Impaired ligase activity.
Mutagenesis99Complete loss of adenylyltransferase activity and ligase activity.
Mutagenesis99Complete loss of ligase activity.
Mutagenesis99About 50% loss of ligase activity.
Mutagenesis100No effect on ligase activity.
Mutagenesis100About 50% loss of ligase activity.
Mutagenesis101Complete loss of ligase activity.
Mutagenesis102Complete loss of adenylyltransferase activity and ligase activity.
Mutagenesis119Increased adenylyltransferase activity. No effect on ligase activity.
Mutagenesis159Complete loss of ligation of 5'-PO4 and 3'-OH termini of the RNA strand and complete loss of tRNA repair.
Mutagenesis165Partial loss of the ligation of 5'-PO4 and 3'-OH termini of the RNA strand; no effect on tRNA repair.
Mutagenesis179Partial loss of the ligation of 5'-PO4 and 3'-OH termini of the RNA strand; no effect on tRNA repair.
Mutagenesis182Complete loss of ligation.
Mutagenesis227Complete loss of adenylyltransferase activity and ligase activity.
Mutagenesis228Complete loss of adenylyltransferase activity and ligase activity.
Mutagenesis230Partial loss of the ligation of 5'-PO4 and 3'-OH termini of the RNA strand; no effect on tRNA repair.
Mutagenesis240Complete loss of adenylyltransferase activity and ligase activity.
Mutagenesis242Complete loss of adenylyltransferase activity and ligase activity.
Mutagenesis246Complete loss of ligation of 5'-PO4 and 3'-OH termini of the RNA strand and complete loss of tRNA repair; no effect on adenylyltransferase activity.
Mutagenesis272No effect on the ligation of 5'-PO4 and 3'-OH termini of the RNA strand and no effect on tRNA repair.
Mutagenesis273No effect on the ligation of 5'-PO4 and 3'-OH termini of the RNA strand and no effect on tRNA repair.

PTM/Processing

Features

Showing features for chain.

TypeIDPosition(s)Description
ChainPRO_00001649761-374RNA ligase 1

Structure

Family & Domains

Domain

The N-terminus contains the nucleotidyltransferase domain (PubMed:17585047).
The C-terminus probably confers tRNA specificity (PubMed:17585047).

Sequence similarities

Belongs to the Tequatrovirus RNA ligase 1 family.

Phylogenomic databases

Family and domain databases

Sequence

  • Sequence status
    Complete
  • Length
    374
  • Mass (Da)
    43,509
  • Last updated
    1986-07-21 v1
  • Checksum
    04388DBA72A8121C
MQELFNNLMELCKDSQRKFFYSDDVSASGRTYRIFSYNYASYSDWLLPDALECRGIMFEMDGEKPVRIASRPMEKFFNLNENPFTMNIDLNDVDYILTKEDGSLVSTYLDGDEILFKSKGSIKSEQALMANGILMNINHHRLRDRLKELAEDGFTANFEFVAPTNRIVLAYQEMKIILLNVRENETGEYISYDDIYKDATLRPYLVERYEIDSPKWIEEAKNAENIEGYVAVMKDGSHFKIKSDWYVSLHSTKSSLDNPEKLFKTIIDGASDDLKAMYADDEYSYRKIEAFETTYLKYLDRALFLVLDCHNKHCGKDRKTYAMEAQGVAKGAGMDHLFGIIMSLYQGYDSQEKVMCEIEQNFLKNYKKFIPEGY

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
X00365
EMBL· GenBank· DDBJ
CAA25107.1
EMBL· GenBank· DDBJ
Genomic DNA
X04140
EMBL· GenBank· DDBJ
CAA27760.1
EMBL· GenBank· DDBJ
Genomic DNA
AF158101
EMBL· GenBank· DDBJ
AAD42514.1
EMBL· GenBank· DDBJ
Genomic DNA
M10160
EMBL· GenBank· DDBJ
-Genomic DNA No translation available.

Genome annotation databases

Similar Proteins

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