ArticleNucleic acids research2016
Structural and mutational analysis of archaeal ATP-dependent RNA ligase identifies amino acids required for RNA binding and catalysis.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 16 citations in OpenAlex.
- Article
- Circular RNAs in Archaea.Advances in experimental medicine and biology · 2025Review
- Influence of Fungicide Application on Rhizosphere Microbiota Structure and Microbial Secreted Enzymes in Diverse Cannabinoid-Rich Hemp Cultivars.International journal of molecular sciences · 2024Article
- Characterisation and engineering of a thermophilic RNA ligase from Palaeococcus pacificus.Nucleic acids research · 2024Article
- Direct adenylation from 5'-OH-terminated oligonucleotides by a fusion enzyme containing Pfu RNA ligase and T4 polynucleotide kinase.Nucleic acids research · 2022Article
- Genetic and Functional Analyses of Archaeal ATP-Dependent RNA Ligase in C/D Box sRNA Circularization and Ribosomal RNA Processing.Frontiers in molecular biosciences · 2022Article
- Article
- Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates.The Journal of biological chemistry · 2019Article
- Structure and two-metal mechanism of fungal tRNA ligase.Nucleic acids research · 2019Article
- Cleavage of 3'-terminal adenosine by archaeal ATP-dependent RNA ligase.Scientific reports · 2017Article
- High-throughput sequencing reveals circular substrates for an archaeal RNA ligase.RNA biology · 2017Article
- Two-metal versus one-metal mechanisms of lysine adenylylation by ATP-dependent and NADProceedings of the National Academy of Sciences of the United States of America · 2017Article
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
An ATP-dependent RNA ligase from Methanobacterium thermoautotrophicum (MthRnl) catalyzes intramolecular ligation of single-stranded RNA to form a closed circular RNA via covalent ligase-AMP and RNA-adenylylate intermediate. Here, we report the X-ray crystal structures of an MthRnl•ATP complex as well as the covalent MthRnl-AMP intermediate. We also performed structure-guided mutational analysis to survey the functions of 36 residues in three component steps of the ligation pathway including ligase-adenylylation (step 1), RNA adenylylation (step 2) and phosphodiester bond synthesis (step 3). Kinetic analysis underscored the importance of motif 1a loop structure in promoting phosphodiester bond synthesis. Alanine substitutions of Thr117 or Arg118 favor the reverse step 2 reaction to deadenylate the 5'-AMP from the RNA-adenylate, thereby inhibiting step 3 reaction. Tyr159, Phe281 and Glu285, which are conserved among archaeal ATP-dependent RNA ligases and are situated on the surface of the enzyme, are required for RNA binding. We propose an RNA binding interface of the MthRnl based on the mutational studies and two sulfate ions that co-crystallized at the active site cleft in the MthRnl-AMP complex.
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