Frontiers in Molecular Biosciences, 2022 RNA ligases play important roles in repairing and circularizing RNAs post-transcriptionally. In this study, we generated an allelic knockout of ATP-dependent RNA ligase (Rnl) in the hyperthermophilic archaeon Thermococcus kodakarensis to identify its ...
Yancheng Liu +7 more
doaj +5 more sources
Structural and mutational analysis of archaeal ATP-dependent RNA ligase identifies amino acids required for RNA binding and catalysis [PDF]
Nucleic Acids Research, 2016 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.
Huiqiong Gu +6 more
semanticscholar +4 more sources
Cleavage of 3′-terminal adenosine by archaeal ATP-dependent RNA ligase [PDF]
Scientific Reports, 2017 Methanothermobacter thermoautotrophicus RNA ligase (MthRnl) catalyzes formation of phosphodiester bonds between the 5′-phosphate and 3′-hydroxyl termini of single-stranded RNAs.
Shigeo Yoshinari +3 more
semanticscholar +4 more sources
Three-dimensional structure model and predicted ATP interaction rewiring of a deviant RNA ligase 2 [PDF]
BMC Structural Biology, 2015 BackgroundRNA ligases 2 are scarce and scattered across the tree of life. Two members of this family are well studied: the mitochondrial RNA editing ligase from the parasitic trypanosomes (Kinetoplastea), a promising drug target, and bacteriophage T4 RNA
Sandrine Moreira +3 more
semanticscholar +4 more sources
Structure-function analysis of Methanobacterium thermoautotrophicum RNA ligase – engineering a thermostable ATP independent enzyme [PDF]
BMC Molecular Biology, 2012 BackgroundRNA ligases are essential reagents for many methods in molecular biology including NextGen RNA sequencing. To prevent ligation of RNA to itself, ATP independent mutant ligases, defective in self-adenylation, are often used in combination with ...
Alexander Zhelkovsky, Larry McReynolds
semanticscholar +5 more sources
Synthesis of bisphosphonate derivatives of ATP by T4 RNA ligase [PDF]
FEBS Letters, 2006 T4 RNA ligase catalyzes the synthesis of ATP β,γ‐bisphosphonate analogues, using the following substrates with the relative velocity rates indicated between brackets: methylenebisphosphonate (pCH2p) (100), clodronate (pCCl2p) (52), and etidronate (pC(OH)(CH3)p) (4). The presence of pyrophosphatase about doubled the rate of these syntheses. Pamidronate (
Marı́a A. Günther Sillero +4 more
semanticscholar +6 more sources
Plant Methods, 2012 Background Deep sequencing is a powerful tool for novel small RNA discovery. Illumina small RNA sequencing library preparation requires a pre-adenylated 3’ end adapter containing a 5’,5’-adenyl pyrophosphoryl moiety.
Chen Yun-Ru +5 more
doaj +2 more sources
Carboxymethylcytosine is a natural base modification and a handle for bacteriophage DNA hypermodification [PDF]
Nature CommunicationsBacteriophages possess a wide array of DNA modifications, with many acting as molecular camouflage to evade host immune defenses. Sequence databases contain numerous bacteriophage enzymes of unknown function, with some potentially involved in yet to be ...
Qiaoyu Yang +16 more
doaj +2 more sources
Development of Allosteric Ribozymes for ATP and l-Histidine Based on the R3C Ligase Ribozyme
LifeDuring the evolution of the RNA, short RNAs are thought to have joined together to form long RNAs, enhancing their function as ribozymes. Previously, the artificial R3C ligase ribozyme (73 nucleotides) was successfully reduced to 46 nucleotides; however,
Yuna Akatsu +2 more
doaj +2 more sources
The adaptability of the fungal tRNA ligase's ATP-binding pocket: a potential target for new antifungal drugs. [PDF]
NAR Mol MedThe transfer RNA (tRNA) ligase (TRL1) is a highly conserved multidomain protein that is the archetype of the recently characterized Rnl6 clade. This clade distinguishes itself through a distinct C-terminal domain that sets it apart from other RNA ligase ...
McEwen AG +6 more
europepmc +2 more sources