Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA

  title={Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA},
  author={Heather C. Losey and Alexander J. Ruthenburg and Gregory L. Verdine},
  journal={Nature Structural \&Molecular Biology},
Bacterial tRNA adenosine deaminases (TadAs) catalyze the hydrolytic deamination of adenosine to inosine at the wobble position of tRNAArg2, a process that enables this single tRNA to recognize three different arginine codons in mRNA. In addition, inosine is also introduced at the wobble position of multiple eukaryotic tRNAs. The genes encoding these deaminases are essential in bacteria and yeast, demonstrating the importance of their biological activity. Here we report the crystallization and… 
The C-terminal end of the Trypanosoma brucei editing deaminase plays a critical role in tRNA binding.
It is shown that deletion of the last 10 amino acids at the C terminus of TbADAT2 abolishes tRNA binding, and the KR-domain provides a first glance at key residues involved in t RNA binding by eukaryotic tRNA editing deaminases.
Sequence-independent substrate selection by the eukaryotic wobble base deaminase ADAT2/3 involves multiple protein domains and distortion of the tRNA anticodon loop
The first structure of a eukaryotic ADAT2/3 deaminase bound to a full-length tRNA is presented, revealing that the enzyme distorts the anticodon loop, but in contrast to the bacterial enzymes, selects its substrate via sequence-independent contacts of eUKaryote-acquired flexible or intrinsically unfolded motifs distal from the conserved catalytic core.
Crystal structure of the yeast heterodimeric ADAT2/3 deaminase
A stepwise model for the pathway of deamination by ADAT2/3 is proposed, providing insight into the molecular mechanism of the A-to-I editing by the eukaryotic ADAT heterodimer, especially the role of ADAT3 in catalysis.
A Single Zinc Ion Is Sufficient for an Active Trypanosoma brucei tRNA Editing Deaminase*
It is shown by kinetic analyses and inductively coupled plasma emission spectrometry that wild type TbADAT2/3 coordinates two Zn2+ per heterodimer, but unlike any other tRNA deaminase, mutation of one of the key Zn 2+-coordinating cysteines in Tb ADAT2 yields a functional enzyme with a single-bound zinc.
Snapshots of dynamics in synthesizing N(6)-isopentenyladenosine at the tRNA anticodon.
The site-specific isopentenylation of RNA is ensured by a characteristic pinch-and-flip mechanism and by a reaction tunnel to confine the substrate selection.
Crystallographic capture of a radical S-adenosylmethionine enzyme in the act of modifying tRNA
The x-ray structure of a key intermediate in the RlmN reaction is reported, in which a Cys118→Ala variant of the protein is cross-linked to a tRNAGlu substrate through the terminal methylene carbon of a formerly methylcysteinyl residue and C2 of A37.
Mechanisms of the tRNA wobble cytidine modification essential for AUA codon decoding in prokaryotes
  • T. Numata
  • Biology, Chemistry
    Bioscience, biotechnology, and biochemistry
  • 2015
In bacteria and archaea, the wobble cytidine of the AUA codon-specific tRNAIle is modified to 2-lysylcytidine and 2-agmatinylcyTidine by TilS and TiaS, respectively.
Molecular basis of cobalamin-dependent RNA modification
This work determined a series of high resolution structures of QueG from Bacillus subtilis and shows how this enzyme uses a HEAT-like domain to recognize the appropriate anticodons and position the hypermodified nucleoside into the enzyme active site, informing the understanding of Cbl dependent nucleic acid modification.
RNA editing in bacteria recodes multiple proteins and regulates an evolutionarily conserved toxin-antitoxin system.
This work focused on hokB, a toxin that confers antibiotic tolerance by growth inhibition, as it demonstrated the highest level of A-to-I RNA editing and identified the tRNA-specific adenosine deaminase (tadA) as the editing enzyme of all these editing sites, thus making it the first identified RNA editing enzyme that modifies both tRNAs and mRNAs.


An adenosine deaminase that generates inosine at the wobble position of tRNAs.
The tRNA-specific adenosine deaminase of Saccharomyces cerevisiae that forms I(34) in tRNAs that provides an evolutionary link between the CDA superfamily and RNA-dependent adenosines deaminases (ADARs/ADATs).
tadA, an essential tRNA‐specific adenosine deaminase from Escherichia coli
It is shown that tadA is an essential gene in E.coli, underscoring the critical function of inosine at the wobble position in prokaryotes.
Crystal Structure of tRNA Adenosine Deaminase (TadA) from Aquifex aeolicus*
This study determined the crystal structure of Aquifex aeolicus TadA at a 1.8-Å resolution, the first structure of a deaminase acting on tRNA, and made a docking model of TadA with the tRNA anticodon stem loop.
Biochemical and structural studies of A-to-I editing by tRNA:A34 deaminases at the wobble position of transfer RNA.
A model of tadA-tRNA interaction that explains the molecular basis of tRNA recognition by tadA is proposed and a conserved FFxxxR motif at the C-terminus, which is unique to tadA, has been identified, and its critical role in tRNA substrate recognition is proposed.
Tad1p, a yeast tRNA‐specific adenosine deaminase, is related to the mammalian pre‐mRNA editing enzymes ADAR1 and ADAR2
Tad1p has significant sequence similarity with the mammalian editing enzymes which act on specific precursor‐mRNAs and on long double‐stranded RNA, suggesting an evolutionary link between pre‐mRNA editing and tRNA modification.
Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase
The refined crystal structure of Escherichia coli glutaminyl transfer RNA synthetase complexed with transfer RNAGln and ATP reveals that the entire anticodon loop provides essential sites for glutaminol tRNA synthetases discrimination among tRNA molecules.
Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate
Interactions between TGT and RNA revealed by the structure provide the molecular basis of the RNA substrate requirements by TGT, and reaction of PreQ1 with the crystallized covalent intermediate provides insight into the necessary structural changes required for the TGT-catalyzed reaction to occur.
Substrate analogues for an RNA-editing adenosine deaminase: mechanistic investigation and inhibitor design.
This and other results indicate that ADAR2 uses a base recognition strategy different from that of ADA, in contrast to adenosine deaminase (ADA), which catalyzes a similar reaction on nucleosides.
The uridine in "U-turn": contributions to tRNA-ribosomal binding.
The results demonstrate that proton donations by the N3-H and 2'OH groups of U33 are not absolutely required for ribosomal binding, and suggest that the overall uridine conformation, including a dynamic (C3'-endo > C2'-endo) sugar pucker, anti-conformation, and ability of uracil to stack between C32 and A35-phosphate, are the contributing factors to a functional U-turn.