Abstract
tRNAs that read codons starting with U are usually modified at their A37 by isopentenyl-tRNA transferases to minimize peptidyl-tRNA slippage in translation. The consensus substrate requirements of the isopentenyl-tRNA transferase of Escherichia coli, MiaA, have been the focus of extensive study. However, the molecular basis of tRNA-MiaA recognition remains unknown. Here we describe the 2.5A crystal structure of MiaA in complex with substrate tRNA(Phe). Comparative structural analysis reveals that the enzymatic reaction involves an RNA-protein mutually induced fit mechanism in which large domain movements in MiaA provoke the partial unfolding of the substrate tRNA anticodon loop. In addition, we show how substrate tRNAs are recognized by MiaA through a combination of direct and indirect sequence readouts.
Highlights
TRNAs that read codons starting with U are usually modified at their A37 by isopentenyl-tRNA transferases to minimize peptidyl-tRNA slippage in translation
Modification is formed by the transfer of an isopentenyl moiety from dimethylallyl pyrophosphate (DMAPP)3 to A37 of tRNAs. This transfer is catalyzed by isopentenyl-tRNA transferases (IPTs; E.C. 2.5.1.8)
ACCELERATED PUBLICATION: MiaA-tRNA(Phe) Complex Structure with the structures of other bacterial IPTs without bound tRNA, we show that the insertion domain moves in toward the core domain as a result of induced fit
Summary
STRUCTURE OF ESCHERICHIA COLI ISOPENTENYL-tRNA TRANSFERASE IN COMPLEX WITH tRNA(Phe)*. The consensus substrate requirements of the isopentenyl-tRNA transferase of Escherichia coli, MiaA, have been the focus of extensive study. In a recent structure of MOD5 in complex with yeast tRNA(Cys) determined to 2.95 Å resolution, MOD5 was shown to bind the tRNA between the core domain and the insertion domain [11]. ACCELERATED PUBLICATION: MiaA-tRNA(Phe) Complex Structure with the structures of other bacterial IPTs without bound tRNA, we show that the insertion domain moves in toward the core domain as a result of induced fit. In this process, the anticodon loop of tRNA unfolds. We compare the MiaA-tRNA cocrystal structure with the MOD5-tRNA(Cys) structure [11] and discuss important regions where the bacterial IPT and eukaryotic IPT differ in light of their different substrate requirements
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