Histidine tRNAs (tRNAHis) are unique in that they possess an extra 5′-base (G-1) not found in other tRNAs. Deletion of G-1 results in at least a 250-fold reduction in the rate of histidine charging in vitro. To better understand the role of the G-1 nucleotide in defining the structure of tRNAHis, and to correlate structure with cognate amino acid charging, NMR and molecular dynamics (MD) studies were performed on the wild-type and a ΔG-1 mutant Escherichia coli histidine tRNA acceptor stem microhelix. Using NMR-derived distance restraints, global structural characteristics are described and interpreted to rationalize experimental observations with respect to aminoacylation activity. The quality of the NMR-derived solution conformations of the wild-type and ΔG-1 histidine microhelices (microhelixHis) is assessed using a variety of MD-based computational protocols. Most of the duplex regions of the acceptor stem and the UUCG tetraloop are well defined and effectively superimposable for the wild-type and ΔG-1 mutant microhelixHis. Differences, however, are observed at the end of the helix and in the single-stranded CCCA-3′ tail. The wild-type microhelixHis structure is more well defined than the mutant and folds into a 'stacked fold-back' conformation. In contrast, we observe fraying of the first two base pairs and looping back of the single-stranded region in the ΔG-1 mutant resulting in a much less well defined conformation. Thus the role of the extra G-1 base of the unique G-1:C73 base pair in tRNAHis may be to prevent end-fraying and stabilize the stacked fold-back conformation of the CCCA-3′ region.
Bibliographical noteFunding Information:
We would like to thank the Minnesota Supercomputing Institute (MSI) for computational resources and technical assistance, and Abbey E. Rosen for critical reading of the manuscript. NMR instrumentation was provided with funds from the NSF (BIR-961477), the University of Minnesota Medical School and the Minnesota Medical Foundation. This research was supported by NIH grant GM49928 (K.M.-F.).