title: Effect of G-1 on histidine tRNA microhelix conformation.
abstract: Histidine tRNAs (tRNA(His)) 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 tRNA(His), and to correlate structure with cognate amino acid charging, NMR and molecular dynamics (MD) studies were performed on the wild-type and a DeltaG-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 DeltaG-1 histidine microhelices (micro helix(His)) 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 DeltaG-1 mutant microhelix(His). Differences, however, are observed at the end of the helix and in the single-stranded CCCA-3' tail. The wild-type microhelix(His) 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 DeltaG-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 tRNA(His) may be to prevent end-fraying and stabilize the stacked fold-back conformation of the CCCA-3' region.
authors.affiliation: Department of Chemistry, University of Minnesota, Minneapolis, MN 55455-0421, USA.
authors.forename: Mahadevan
authors.initials: M
authors.lastname: Seetharaman
authors.forename: Caroline
authors.initials: C
authors.lastname: Williams
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Cramer
authors.forename: Karin
authors.initials: K
authors.lastname: Musier-Forsyth
mesh_terms: D001483:Base Sequence; D004926:Escherichia coli / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D017354:Point Mutation / Q000235:genetics*; D020871:RNA Stability; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry* / Q000235:genetics*
chemical_list: D012329:RNA, Bacterial; D012346:RNA, Transfer, Amino Acyl