Catalysis by RNase P RNA: unique features and unprecedented active site plasticity.
Metal ions are essential cofactors for precursor tRNA (ptRNA) processing by bacterial RNase P. The ribose 2'-OH at nucleotide (nt) -1 of ptRNAs is known to contribute to positioning of catalytic Me2+. To investigate the catalytic process, we used ptRNAs with single 2'-deoxy (2'-H), 2'-amino (2'-N), or 2'-fluoro (2'-F) modifications at the cleavage site (nt -1). 2' modifications had small (2.4-7.7-fold) effects on ptRNA binding to E. coli RNase P RNA in the ground state, decreasing substrate affinity in the order 2'-OH > 2'-F > 2'-N > 2'-H. Effects on the rate of the chemical step (about 10-fold for 2'-F, almost 150-fold for 2'-H and 2'-N) were much stronger, and, except for the 2'-N modification, resembled strikingly those observed in the Tetrahymena ribozyme-catalyzed reaction at corresponding position. Mn2+ rescued cleavage of the 2'-N but also the 2'-H-modified ptRNA, arguing against a direct metal ion coordination at this location. Miscleavage between nt -1 and -2 was observed for the 2'-N-ptRNA at low pH (further influenced by the base identities at nt -1 and +73), suggesting repulsion of a catalytic metal ion due to protonation of the amino group. Effects caused by the 2'-N modification at nt -1 of the substrate allowed us to substantiate a mechanistic difference in phosphodiester hydrolysis catalyzed by Escherichia coli RNase P RNA and the Tetrahymena ribozyme: a metal ion binds next to the 2' substituent at nt -1 in the reaction catalyzed by RNase P RNA, but not at the corresponding location in the Tetrahymena ribozyme reaction.
Persson
Tina
T
Universität zu Lübeck, Institut für Biochemie, Ratzeburger Allee 160, D-23538 Lübeck, Germany.
Cuzic
Simona
S
Hartmann
Roland K
RK
D000818:Animals; D001665:Binding Sites; D002384:Catalysis; D004926:Escherichia coli / Q000201:enzymology / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D007477:Ions; D007700:Kinetics; D008274:Magnesium / Q000378:metabolism; D008345:Manganese / Q000378:metabolism; D008954:Models, Biological; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012313:RNA / Q000378:metabolism; D016337:RNA, Catalytic / Q000378:metabolism; D043262:Ribonuclease P / Q000737:chemistry*; D012260:Ribonucleases / Q000378:metabolism; D013379:Substrate Specificity; D013768:Tetrahymena / Q000378:metabolism
D007477:Ions; D016337:RNA, Catalytic; D008345:Manganese; D012313:RNA; D012260:Ribonucleases; D043262:Ribonuclease P; D008274:Magnesium