A three-dimensional model of RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3

摘要

Abstract Ribonuclease P (RNase P) is an endoribonuclease involved in maturation of the 5′-end of tRNA. We found previously that RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 consists of a catalytic RNase P RNA ( Pho pRNA) and five protein cofactors designated Pho Pop5, Pho Rpp21, Pho Rpp29, Pho Rpp30, and Pho Rpp38. The crystal structures of the five proteins have been determined, a three-dimensional (3-D) model of Pho pRNA has been constructed, and biochemical data, including protein-RNA interaction sites, have become available. Here, this information was combined to orient the crystallographic structures of the proteins relative to their RNA binding sites in the Pho pRNA model. Some alterations were made to the Pho pRNA model to improve the fit. In the resulting structure, a heterotetramer composed of Pho Pop5 and Pho Rpp30 bridges helices P3 and P16 in the Pho pRNA C-domain, thereby probably stabilizing a double-stranded RNA structure (helix P4) containing catalytic Mg 2+ ions, while a heterodimer of Pho Rpp21 and Pho Rpp29 locates on a single-stranded loop connecting helices P11 and P12 in the specificity domain (S-domain) in Pho pRNA, probably forming an appropriate conformation of the precursor tRNA (pre-tRNA) binding site. The fifth protein Pho Rpp38 binds each kink-turn (K-turn) motif in helices P12.1, P12.2, and P16 in Pho pRNA. Comparison of the structure of the resulting 3-D model with that of bacterial RNase P suggests transition from RNA-RNA interactions in bacterial RNase P to protein-RNA interactions in archaeal RNase P. The proposed 3-D model of P.?horikoshii RNase P will serve as a framework for further structural and functional studies on archaeal, as well as eukaryotic, RNase Ps. Graphical abstract The proteins are represented by their molecular surfaces, while the RNA is shown in stick form. Pho Pop5, Pho Rpp21, Pho Rpp29, Pho Rpp30, and Pho Rpp38 are colored in red, yellow, magenta, cyan, and green, respectively. Display Omitted Highlights ? An archaeal RNase P consists of RNA and five protein cofactors. ? A three-dimensional (3-D) model of the archaeal RNase P was constructed. ? The 3-D model was compared with the crystal structure of the bacterial RNase P. ? RNA-RNA in bacterial RNase P is replaced by protein-RNA in archaeal RNase P. ? The 3-D model will serve as a framework for further studies on archaeal RNase Ps.