Ribonuclease P RNA: models of the 15/16 bulge from Escherichia coli and the P15 stem loop of Bacillus subtilis.
The Escherichia coli ribonuclease P RNA 15/16 internal bulge loop and the Bacillus subtilis P15 stem loop are important substrate binding sites for the CCA-3' terminus of pre-tRNA. Models of E. coli 15/16 bulge loop and the B. subtilis P15 stem loop have been constructed using MC-SYM, a constraint satisfaction program. The models use covariation analysis data for suggesting initial base pairings, chemical probing, and protection/modification results to determine particular pairing orientations, and mutational experimental analysis data for tRNA-RNase P RNA contacts. The structures from E. coli and B. subtilis, although different in secondary structure, have similar sequence and function. Using MC-SYM, we are able to illustrate how the 3' end of the pre-tRNA is able to interact with this segment of the catalytic RNase P RNA. In addition, we propose additional hydrogen bonding between A76 in the 3' terminus of the tRNA and the 15/16 region of E. coli and to the loop of B. subtilis.
Easterwood
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Department of Biochemistry & Molecular Genetics, University of Alabama at Birmingham, 35294, USA.
Harvey
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D001412:Bacillus subtilis / Q000737:chemistry; D001483:Base Sequence; D001665:Binding Sites; D003198:Computer Simulation; D004722:Endoribonucleases / Q000737:chemistry*; D004926:Escherichia coli / Q000737:chemistry; D029968:Escherichia coli Proteins; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012322:RNA Precursors; D012329:RNA, Bacterial / Q000737:chemistry*; D016337:RNA, Catalytic / Q000737:chemistry*; D012343:RNA, Transfer; D043262:Ribonuclease P; D013045:Species Specificity
D029968:Escherichia coli Proteins; D012322:RNA Precursors; D012329:RNA, Bacterial; D016337:RNA, Catalytic; D012343:RNA, Transfer; D004722:Endoribonucleases; D043262:Ribonuclease P; C470865:ribonuclease P, E coli