Substrate-assisted catalysis of peptide bond formation by the ribosome (original) (raw)
References
Rodnina, M.V. & Wintermeyer, W. Peptide bond formation on the ribosome: structure and mechanism. Curr. Opin. Struct. Biol.13, 334–340 (2003). ArticleCAS Google Scholar
Schmeing, T.M. et al. A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits. Nat. Struct. Biol.9, 225–230 (2002). CASPubMed Google Scholar
Bruice, T.C. & Fife, T.H. Hydroxyl group catalysis 3. Nature of neighboring hydroxyl group assistance in alkaline hydrolysis of ester bond. J. Am. Chem. Soc.84, 1973–1979 (1962). ArticleCAS Google Scholar
Nissen, P., Hansen, J., Ban, N., Moore, P.B. & Steitz, T.A. The structural basis of ribosome activity in peptide bond synthesis. Science289, 920–930 (2000). ArticleCAS Google Scholar
Muth, G.W., Ortoleva-Donnelly, L. & Strobel, S.A. A single adenosine with a neutral pK(a) in the ribosomal peptidyl transferase center. Science289, 947–950 (2000). ArticleCAS Google Scholar
Polacek, N., Gaynor, M., Yassin, A. & Mankin, A.S. Ribosomal peptidyl transferase can withstand mutations at the putative catalytic nucleotide. Nature411, 498–501 (2001). ArticleCAS Google Scholar
Youngman, E.M., Brunelle, J.L., Kochaniak, A.B. & Green, R. The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release. Cell117, 589–599 (2004). ArticleCAS Google Scholar
Beringer, M., Adio, S., Wintermeyer, W. & Rodnina, M. The G2447A mutation does not affect ionization of a ribosomal group taking part in peptide bond formation. RNA9, 919–922 (2003). ArticleCAS Google Scholar
Thompson, J. et al. Analysis of mutations at residues A2451 and G2447 of 23S rRNA in the peptidyltransferase active site of the 50S ribosomal subunit. Proc. Natl. Acad. Sci. USA98, 9002–9007 (2001). ArticleCAS Google Scholar
Sievers, A., Beringer, M., Rodnina, M.V. & Wolfenden, R. The ribosome as an entropy trap. Proc. Natl. Acad. Sci. USA101, 7897–7901 (2004). ArticleCAS Google Scholar
Hecht, S.M., Kozarich, J.W. & Schmidt, F.J. Isomeric phenylalanyl-transfer-RNAs—position of aminoacyl moiety during protein-biosynthesis. Proc. Natl. Acad. Sci. USA71, 4317–4321 (1974). ArticleCAS Google Scholar
Wagner, T., Cramer, F. & Sprinzl, M. Activity of the 2′ and 3′ isomers of aminoacyl transfer ribonucleic-acid in the in vitro peptide elongation on Escherichia coli ribosomes. Biochemistry21, 1521–1529 (1982). ArticleCAS Google Scholar
Wagner, T. & Sprinzl, M. Inhibition of ribosomal translocation by peptidyl transfer ribonucleic-acid analogs. Biochemistry22, 94–98 (1983). ArticleCAS Google Scholar
Quiggle, K., Kumar, G., Ott, T.W., Ryu, E.K. & Chladek, S. Amindacyl derivates of nucleosides, nucleotides and polynucleotides 34. Donor site of ribosomal peptidyltransferase - investigation of substrate-specificity using 2′(3′)-_O_-(_N_-acylaminoacyl)dinucleoside phosphates as models of the 3′ terminus of _N_-acylaminoacyl transfer ribonucleic-acid. Biochemistry20, 3480–3485 (1981). ArticleCAS Google Scholar
Dorner, S., Panuschka, C., Schmid, W. & Barta, A. Mononucleotide derivatives as ribosomal P-site substrates reveal an important contribution of the 2′-OH to activity. Nucleic Acids Res.31, 6536–6542 (2003). ArticleCAS Google Scholar
Griffin, B.E. & Reese, C.B. Some observations on mechanism of acylation process in protein synthesis. Proc. Natl. Acad. Sci. USA51, 440–444 (1964). ArticleCAS Google Scholar
Hansen, J.L., Schmeing, T.M., Moore, P.B. & Steitz, T.A. Structural insights into peptide bond formation. Proc. Natl. Acad. Sci. USA99, 11670–11675 (2002). ArticleCAS Google Scholar
Das, G.K., Bhattacharyya, D. & Burma, D.P. A possible mechanism of peptide bond formation on ribosome without mediation of peptidyl transferase. J. Theor. Biol.200, 193–205 (1999). ArticleCAS Google Scholar
Chamberlin, S.I., Merino, E.J. & Weeks, K.M. Catalysis of amide synthesis by RNA phosphodiester and hydroxyl groups. Proc. Natl. Acad. Sci. USA99, 14688–14693 (2002). ArticleCAS Google Scholar
Katunin, V.I., Muth, G.W., Strobel, S.A., Wintermeyer, W. & Rodnina, M.V. Important contribution to catalysis of peptide bond formation by a single ionizing group within the ribosome. Mol. Cell10, 339–346 (2002). ArticleCAS Google Scholar
Sprinzl, M. & Sternbach, H. Enzymic modification of the C-C-A terminus of tRNA. 59, 182–190 (1979).
Fredrick, K. & Noller, H.F. Catalysis of ribosomal translocation by sparsomycin. Science300, 1159–1162 (2003). ArticleCAS Google Scholar
Moazed, D. & Noller, H.F. Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites. 57, 585–597 (1989).
Strobel, S.A. & Ortoleva-Donnelly, L. A hydrogen-bonding triad stabilizes the chemical transition state of a group I ribozyme. Chem. Biol.6, 153–165 (1999). ArticleCAS Google Scholar
Herschlag, D., Eckstein, F. & Cech, T.R. Contributions of 2′-hydroxyl groups of the RNA substrate to binding and catalysis by the Tetrahymena ribozyme—n energetic picture of an active-site composed of RNA. Biochemistry32, 8299–8311 (1993). ArticleCAS Google Scholar
Herschlag, D., Eckstein, F. & Cech, T.R. The importance of being ribose at the cleavage site in the Tetrahymena ribozyme reaction. Biochemistry32, 8312–8321 (1993). ArticleCAS Google Scholar
Hocquet, A., Leulliot, N. & Ghomi, M. Ground-state properties of nucleic acid constituents studied by density functional calculations. 3. Role of sugar puckering and base orientation on the energetics and geometry of 2′-deoxyribonucleosides and ribonucleosides. J. Phys. Chem. B104, 4560–4568 (2000). ArticleCAS Google Scholar
Uesugi, S., Miki, H., Ikehara, M., Iwahashi, H. & Kyogoku, Y. Linear relationship between electronegativity of 2′-substituents and conformation of adenine nucleosides. Tetrahedron Lett.20, 4073–4076 (1979). Article Google Scholar
Sjogren, A.S., Pettersson, E., Sjoberg, B.M. & Stromberg, R. Metal ion interaction with cosubstrate in self-splicing of group I introns. Nucleic Acids Res.25, 648–653 (1997). ArticleCAS Google Scholar
Shan, S.O. & Herschlag, D. Probing the role of metal ions in RNA catalysis: Kinetic and thermodynamic characterization of a metal ion interaction with the 2′-moiety of the guanosine nucleophile in the Tetrahymena group I ribozyme. Biochemistry38, 10958–10975 (1999). ArticleCAS Google Scholar
Adams, P.L., Stahley, M.R., Kosek, A.B., Wang, J. & Strobel, S.A. Crystal structure of a self-splicing group I intron with both exons. Nature430, 45–50 (2004). ArticleCAS Google Scholar
Bass, B.L. & Cech, T.R. Ribozyme inhibitors: deoxyguanosine and dideoxyguanosine are competitive inhibitors of self-splicing of the Tetrahymena ribosomal ribonucleic acid precursor. Biochemistry25, 4473–4477 (1986). ArticleCAS Google Scholar
Moran, S., Kierzek, R. & Turner, D.H. Binding of guanosine and 3′ splice site analogs to a group-I ribozyme—interactions with functional-groups of guanosine and with additional nucleotides. Biochemistry32, 5247–5256 (1993). ArticleCAS Google Scholar
Nakano, S., Chadalavada, D.M. & Bevilacqua, P.C. General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme. Science287, 1493–1497 (2000). ArticleCAS Google Scholar
Perrotta, A.T., Shih, I.H. & Been, M.D. Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme. Science286, 123–126 (1999). ArticleCAS Google Scholar
Bevilacqua, P.C., Brown, T.S., Nakano, S. & Yajima, R. Catalytic roles for proton transfer and protonation in ribozymes. Biopolymers73, 90–109 (2004). ArticleCAS Google Scholar
Dall'Acqua, W. & Carter, P. Substrate-assisted catalysis: Molecular basis and biological significance. Protein Sci.9, 1–9 (2000). ArticleCAS Google Scholar
Carter, P. & Wells, J.A. Engineering enzyme specificity by substrate-assisted catalysis. Science237, 394–399 (1987). ArticleCAS Google Scholar
Woese, C.R. Tanslation: In retrospect and prospect. RNA7, 1055–1067 (2001). ArticleCAS Google Scholar
Zakharova, O.D. et al. Structural constraints in the HIV-1 reverse trancriptase-primer/template complex for the initiation of DNA synthesis from primer tRNA(Lys3). Biochemistry37, 13343–13348 (1998). ArticleCAS Google Scholar
Pawlik, R.T., Littlechild, J., Pon, C. & Gualerzi, C. Purification and properties of Escherichia-coli translational initiation-factors. Biochemistry Int.2, 421–428 (1981). CAS Google Scholar
Schmitt, E., Mechulam, Y., Fromant, M., Plateau, P. & Blanquet, S. Crystal structure at 1.2 angstrom resolution and active site mapping of Escherichia coli peptidyl-tRNA hydrolase. EMBO J.16, 4760–4769 (1997). ArticleCAS Google Scholar
Moazed, D. & Noller, H.F. Sites of interaction of the CCA end of peptidyl-transfer RNA with 23s ribosomal-RNA. Proc. Natl. Acad. Sci. USA88, 3725–3728 (1991). ArticleCAS Google Scholar