Importance of tRNA interactions with 23S rRNA for peptide bond formation on the ribosome: Studies with substrate analogs

Biological Chemistry

Volumn 388, Issue 7, 2007, Pages 687-691

  Beringer, Malte ^a   Rodnina, Marina V ^a  

^a UNIVERSITY OF WITTEN HERDECKE   (Germany)

Author keywords

Peptide bond formation; Puromycin; Ribosome; tRNA

Indexed keywords

CYSTEINE; PEPTIDYLTRANSFERASE; PUROMYCIN; RNA 23S; TRANSFER RNA;

BASE PAIRING; CHEMICAL BOND; CHEMICAL REACTION; GENE INTERACTION; MOLECULAR MIMICRY; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PH; PRIORITY JOURNAL; RIBOSOME; SHORT SURVEY;

PEPTIDES; PROTEIN BIOSYNTHESIS; RIBOSOMES; RNA, RIBOSOMAL, 23S; RNA, TRANSFER; SUBSTRATE SPECIFICITY;

EID: 34250644283     PISSN: 14316730     EISSN: 14374315     Source Type: Journal    
DOI: 10.1515/BC.2007.077     Document Type: Short Survey

References (35)

1. Bashan, A., Agmon, I., Zarivach, R., Schluenzen, F., Harms, J., Berisio, R., Bartels, H., Franceschi, F., Auerbach, T., Hansen, H.A., et al. (2003). Structural basis of the ribosomal machinery for peptide bond formation, translocation, and nascent chain progression. Mol. Cell 11, 91-102.
2. Bayfield, M.A., Dahlberg, A.E., Schulmeister, U., Dorner, S., and Barta, A. (2001). A conformational change in the ribosomal peptidyl transferase center upon active/inactive transition. Proc. Natl. Acad. Sci. USA 98, 10096-10101.
3. Bayfield, M.A., Thompson, J., and Dahlberg, A.E. (2004). The A2453-C2499 wobble base pair in Escherichia coli 23S ribosomal RNA is responsible for pH sensitivity of the peptidyl-transferase active site conformation. Nucleic Acids Res. 32, 5512-5518.
4. Beringer, M., Adio, S., Wintermeyer, W., and Rodnina, M.V. (2003). The G2447A mutation does not affect ionization of a ribosomal group taking part in peptide bond formation. RNA 9, 919-922.
5. Beringer, M., Bruell, C., Xiong, L., Pfister, P., Bieling, P., Katunin, V.I., Mankin, A.S., Bottger, E.C., and Rodnina, M.V. (2005). Essential mechanisms in the catalysis of peptide bond formation on the ribosome. J. Biol. Chem. 280, 36065-36072.
6. Bieling, P., Beringer, M., Adio, S., and Rodnina, M.V. (2006). Peptide bond formation does not involve acid-base catalysis by ribosomal residues. Nat. Struct. Mol. Biol. 13, 423-428.
7. Brunelle, J.L., Youngman, E.M., Sharma, D., and Green, R. (2006). The interaction between C75 of tRNA and the A loop of the ribosome stimulates peptidyl transferase activity. RNA 12, 33-39.
8. Cai, Z. and Tinoco, I. Jr. (1996). Solution structure of loop A from the hairpin ribozyme from tobacco ringspot virus satellite. Biochemistry 35, 6026-6036.
9. Feinberg, J.S. and Joseph, S. (2006). A conserved base-pair between tRNA and 23S rRNA in the peptidyl transferase center is important for peptide release. J. Mol. Biol. 364, 1010-1020.
10. Hansen, J.L., Schmeing, T.M., Moore, P.B., and Steitz, T.A. (2002). Structural insights into peptide bond formation. Proc. Natl. Acad. Sci. USA 99, 11670-11675.
11. Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F., and Yonath, A. (2001). High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell 107, 679-688.
12. +C wobble pair within the ribosomal peptidyl transferase center using affinity purified mutant ribosomes. Nucleic Acids Res. 32, 3760-3770.
13. Katunin, V.I., Muth, G.W., Strobel, S.A., Wintermeyer, W., and Rodnina, M.V. (2002). Important contribution to catalysis of peptide bond formation by a single ionizing group within the ribosome. Mol. Cell 10, 339-346.
14. Kim, D.F. and Green, R. (1999). Base-pairing between 23S rRNA and tRNA in the ribosomal A site. Mol. Cell 4, 859-864.
15. Korostelev, A., Trakhanov, S., Laurberg, M., and Noller, H.F. (2006). Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell 126, 1065-1077.
16. Maden, B.E. and Monro, R.E. (1968). Ribosome-catalyzed peptidyl transfer. Effects of cations and pH value. Eur. J. Biochem. 6, 309-316.
17. Muth, G.W., Chen, L., Kosek, A.B., and Strobel, S.A. (2001). pH-dependent conformational flexibility within the ribosomal peptidyl transferase center. RNA 7, 1403-1415.
18. Nissen, P., Hansen, J., Ban, N., Moore, P.B., and Steitz, T.A. (2000). The structural basis of ribosome activity in peptide bond synthesis. Science 289, 920-930.
19. a of the ribosomal peptidyl transferase reaction utilizing a fluorinated puromycin derivative. Biochemistry 44, 6675-6684.
20. Pape, T., Wintermeyer, W., and Rodnina, M.V. (1998). Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-tRNA to the A site of the E. coli ribosome. EMBO J. 17, 7490-7497.
21. Rodnina, M.V. and Wintermeyer, W. (1995). GTP consumption of elongation factor Tu during translation of heteropolymeric mRNAs. Proc. Natl. Acad. Sci. USA 92, 1945-1949.
22. Rodnina, M.V., Savelsbergh, A., Matassova, N.B., Katunin, V.I., Semenkov, Y.P., and Wintermeyer, W. (1999). Thiostrepton inhibits the turnover but not the GTPase of elongation factor G on the ribosome. Proc. Natl. Acad. Sci. USA 96, 9586-9590.
23. Rodnina, M.V., Gromadski, K.B., Kothe, U., and Wieden, H.J. (2005). Recognition and selection of tRNA in translation. FEBS Lett. 579, 938-942.
24. Samaha, R.R., Green, R., and Noller, H.F. (1995). A base pair between tRNA and 23S rRNA in the peptidyl transferase centre of the ribosome. Nature 377, 309-314.
25. Schmeing, T.M., Seila, A.C., Hansen, J.L., Freeborn, B., Soukup, J.K., Scaringe, S.A., Strobel, S.A., Moore, P.B., and Steitz, T.A. (2002). A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits. Nat. Struct. Biol. 9, 225-230.
26. Schmeing, T.M., Huang, K.S., Kitchen, D.E., Strobel, S.A., and Steitz, T.A. (2005a). Structural insights into the roles of water and the 2′ hydroxyl of the P site tRNA in the peptidyl transferase reaction. Mol. Cell 20, 437-448.
27. Schmeing, T.M., Huang, K.S., Strobel, S.A., and Steitz, T.A. (2005b). An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature 438, 520-524.
28. Schuwirth, B.S., Borovinskaya, M.A., Hau, C.W., Zhang,W., Vila-Sanjurjo, A., Holton, J.M., and Cate, J.H. (2005). Structures of the bacterial ribosome at 3.5 Å resolution. Science 310, 827-834.
29. Selmer, M., Dunham, C.M., Murphy, F.V.T., Weixlbaumer, A., Petry, S., Kelley, A.C., Weir, J.R., and Ramakrishnan, V. (2006). Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313, 1935-1942.
30. Sievers, A., Beringer, M., Rodnina, M.V., and Wolfenden, R. (2004). The ribosome as an entropy trap. Proc. Natl. Acad. Sci. USA 101, 7897-7901.
31. Trobro, S. and Åqvist, J. (2005). Mechanism of peptide bond synthesis on the ribosome. Proc. Natl. Acad. Sci. USA 102, 12395-12400.
32. Trobro, S. and Åqvist, J. (2006). Analysis of predictions for the catalytic mechanism of ribosomal peptidyl transfer. Biochemistry 45, 7049-7056.
33. a of adenine 2451 in the ribosomal peptidyl transferase center remains elusive. RNA 7, 1365-1369.
34. Youngman, E.M., Brunelle, J.L., Kochaniak, A.B., and Green, R. (2004). The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release. Cell 117, 589-599.
35. Yusupov, M.M., Yusupova, G.Z., Baucom, A., Lieberman, K., Earnest, T.N., Cate, J.H., and Noller, H.F. (2001). Crystal structure of the ribosome at 5.5 Å resolution. Science 292, 883-896.