The interaction between C75 of tRNA and the A loop of the ribosome stimulates peptidyl transferase activity

RNA

Volumn 12, Issue 1, 2006, Pages 33-39

  Brunelle, Julie L ^a   Youngman, Elaine M ^a   Sharma, Divya ^a   Green, Rachel ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

A loop; Peptidyl transfer; pH rate profile; Ribosome; tRNA

Indexed keywords

CYTIDINE; PEPTIDYLTRANSFERASE; PUROMYCIN; TRANSFER RNA;

ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME BINDING; ENZYME CONFORMATION; ENZYME INHIBITION; ENZYME SUBSTRATE; PH MEASUREMENT; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; PROTEIN VARIANT; RIBOSOME;

BINDING SITES; CATALYSIS; HYDROGEN-ION CONCENTRATION; MUTATION; PEPTIDYL TRANSFERASES; PUROMYCIN; RIBOSOMES; RNA, RIBOSOMAL;

EID: 29844448116     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2256706     Document Type: Article

References (28)

1. 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. 98: 10096-10101.
2. Beringer, M., Adio, S., Wintermeyer, W., and Rodnina, M. 2003. The G2447A mutation does not affect ionization of a ribosomal group taking part in peptide bond formation. RNA 9: 919-922.
3. Caskey, C.T., Beaudet, A.L., Scolnick, E.M., and Rosman, M. 1971. Hydrolysis of fMet-tRNA by peptidyl transferase. Proc. Natl. Acad. Sci. 68: 3163-3167.
4. Cate, J.H., Yusupov, M.M., Yusupova, G.Z., Earnest, T.N., and Noller, H.F. 1999. X-ray crystal structures of 70S ribosome functional complexes. Science 285: 2095-2104.
5. Dahlquist, K.D. and Puglisi, J.D. 2000. Interaction of translation initiation factor IF1 with the E. coli ribosomal A site. J. Mol. Biol. 299: 1-15.
6. Dallas, A. and Noller, H.F. 2001. Interaction of translation initiation factor 3 with the 30S ribosomal subunit. Mol. Cell 8: 855-864.
7. Fersht, A. 1984. Enzyme structure and mechanism. W.H. Freeman and Company, New York.
8. Hesslein, A.E., Katunin, V.I., Beringer, M., Kosek, A.B., Rodnina, M.V., and Strobel, S.A. 2004. Exploration of the conserved A + C wobble pair within the ribosomal peptidyl transferase center using affinity purified mutant ribosomes. Nucleic Acids Res. 32: 3760-3770.
9. 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: 1-20.
10. Kim, D.F. and Green, R. 1999. Base-pairing between 23S rRNA and tRNA in the ribosomal A site. Mol. Cell 4: 859-864.
11. Knitt, D.S. and Herschlag, D. 1996. pH dependencies of the Tetrahymena ribozyme reveal an unconventional origin of an apparent pKa. Biochemistry 35: 1560-1570.
12. Merryman, C., Moazed, D., McWhirter, J., and Noller, H.F. 1999. Nucleotides in 16S rRNA protected by the association of 30S and 50S ribosomal subunits. J. Mol. Biol. 285: 97-105.
13. Miskin, R., Zamir, A., and Elson, D. 1968. The inactivation and reactivation of ribosomal-peptidyl transferase of E. coli. Biochem. Biophys. Res. Commun. 33: 551-557.
14. Moazed, D. and Noller, H.F. 1986. Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes. Cell 47: 985-994.
15. 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.
16. Nissen, P., Hansen, J., Ban, N., Moore, P.B., and Steitz, T.A. 2000. The structural basis of ribosome activity in peptide bond synthesis. [See comments.] Science 289: 920-930.
17. Okuda, K., Seila, A.C., and Strobel, S.A. 2005. Uncovering the enzymatic pKa of the ribosomal peptidyl transferase reaction utilizing a fluorinated puromycin derivative. Biochemistry 44: 6675-6684.
18. Rodriguez-Fonseca, C., Phan, H., Long, K.S., Porse, B.T., Kirillov, S.V., Amils, R., and Garrett, R.A. 2000. Puromycin-rRNA interaction sites at the peptidyl transferase center. RNA 6: 744-754.
19. 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.
20. Schmeing, T.M., Huang, K., Strobel, S.A., and Steitz, T.A. 2005. An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature (in press).
21. Seila, A.C., Okuda, K., Nunez, S., Seila, A.F., and Strobel, S.A. 2005. Kinetic isotope effect analysis of the ribosomal peptidyl transferase reaction. Biochemistry 44: 4018-4027.
22. Sievers, A., Beringer, M., Rodnina, M.V., and Wolfenden, R. 2004. The ribosome as an entropy trap. Proc. Natl. Acad. Sci. 101: 7897-7901.
23. Soffientini A.L.R., Gastaldo L., Parlett, J.H., Spurio, R., Lateana, A., and Islam, K. 1994. Purification procedure for bacterial translational initiation factors IF2 and IF3. Protein Expr. Purif. 5: 118-124.
24. Spurio, R., Paci, M., Pawlik, R.T., La Teana, A., DiGiacco, B.V., Pon, C.L., and Gualerzi, C.O. 1991. Site-directed mutagenesis and NMR spectroscopic approaches to the elucidation of the structure-function relationships in translation initiation factors IF1 and IF3. Biochimie 73: 1001-1006.
25. Starck, S.R. and Roberts, R.W. 2002. Puromycin oligonucleotides reveal steric restrictions for ribosome entry and multiple modes of translation inhibition. RNA 8: 890-903.
26. Weinger, J.S., Parnell, K.M., Dorner, S., Green, R., and Strobel, S.A. 2004. Substrate-assisted catalysis of peptide bond formation by the ribosome. Nat. Struct. Mol. Biol. 11: 1101-1106.
27. Youngman, E.M. and Green, R. 2005. Affinity purification of in vivo-assembled ribosomes for in vitro biochemical analysis. Methods 36: 305-312.
28. 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.