Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3′-hydroxyl group of A76 of the unacylated A-site tRNA

RNA

Volumn 14, Issue 11, 2008, Pages 2372-2378

  Simonović, Miljan ^a,b,c   Steitz, Thomas A ^a,b  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^b YALE UNIVERSITY   (United States)

^c UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

CCA; Peptide release; Peptidyl tRNA hydrolysis; Ribosome; Unacylated tRNA

Indexed keywords

CARBON; CARBONYL DERIVATIVE; HEXANOIC ACID; HYDROXYL GROUP; OLIGONUCLEOTIDE; PEPTIDYL CAPROIC ACID; PEPTIDYLTRANSFERASE; POLYPEPTIDE; PROTEIN SUBUNIT; TRANSFER RNA; UNCLASSIFIED DRUG; WATER;

ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; DEACYLATION; GENE SEQUENCE; HALOARCULA MARISMORTUI; HYDROLYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; RIBOSOME;

ACYLATION; BINDING SITES; CATALYSIS; CRYSTALLOGRAPHY; DINUCLEOSIDE PHOSPHATES; HALOARCULA; HYDROLYSIS; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; PROTEIN BIOSYNTHESIS; RIBOSOME SUBUNITS, LARGE, ARCHAEAL; RNA, TRANSFER, AMINO ACYL; WATER;

HALOARCULA MARISMORTUI;

EID: 55549147922     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1118908     Document Type: Article

References (26)

1. Ban, N., Nissen, P., Hansen, J., Moore, P.B., and Steitz, T.A. 2000. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289: 905-920.
2. 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.
3. 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.
4. Brunelle, J.L., Shaw, J.J., Youngman, E.M., and Green, R. 2008. Peptide release on the ribosome depends critically on the 2′ OH of the peptidyl tRNA substrate. RNA 14: 1526-1531.
5. Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., et al. 1998. Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54: 905-921.
6. Caskey, C.T., Beaudet, A.L., Scolnik, E.M., and Rosman, M. 1971. Hydrolysis of fMet-tRNA by peptidyl transferase. Proc. Natl. Acad. Sci. 68: 3163-3167.
7. DeLano, W.L. 2002. The PyMOL user's manual. DeLano Scientific, Palo Alto, CA.
8. Dorner, S., Panuschka, C., Schmid, W., and Barta, A. 2003. Mononucleotide derivatives as ribosomal P-site substrates reveal an important contribution of the 2′-OH to activity. Nucleic Acids Res. 31: 6536-6542.
9. Emsley, P. and Cowtan, K. 2004. Coot: Model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60: 2126-2132.
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. 99: 11670-11675.
11. Klein, D.J., Moore, P.B., and Steitz, T.A. 2004. The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. J. Mol. Biol. 340: 141-177.
12. Laurberg, M, Asahara, H, Korostelev, A, Zhu, J, Trakhanov, S, and Noller, HF 2008. Structural basis for translation termination on the 70S ribosome. Nature 454: 852-857.
13. Ogle, J.M., Brodersen, D.E., Clemons Jr., W.M., Tarry, M.J., Carter, A.P., and Ramakrishnan, V. 2001. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292: 897-902.
14. Otwinowski, Z. and Minor, W. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276: 307-326.
15. Petry, S., Brodersen, D.E., Murphy, F.V.T., Dunham, C.M., Selmer, M., Tarry, M.J., Kelley, A.C., and Ramakrishnan, V. 2005. Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon. Cell 123: 1255-1266.
16. Polacek, N., Gomez, M.J., Ito, K., Xiong, L., Nakamura, Y., and Mankin, A. 2003. The critical role of the universally conserved A2602 of 23S ribosomal RNA in the release of the nascent peptide during translation termination. Mol. Cell 11: 103-112.
17. Rawat, U.B., Zavialov, A.V., Sengupta, J., Valle, M., Grassucci, R.A., Linde, J., Vestergaard, B., Ehrenberg, M., and Frank, J. 2003. A cryo-electron microscopic study of ribosome-bound termination factor RF2. Nature 421: 87-90.
18. Rawat, U., Gao, H., Zavialov, A., Gursky, R., Ehrenberg, M., and Frank, J. 2006. Interactions of the release factor RF1 with the ribosome as revealed by cryo-EM. J. Mol. Biol. 357: 1144-1153.
19. 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 29 hydroxyl of the P site tRNA in the peptidyl transferase reaction. Mol. Cell 20: 437-448.
20. 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.
21. Shaw, J.J. and Green, R. 2007. Two distinct components of release factor function uncovered by nucleophile partitioning analysis. Mol. Cell 28: 458-467.
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. Trobro, S. and Åqvist, J. 2006. Analysis of predictions for the catalytic mechanism of ribosomal peptidyl transfer. Biochemistry 45: 7049-7056.
24. 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.
25. 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.
26. Zavialov, A.V., Mora, L., Buckingham, R.H., and Ehrenberg, M. 2002. Release of peptide promoted by the GGQ motif of class 1 release factors regulates the GTPase activity of RF3. Mol. Cell 10: 789-798.