The conserved A-site finger of the 23 S rRNA: Just one of the intersubunit bridges or a part of the allosteric communication pathway?

Journal of Molecular Biology

Volumn 353, Issue 1, 2005, Pages 116-123

  Sergiev, Petr V ^a   Kiparisov, Sergey V ^a   Burakovsky, Dmitry E ^a   Lesnyak, Dmitry V ^a   Leonov, Andrei A ^a   Bogdanov, Alexey A ^a   Dontsova, Olga A ^a  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

EF G; Intersubunit bridges; Mutation; Ribosome; Translocation

Indexed keywords

ELONGATION FACTOR; GUANOSINE TRIPHOSPHATASE; PEPTIDYLTRANSFERASE; PROTEIN SUBUNIT; TRANSFER RNA;

ALLOSTERISM; ARTICLE; BINDING SITE; DEACYLATION; ENZYME ACTIVATION; GENE MUTATION; PRIORITY JOURNAL; RIBOSOME; RNA BINDING;

EID: 25144497020     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.08.006     Document Type: Article

References (35)

1. I.S. Gabashvili, R.K. Agrawal, C.M.T. Spahn, R.A. Grassucci, D.I. Svergun, J. Frank, and P. Penczek Solution structure of the E. coli 70 S ribosome at 11.5 Å resolution Cell 100 2000 537 549
2. M.M. Yusupov, G.Z. Yusupova, A. Baucom, K. Lieberman, T.N. Earnest, J.H.D. Cate, and H.F. Noller Crystal structure of the ribosome at 5.5 Å resolution Science 292 2001 883 896
3. H. Stark, E.V. Orlova, J. Rinke-Appel, N. Junke, F. Mueller, and M. Rodnina Arrangement of tRNAs in pre- and posttranslocational ribosomes revealed by electron cryomicroscopy Cell 88 1997 19 28
4. C. Meryman, D. Moazed, G. Daubresse, and H.F. Noller Nucleotides in 23 S rRNA protected by the association of 30 S and 50 S ribosomal subunits J. Mol. Biol. 285 1999 107 113
5. P. Penczek, N. Ban, R.A. Grassucci, R.K. Agrawal, and J. Frank Haloarcula marismortui 50 S subunit-complementarity of electron microscopy and X-ray crystallographic information J. Struct. Biol. 128 1999 44 50
6. C.M.T. Spahn, R. Beckmann, N. Eswar, P.A. Penczek, A. Sali, G. Blobel, and J. Frank Structure of the 80 S ribosome from Saccharomyces cerevisiae-tRNA-ribosome and subunit-subunit interactions Cell 107 2001 373 386
7. M.R. Sharma, E.C. Koc, P.P. Datta, T.M. Booth, L.L. Spremulli, and R.K. Agrawal Structure of the mammalian mitochondrial ribosome reveals an expanded functional role for its component proteins Cell 115 2003 97 108
8. J. Rinke-Appel, N. Junke, M. Osswald, and R. Brimacombe The ribosomal environment of tRNA: crosslinks to rRNA from positions 8 and 20:1 in the central fold of tRNA located at the A, P, or E site RNA 1 1995 1018 1028
9. M. Osswald, T. Doring, and R. Brimacombe The ribosomal neighbourhood of the central fold of tRNA: cross-links from position 47 of tRNA located at the A, P or E site Nucl. Acids Res. 23 1995 4635 4641
10. M. Valle, A. Zavialov, J. Sengupta, U. Rawat, M. Ehrenberg, and J. Frank Locking and unlocking of ribosomal motions Cell 114 2003 123 134
11. O. Dontsova, V. Tishkov, S. Dokudovskaya, A. Bogdanov, T. Doring, and J. Rinke-Appel Stem-loop IV of 5 S rRNA lies close to the peptidyltransferase center Proc. Natl Acad. Sci. USA 91 1994 4125 4129
12. S. Dokudovskaya, O. Dontsova, O. Shpanchenko, A. Bogdanov, and R. Brimacombe Loop IV of 5 S ribosomal RNA has contacts both to domain II and to domain V of the 23 S RNA RNA 2 1996 146 152
13. P. Sergiev, S. Dokudovskaya, E. Romanova, A. Topin, A. Bogdanov, R. Brimacombe, and O. Dontsova The environment of 5 S rRNA in the ribosome: cross-links to the GTPase-associated area of 23 S rRNA Nucl. Acids Res. 26 1998 2519 2525
14. N. Ban, P. Nissen, J. Hansen, P.B. Moore, and T.A. Steitz The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution Science 289 2000 905 920
15. A.A. Bogdanov, O.A. Dontsova, S.S. Dokudovskaya, and I.N. Lavrik Structure and function of 5 S rRNA in the ribosome Biochem. Cell Biol. 73 1996 869 876
16. T. Powers, and H.F. Noller Dominant lethal mutations in a conserved loop in 16 S rRNA Proc. Natl Acad. Sci. USA 87 1990 1042 1046
17. T. Asai, D. Zaporojets, C. Squires, and C.L. Squires An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria Proc. Natl Acad. Sci. USA 96 1999 1971 1976
18. M. O'Connor, and A.E. Dahlberg Mutations at U2555, a tRNA-protected base in 23 S rRNA, affect translational fidelity Proc. Natl Acad. Sci. USA 90 1993 9214 9218
19. +/polyamine system for polyuridine-dependent polyphenylalanine synthesis with near in vivo characteristics Methods Enzymol. 164 1988 650 658
20. R. Lill, J.M. Robertson, and W. Wintermeyer Binding of the 3′ terminus of tRNA to 23 S rRNA in the ribosomal exit site actively promotes translocation EMBO J. 8 1989 3933 3938
21. A.V. Zavialov, and M. Ehrenberg Peptidyl-tRNA regulates the GTPase activity of translation factors Cell 114 2003 113 122
22. A.A. Leonov, P.V. Sergiev, A.A. Bogdanov, R. Brimacombe, and O.A. Dontsova Affinity purification of ribosomes with a lethal G2655C mutation in 23 S rRNA that affects the translocation J. Biol. Chem. 278 2003 25664 25670
23. M.R. Macbeth, and I.G. Wool The phenotype of mutations of G2655 in the sarcin/ricin domain of 23 S ribosomal RNA J. Mol. Biol. 285 1999 965 975
24. C.M.T. Spahn, J. Remme, M.A. Schafer, and K.H. Nierhaus Mutational analysis of two highly conserved UGG sequences of 23 S rRNA from Escherichia coli J. Biol. Chem. 271 1996 32849 32856
25. D. Moazed, and H.F. Noller Interaction of tRNA with 23 S rRNA in the ribosomal A, P, and E sites Cell 57 1989 585 597
26. U. Maivali, and J. Remme Definition of bases in 23 S rRNA essential for ribosomal subunit association RNA 10 2004 600 604
27. S.T. Gregory, and A.E. Dahlberg Mutations in the conserved P loop perturb the conformation of two structural elements in the peptidyl transferase center of 23 S ribosomal RNA J. Mol. Biol. 285 1999 1475 1483
28. P.V. Sergiev, A.A. Bogdanov, A.E. Dahlberg, and O. Dontsova Mutations at position A960 of E. coli 23 S ribosomal RNA influence the structure of 5 S ribosomal RNA and the peptidyltransferase region of 23 S ribosomal RNA J. Mol. Biol. 299 2000 379 389
29. C.G. Cupples, and J.H. Miller A set of lacZ mutations in Escherichia coli that allow rapid detection of each of the six base substitutions Proc. Natl Acad. Sci. USA 86 1989 5345 5349
30. G. Blaha, U. Stelzl, C.M. Spahn, R.K. Agrawal, J. Frank, and K.H. Nierhaus Preparation of functional ribosomal complexes and effect of buffer conditions on tRNA positions observed by cryoelectron microscopy Methods Enzymol. 317 2000 292 309
31. Y. Shimizu, A. Inoue, Y. Tomari, T. Suzuki, T. Yokogawa, K. Nishikawa, and T. Ueda Cell-free translation reconstituted with purified components Nature Biotechnol. 19 2001 751 755
32. D. Hartz, D.S. McPheeters, R. Traut, and L. Gold Extension inhibition analysis of translation initiation complexes Methods Enzymol. 164 1988 419 425
33. M. Ehrenberg, N. Bilgin, and C.G. Kurland Design and use of fast and accurate in vitro translation system G. Spedding Ribosomes and Protein Synthesis: A Practical Approach 1990 Oxford University Press Oxford 101 129
34. R.R. Gutell Comparative sequence analysis and the structure of 16 S and 23 S rRNA R.A. Zimmermann A.E. Dahlberg Ribosomal RNA: Structure, Evolution, Processing and Function in Protein Biosynthesis 1996 CRC Press Boca Raton, FL 111 128
35. N. Guex, and M.C. Peitsch SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling Electrophoresis 18 1997 2714 2723