Journal of Molecular Biology, volume 353, issue 1, pages 116-123

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

Sergiev Petr V. ¹

Kiparisov Sergey V ¹

Burakovsky Dmitry E ¹

Lesnyak Dmitry V ²

Leonov Andrei A. ¹

Bogdanov Alexey A. ¹

Dontsova Olga A. ¹

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Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russian Federation |

Department of Bioinformatics and Bioengineering, Moscow State University, Moscow 119899, Russian Federation |

Publication type: Journal Article

Publication date: 2005-10-01

Elsevier

Journal: Journal of Molecular Biology

Quartile SCImago

Quartile WOS

Impact factor: 5.6

ISSN: 00222836, 10898638

DOI: 10.1016/j.jmb.2005.08.006

Copy DOI

Molecular Biology

Structural Biology

Abstract

During the translocation of tRNAs and mRNA relative to the ribosome, the B1a, B1b and B1c bridges undergo the most extensive conformational changes among the bridges between the large and the small ribosomal subunits. The B1a bridge, also called the "A-site finger" (ASF), is formed by the 23S rRNA helix 38, which is located right above the ribosomal A-site. Here, we deleted part of the ASF so that the B1a intersubunit bridge could not be formed (DeltaB1a). The mutation led to a less efficient subunit association. A number of functional activities of the DeltaB1a ribosomes, such as tRNA binding to the P and A-sites, translocation and EF-G-related GTPase reaction were preserved. A moderate decrease in EF-G-related GTPase stimulation by the P-site occupation by deacylated tRNA was observed. This suggests that the B1a bridge is not involved in the most basic steps of the elongation cycle, but rather in the fine-tuning of the ribosomal activity. Chemical probing of ribosomes carrying the ASF truncation revealed structural differences in the 5S rRNA and in the 23S rRNA helices located between the peptidyltransferase center and the binding site of the elongation factors. Interestingly, reactivity changes were found in the P-loop, an important functional region of the 23S rRNA. It is likely that the A-site finger, in addition to its role in subunit association, forms part of the system of allosteric signal exchanges between the small subunit decoding center and the functional centers on the large subunit.

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Citations by journals

	2 4 6 8 10
Nucleic Acids Research	Nucleic Acids Research, 10, 28.57% Nucleic Acids Research 10 publications, 28.57%
Journal of Biological Chemistry	Journal of Biological Chemistry, 4, 11.43% Journal of Biological Chemistry 4 publications, 11.43%
Biochemistry (Moscow)	Biochemistry (Moscow), 3, 8.57% Biochemistry (Moscow) 3 publications, 8.57%
Molecular Biology	Molecular Biology, 2, 5.71% Molecular Biology 2 publications, 5.71%
Journal of Molecular Biology	Journal of Molecular Biology, 1, 2.86% Journal of Molecular Biology 1 publication, 2.86%
RNA	RNA, 1, 2.86% RNA 1 publication, 2.86%
Molecular Genetics and Genomics	Molecular Genetics and Genomics, 1, 2.86% Molecular Genetics and Genomics 1 publication, 2.86%
PLoS ONE	PLoS ONE, 1, 2.86% PLoS ONE 1 publication, 2.86%
Biophysical Journal	Biophysical Journal, 1, 2.86% Biophysical Journal 1 publication, 2.86%
Biochimica et Biophysica Acta - General Subjects	Biochimica et Biophysica Acta - General Subjects, 1, 2.86% Biochimica et Biophysica Acta - General Subjects 1 publication, 2.86%
Structure	Structure, 1, 2.86% Structure 1 publication, 2.86%
Molecular Cell	Molecular Cell, 1, 2.86% Molecular Cell 1 publication, 2.86%
Chemical Reviews	Chemical Reviews, 1, 2.86% Chemical Reviews 1 publication, 2.86%
Molecular and Cellular Biology	Molecular and Cellular Biology, 1, 2.86% Molecular and Cellular Biology 1 publication, 2.86%
Nucleic Acids and Molecular Biology	Nucleic Acids and Molecular Biology, 1, 2.86% Nucleic Acids and Molecular Biology 1 publication, 2.86%
Journal of Bacteriology	Journal of Bacteriology, 1, 2.86% Journal of Bacteriology 1 publication, 2.86%
Proceedings of the National Academy of Sciences of the United States of America	Proceedings of the National Academy of Sciences of the United States of America, 1, 2.86% Proceedings of the National Academy of Sciences of the United States of America 1 publication, 2.86%
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Citations by publishers

	2 4 6 8 10
Oxford University Press	Oxford University Press, 10, 28.57% Oxford University Press 10 publications, 28.57%
Pleiades Publishing	Pleiades Publishing, 5, 14.29% Pleiades Publishing 5 publications, 14.29%
Elsevier	Elsevier, 4, 11.43% Elsevier 4 publications, 11.43%
American Society for Biochemistry and Molecular Biology	American Society for Biochemistry and Molecular Biology, 4, 11.43% American Society for Biochemistry and Molecular Biology 4 publications, 11.43%
Springer Nature	Springer Nature, 2, 5.71% Springer Nature 2 publications, 5.71%
American Society for Microbiology	American Society for Microbiology, 2, 5.71% American Society for Microbiology 2 publications, 5.71%
Cold Spring Harbor Laboratory	Cold Spring Harbor Laboratory, 1, 2.86% Cold Spring Harbor Laboratory 1 publication, 2.86%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 1, 2.86% Public Library of Science (PLoS) 1 publication, 2.86%
Biophysical Society	Biophysical Society, 1, 2.86% Biophysical Society 1 publication, 2.86%
American Chemical Society (ACS)	American Chemical Society (ACS), 1, 2.86% American Chemical Society (ACS) 1 publication, 2.86%
Proceedings of the National Academy of Sciences (PNAS)	Proceedings of the National Academy of Sciences (PNAS), 1, 2.86% Proceedings of the National Academy of Sciences (PNAS) 1 publication, 2.86%
	2 4 6 8 10

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Sergiev P. V. et al. 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. 2005. Vol. 353. No. 1. pp. 116-123.

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Sergiev P. V., Kiparisov S. V., Burakovsky D. E., Lesnyak D. V., Leonov A. A., Bogdanov A. A., Dontsova O. A. 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. 2005. Vol. 353. No. 1. pp. 116-123.

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