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Induced fit of the peptidyl-transferase center of the ribosome and conformational freedom of the esterified amino acids
The catalytic site of most enzymes can efficiently handle only one substrate. In contrast, the ribosome is capable of polymerizing at a similar rate at least 20 different kinds of amino acids from aminoacyl-tRNA carriers while using just one catalytic site, the peptidyl-transferase center (PTC). An...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Cold Spring Harbor Laboratory Press
2017
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5238797/ https://www.ncbi.nlm.nih.gov/pubmed/27879432 http://dx.doi.org/10.1261/rna.057273.116 |
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author | Lehmann, Jean |
author_facet | Lehmann, Jean |
author_sort | Lehmann, Jean |
collection | PubMed |
description | The catalytic site of most enzymes can efficiently handle only one substrate. In contrast, the ribosome is capable of polymerizing at a similar rate at least 20 different kinds of amino acids from aminoacyl-tRNA carriers while using just one catalytic site, the peptidyl-transferase center (PTC). An induced-fit mechanism has been uncovered in the PTC, but a possible connection between this mechanism and the uniform handling of the substrates has not been investigated. We present an analysis of published ribosome structures supporting the hypothesis that the induced fit eliminates unreactive rotamers predominantly populated for some A-site aminoacyl esters before induction. We show that this hypothesis is fully consistent with the wealth of kinetic data obtained with these substrates. Our analysis reveals that induction constrains the amino acids into a reactive conformation in a side-chain independent manner. It allows us to highlight the rationale of the PTC structural organization, which confers to the ribosome the very unusual ability to handle large as well as small substrates. |
format | Online Article Text |
id | pubmed-5238797 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-52387972018-02-01 Induced fit of the peptidyl-transferase center of the ribosome and conformational freedom of the esterified amino acids Lehmann, Jean RNA Article The catalytic site of most enzymes can efficiently handle only one substrate. In contrast, the ribosome is capable of polymerizing at a similar rate at least 20 different kinds of amino acids from aminoacyl-tRNA carriers while using just one catalytic site, the peptidyl-transferase center (PTC). An induced-fit mechanism has been uncovered in the PTC, but a possible connection between this mechanism and the uniform handling of the substrates has not been investigated. We present an analysis of published ribosome structures supporting the hypothesis that the induced fit eliminates unreactive rotamers predominantly populated for some A-site aminoacyl esters before induction. We show that this hypothesis is fully consistent with the wealth of kinetic data obtained with these substrates. Our analysis reveals that induction constrains the amino acids into a reactive conformation in a side-chain independent manner. It allows us to highlight the rationale of the PTC structural organization, which confers to the ribosome the very unusual ability to handle large as well as small substrates. Cold Spring Harbor Laboratory Press 2017-02 /pmc/articles/PMC5238797/ /pubmed/27879432 http://dx.doi.org/10.1261/rna.057273.116 Text en © 2017 Lehmann; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/. |
spellingShingle | Article Lehmann, Jean Induced fit of the peptidyl-transferase center of the ribosome and conformational freedom of the esterified amino acids |
title | Induced fit of the peptidyl-transferase center of the ribosome and conformational freedom of the esterified amino acids |
title_full | Induced fit of the peptidyl-transferase center of the ribosome and conformational freedom of the esterified amino acids |
title_fullStr | Induced fit of the peptidyl-transferase center of the ribosome and conformational freedom of the esterified amino acids |
title_full_unstemmed | Induced fit of the peptidyl-transferase center of the ribosome and conformational freedom of the esterified amino acids |
title_short | Induced fit of the peptidyl-transferase center of the ribosome and conformational freedom of the esterified amino acids |
title_sort | induced fit of the peptidyl-transferase center of the ribosome and conformational freedom of the esterified amino acids |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5238797/ https://www.ncbi.nlm.nih.gov/pubmed/27879432 http://dx.doi.org/10.1261/rna.057273.116 |
work_keys_str_mv | AT lehmannjean inducedfitofthepeptidyltransferasecenteroftheribosomeandconformationalfreedomoftheesterifiedaminoacids |