Nature, volume 438, issue 7067, pages 520-524

An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA

Martin Schmeing T ¹

Huang Kevin S ¹

Strobel Scott A. ^{1, 2}

Steitz Thomas A. ^{1, 2, 3}

Hide authors affiliations Show authors affiliations: 3 affiliations

Department of Molecular Biophysics and Biochemistry,

Department of Chemistry, Yale University, |

Howard Hughes Medical Institute, New Haven, USA |

Publication type: Journal Article

Publication date: 2005-11-24

Springer Nature

Journal: Nature

Quartile SCImago

Quartile WOS

Impact factor: 64.8

ISSN: 00280836, 14764687

DOI: 10.1038/nature04152

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Multidisciplinary

Abstract

Many kinds of enzymes need to protect their substrates from unwanted hydrolysis. Koshland proposed more than 40 years ago that these enzymes — he was looking specifically at hexokinase — adopt the catalytically competent conformation only when the appropriate substrates are bound and produce an ‘induced fit’ conformational change. Later work showed that it is indeed ‘induced fit’ that stops hexokinase from hydrolysing ATP when there is no glucose about. Structural studies of the large ribosomal subunit now show that a similar fit mechanism operates here too. This provides the answer to the long-standing question of how the nascent peptide in the P site of the ribosome avoids hydrolysis by peptidyl tRNA until the termination step of protein synthesis. This mechanism may well have been available to the ribozymes in an RNA world before proteins came on the scene. The large ribosomal subunit catalyses the reaction between the α-amino group of the aminoacyl-tRNA bound to the A site and the ester carbon of the peptidyl-tRNA bound to the P site1, while preventing the nucleophilic attack of water on the ester, which would lead to unprogrammed deacylation of the peptidyl-tRNA. Here we describe three new structures of the large ribosomal subunit of Haloarcula marismortui (Hma) complexed with peptidyl transferase substrate analogues that reveal an induced-fit mechanism in which substrates and active-site residues reposition to allow the peptidyl transferase reaction. Proper binding of an aminoacyl-tRNA analogue to the A site induces specific movements of 23S rRNA nucleotides 2618–2620 (Escherichia coli numbering 2583–2585) and 2541(2506), thereby reorienting the ester group of the peptidyl-tRNA and making it accessible for attack. In the absence of the appropriate A-site substrate, the peptidyl transferase centre positions the ester link of the peptidyl-tRNA in a conformation that precludes the catalysed nucleophilic attack by water. Protein release factors2 may also function, in part, by inducing an active-site rearrangement similar to that produced by the A-site aminoacyl-tRNA, allowing the carbonyl group and water to be positioned for hydrolysis.

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	2 4 6 8 10 12 14 16 18
Nucleic Acids Research	Nucleic Acids Research, 18, 6% Nucleic Acids Research 18 publications, 6%
Molecular Cell	Molecular Cell, 13, 4.33% Molecular Cell 13 publications, 4.33%
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, 12, 4% Proceedings of the National Academy of Sciences of the United States of America 12 publications, 4%
RNA	RNA, 11, 3.67% RNA 11 publications, 3.67%
Nature Communications	Nature Communications, 9, 3% Nature Communications 9 publications, 3%
Nature Structural and Molecular Biology	Nature Structural and Molecular Biology, 9, 3% Nature Structural and Molecular Biology 9 publications, 3%
Journal of Molecular Biology	Journal of Molecular Biology, 8, 2.67% Journal of Molecular Biology 8 publications, 2.67%
Current Opinion in Structural Biology	Current Opinion in Structural Biology, 8, 2.67% Current Opinion in Structural Biology 8 publications, 2.67%
Biochemistry	Biochemistry, 6, 2% Biochemistry 6 publications, 2%
Journal of Biological Chemistry	Journal of Biological Chemistry, 6, 2% Journal of Biological Chemistry 6 publications, 2%
Nature	Nature, 5, 1.67% Nature 5 publications, 1.67%
Chemistry & Biology	Chemistry & Biology, 5, 1.67% Chemistry & Biology 5 publications, 1.67%
Science	Science, 5, 1.67% Science 5 publications, 1.67%
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Angewandte Chemie - International Edition	Angewandte Chemie - International Edition, 4, 1.33% Angewandte Chemie - International Edition 4 publications, 1.33%
EMBO Journal	EMBO Journal, 4, 1.33% EMBO Journal 4 publications, 1.33%
Journal of the American Chemical Society	Journal of the American Chemical Society, 4, 1.33% Journal of the American Chemical Society 4 publications, 1.33%
Trends in Biochemical Sciences	Trends in Biochemical Sciences, 3, 1% Trends in Biochemical Sciences 3 publications, 1%
FEBS Letters	FEBS Letters, 3, 1% FEBS Letters 3 publications, 1%
eLife	eLife, 3, 1% eLife 3 publications, 1%
Annual Review of Biochemistry	Annual Review of Biochemistry, 3, 1% Annual Review of Biochemistry 3 publications, 1%
NATO Science for Peace and Security Series A: Chemistry and Biology	NATO Science for Peace and Security Series A: Chemistry and Biology, 3, 1% NATO Science for Peace and Security Series A: Chemistry and Biology 3 publications, 1%
Journal of Chemical Physics	Journal of Chemical Physics, 2, 0.67% Journal of Chemical Physics 2 publications, 0.67%
Biochemical Society Transactions	Biochemical Society Transactions, 2, 0.67% Biochemical Society Transactions 2 publications, 0.67%
Molecules	Molecules, 2, 0.67% Molecules 2 publications, 0.67%
Frontiers in Molecular Biosciences	Frontiers in Molecular Biosciences, 2, 0.67% Frontiers in Molecular Biosciences 2 publications, 0.67%
Scientific Reports	Scientific Reports, 2, 0.67% Scientific Reports 2 publications, 0.67%
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	2 4 6 8 10 12 14 16 18

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	10 20 30 40 50 60
Elsevier	Elsevier, 60, 20% Elsevier 60 publications, 20%
Springer Nature	Springer Nature, 39, 13% Springer Nature 39 publications, 13%
Wiley	Wiley, 21, 7% Wiley 21 publications, 7%
Oxford University Press	Oxford University Press, 20, 6.67% Oxford University Press 20 publications, 6.67%
American Chemical Society (ACS)	American Chemical Society (ACS), 18, 6% American Chemical Society (ACS) 18 publications, 6%
Cold Spring Harbor Laboratory	Cold Spring Harbor Laboratory, 15, 5% Cold Spring Harbor Laboratory 15 publications, 5%
Proceedings of the National Academy of Sciences (PNAS)	Proceedings of the National Academy of Sciences (PNAS), 12, 4% Proceedings of the National Academy of Sciences (PNAS) 12 publications, 4%
Annual Reviews	Annual Reviews, 7, 2.33% Annual Reviews 7 publications, 2.33%
American Society for Biochemistry and Molecular Biology	American Society for Biochemistry and Molecular Biology, 6, 2% American Society for Biochemistry and Molecular Biology 6 publications, 2%
EMBO press	EMBO press, 6, 2% EMBO press 6 publications, 2%
American Association for the Advancement of Science (AAAS)	American Association for the Advancement of Science (AAAS), 6, 2% American Association for the Advancement of Science (AAAS) 6 publications, 2%
American Society for Microbiology	American Society for Microbiology, 6, 2% American Society for Microbiology 6 publications, 2%
Taylor & Francis	Taylor & Francis, 5, 1.67% Taylor & Francis 5 publications, 1.67%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 4, 1.33% Multidisciplinary Digital Publishing Institute (MDPI) 4 publications, 1.33%
American Institute of Physics (AIP)	American Institute of Physics (AIP), 3, 1% American Institute of Physics (AIP) 3 publications, 1%
The Royal Society	The Royal Society, 3, 1% The Royal Society 3 publications, 1%
Pleiades Publishing	Pleiades Publishing, 3, 1% Pleiades Publishing 3 publications, 1%
Frontiers Media S.A.	Frontiers Media S.A., 3, 1% Frontiers Media S.A. 3 publications, 1%
Royal Society of Chemistry (RSC)	Royal Society of Chemistry (RSC), 3, 1% Royal Society of Chemistry (RSC) 3 publications, 1%
eLife Sciences Publications	eLife Sciences Publications, 3, 1% eLife Sciences Publications 3 publications, 1%
Portland Press	Portland Press, 2, 0.67% Portland Press 2 publications, 0.67%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 2, 0.67% Public Library of Science (PLoS) 2 publications, 0.67%
Beilstein-Institut	Beilstein-Institut, 1, 0.33% Beilstein-Institut 1 publication, 0.33%
The Chemical Society of Japan	The Chemical Society of Japan, 1, 0.33% The Chemical Society of Japan 1 publication, 0.33%
Canadian Science Publishing	Canadian Science Publishing, 1, 0.33% Canadian Science Publishing 1 publication, 0.33%
Biophysical Society	Biophysical Society, 1, 0.33% Biophysical Society 1 publication, 0.33%
Cambridge University Press	Cambridge University Press, 1, 0.33% Cambridge University Press 1 publication, 0.33%
Keio Gijuku Daigaku	Keio Gijuku Daigaku, 1, 0.33% Keio Gijuku Daigaku 1 publication, 0.33%
Walter de Gruyter	Walter de Gruyter, 1, 0.33% Walter de Gruyter 1 publication, 0.33%
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Martin Schmeing T. et al. An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA // Nature. 2005. Vol. 438. No. 7067. pp. 520-524.

GOST all authors (up to 50) Copy

Martin Schmeing T., Huang K. S., Strobel S. A., Steitz T. A. An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA // Nature. 2005. Vol. 438. No. 7067. pp. 520-524.

RIS |

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RIS Copy

TY - JOUR

DO - 10.1038/nature04152

UR - https://doi.org/10.1038%2Fnature04152

TI - An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA

T2 - Nature

AU - Martin Schmeing, T

AU - Huang, Kevin S

AU - Strobel, Scott A.

AU - Steitz, Thomas A.

PY - 2005

DA - 2005/11/24 00:00:00

PB - Springer Nature

SP - 520-524

IS - 7067

VL - 438

SN - 0028-0836

SN - 1476-4687

ER -

BibTex |

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BibTex Copy

@article{2005_Martin Schmeing,

author = {T Martin Schmeing and Kevin S Huang and Scott A. Strobel and Thomas A. Steitz},

title = {An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA},

journal = {Nature},

year = {2005},

volume = {438},

publisher = {Springer Nature},

month = {nov},

url = {https://doi.org/10.1038%2Fnature04152},

number = {7067},

pages = {520--524},

doi = {10.1038/nature04152}

}

MLA

Cite this

MLA Copy

Martin Schmeing, T., et al. “An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA.” Nature, vol. 438, no. 7067, Nov. 2005, pp. 520-524. https://doi.org/10.1038%2Fnature04152.

Found error?

Publisher

Springer Nature

Journal

Nature

Quartile SCImago

Quartile WOS

Impact factor

64.8

ISSN

00280836 (Print)
14764687 (Electronic)