YoeB-ribosome structure: a canonical RNase that requires the ribosome for its specific activity
As a typical endoribonuclease, YoeB mediates cellular adaptation in diverse bacteria by degrading mRNAs on its activation. Although the catalytic core of YoeB is thought to be identical to well-studied nucleases, this enzyme specifically targets mRNA substrates that are associated with ribosomes in...
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sg-ntu-dr.10356-1014162023-02-28T16:55:58Z YoeB-ribosome structure: a canonical RNase that requires the ribosome for its specific activity Tang, Kai Wang, Meitian Feng, Shu Chen, Yun Kamada, Katsuhiko Wang, Han Gao, Yong-Gui School of Biological Sciences DRNTU::Science::Biological sciences As a typical endoribonuclease, YoeB mediates cellular adaptation in diverse bacteria by degrading mRNAs on its activation. Although the catalytic core of YoeB is thought to be identical to well-studied nucleases, this enzyme specifically targets mRNA substrates that are associated with ribosomes in vivo. However, the molecular mechanism of mRNA recognition and cleavage by YoeB, and the requirement of ribosome for its optimal activity, largely remain elusive. Here, we report the structure of YoeB bound to 70S ribosome in pre-cleavage state, revealing that both the 30S and 50S subunits participate in YoeB binding. The mRNA is recognized by the catalytic core of YoeB, of which the general base/acid (Glu46/His83) are within hydrogen-bonding distance to their reaction atoms, demonstrating an active conformation of YoeB on ribosome. Also, the mRNA orientation involves the universally conserved A1493 and G530 of 16S rRNA. In addition, mass spectrometry data indicated that YoeB cleaves mRNA following the second position at the A-site codon, resulting in a final product with a 3′–phosphate at the newly formed 3′ end. Our results demonstrate a classical acid-base catalysis for YoeB-mediated RNA hydrolysis and provide insight into how the ribosome is essential for its specific activity. Published version 2014-01-03T08:20:00Z 2019-12-06T20:38:22Z 2014-01-03T08:20:00Z 2019-12-06T20:38:22Z 2013 2013 Journal Article Feng, S., Chen, Y., Kamada, K., Wang, H., Tang, K., Wang, M., et al. (2013). YoeB-ribosome structure: a canonical RNase that requires the ribosome for its specific activity. Nucleic acids research, 41(20), 9549-9556. https://hdl.handle.net/10356/101416 http://hdl.handle.net/10220/18397 10.1093/nar/gkt742 23945936 en Nucleic acids research © 2013 The Authors. This paper was published in Nucleic Acids Research and is made available as an electronic reprint (preprint) with permission of the authors. The paper can be found at the following official DOI: [http://dx.doi.org/10.1093/nar/gkt742]. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper is prohibited and is subject to penalties under law. application/pdf |
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DRNTU::Science::Biological sciences Tang, Kai Wang, Meitian Feng, Shu Chen, Yun Kamada, Katsuhiko Wang, Han Gao, Yong-Gui YoeB-ribosome structure: a canonical RNase that requires the ribosome for its specific activity |
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As a typical endoribonuclease, YoeB mediates cellular adaptation in diverse bacteria by degrading mRNAs on its activation. Although the catalytic core of YoeB is thought to be identical to well-studied nucleases, this enzyme specifically targets mRNA substrates that are associated with ribosomes in vivo. However, the molecular mechanism of mRNA recognition and cleavage by YoeB, and the requirement of ribosome for its optimal activity, largely remain elusive. Here, we report the structure of YoeB bound to 70S ribosome in pre-cleavage state, revealing that both the 30S and 50S subunits participate in YoeB binding. The mRNA is recognized by the catalytic core of YoeB, of which the general base/acid (Glu46/His83) are within hydrogen-bonding distance to their reaction atoms, demonstrating an active conformation of YoeB on ribosome. Also, the mRNA orientation involves the universally conserved A1493 and G530 of 16S rRNA. In addition, mass spectrometry data indicated that YoeB cleaves mRNA following the second position at the A-site codon, resulting in a final product with a 3′–phosphate at the newly formed 3′ end. Our results demonstrate a classical acid-base catalysis for YoeB-mediated RNA hydrolysis and provide insight into how the ribosome is essential for its specific activity. |
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School of Biological Sciences |
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School of Biological Sciences Tang, Kai Wang, Meitian Feng, Shu Chen, Yun Kamada, Katsuhiko Wang, Han Gao, Yong-Gui |
format |
Article |
author |
Tang, Kai Wang, Meitian Feng, Shu Chen, Yun Kamada, Katsuhiko Wang, Han Gao, Yong-Gui |
author_sort |
Tang, Kai |
title |
YoeB-ribosome structure: a canonical RNase that requires the ribosome for its specific activity |
title_short |
YoeB-ribosome structure: a canonical RNase that requires the ribosome for its specific activity |
title_full |
YoeB-ribosome structure: a canonical RNase that requires the ribosome for its specific activity |
title_fullStr |
YoeB-ribosome structure: a canonical RNase that requires the ribosome for its specific activity |
title_full_unstemmed |
YoeB-ribosome structure: a canonical RNase that requires the ribosome for its specific activity |
title_sort |
yoeb-ribosome structure: a canonical rnase that requires the ribosome for its specific activity |
publishDate |
2014 |
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https://hdl.handle.net/10356/101416 http://hdl.handle.net/10220/18397 |
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1759855159492476928 |