The functional exchangeability of pk- and k-turns in RNA structure
Ribonuclease P RNA requires a sharply kinked RNA helix to make a loop-receptor interaction that creates the binding site for the substrate. In some forms of the ribozyme, this is accomplished by a k-turn, while others have a different element called the pk-turn. The structure of the pk-turn in RNase...
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Landes Bioscience
2013
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3672288/ |
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pubmed-36722882013-06-27 The functional exchangeability of pk- and k-turns in RNA structure Daldrop, Peter Masquida, Benoît Lilley, David M.J. Research Paper Ribonuclease P RNA requires a sharply kinked RNA helix to make a loop-receptor interaction that creates the binding site for the substrate. In some forms of the ribozyme, this is accomplished by a k-turn, while others have a different element called the pk-turn. The structure of the pk-turn in RNase P of Thermotoga maritima is globally very similar to a k-turn, but lacks all the standard features of that structure, including long-range hydrogen bonds between the two helical arms. We show here that in an isolated RNA duplex, the pk-turn fails to adopt a tightly kinked structure, but rather is a flexible element. This suggests that the tertiary contacts of RNase P assist its folding into the required kinked structure. We find that we can replace the k-turn of the SAM-I riboswitch with the pk-turn, such that the resulting RNA retains its ability to bind SAM, although with lower affinity. We also find that we can replace the pk-turn of T. maritima RNase P with a standard k-turn (in either orientation) with retention of ribozyme activity. Thus, although the pk-turn cannot intrinsically fold into the kinked structure, it can be induced to fold correctly in context. And the pk-turn and k-turns can substitute functionally for one another. Landes Bioscience 2013-03-01 2013-01-30 /pmc/articles/PMC3672288/ /pubmed/23364423 http://dx.doi.org/10.4161/rna.23673 Text en Copyright © 2013 Landes Bioscience http://creativecommons.org/licenses/by-nc/3.0/ This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Daldrop, Peter Masquida, Benoît Lilley, David M.J. |
| spellingShingle |
Daldrop, Peter Masquida, Benoît Lilley, David M.J. The functional exchangeability of pk- and k-turns in RNA structure |
| author_facet |
Daldrop, Peter Masquida, Benoît Lilley, David M.J. |
| author_sort |
Daldrop, Peter |
| title |
The functional exchangeability of pk- and k-turns in RNA structure |
| title_short |
The functional exchangeability of pk- and k-turns in RNA structure |
| title_full |
The functional exchangeability of pk- and k-turns in RNA structure |
| title_fullStr |
The functional exchangeability of pk- and k-turns in RNA structure |
| title_full_unstemmed |
The functional exchangeability of pk- and k-turns in RNA structure |
| title_sort |
functional exchangeability of pk- and k-turns in rna structure |
| description |
Ribonuclease P RNA requires a sharply kinked RNA helix to make a loop-receptor interaction that creates the binding site for the substrate. In some forms of the ribozyme, this is accomplished by a k-turn, while others have a different element called the pk-turn. The structure of the pk-turn in RNase P of Thermotoga maritima is globally very similar to a k-turn, but lacks all the standard features of that structure, including long-range hydrogen bonds between the two helical arms. We show here that in an isolated RNA duplex, the pk-turn fails to adopt a tightly kinked structure, but rather is a flexible element. This suggests that the tertiary contacts of RNase P assist its folding into the required kinked structure. We find that we can replace the k-turn of the SAM-I riboswitch with the pk-turn, such that the resulting RNA retains its ability to bind SAM, although with lower affinity. We also find that we can replace the pk-turn of T. maritima RNase P with a standard k-turn (in either orientation) with retention of ribozyme activity. Thus, although the pk-turn cannot intrinsically fold into the kinked structure, it can be induced to fold correctly in context. And the pk-turn and k-turns can substitute functionally for one another. |
| publisher |
Landes Bioscience |
| publishDate |
2013 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3672288/ |
| _version_ |
1611983590179995648 |