Crucial Roles of Two Hydrated Mg2+ Ions in Reaction Catalysis of the Pistol Ribozyme

Teplova, Marianna; Falschlunger, Christoph; Krasheninina, Olga; Egger, Michaela; Ren, Aiming; Patel, Dinshaw J.; Micura, Ronald

doi:10.1002/anie.201912522

Crucial Roles of Two Hydrated Mg²⁺ Ions in Reaction Catalysis of the Pistol Ribozyme

Journal Article · Thu Dec 05 00:00:00 EST 2019 · Angewandte Chemie (International Edition)

DOI:https://doi.org/10.1002/anie.201912522· OSTI ID:1598035

Teplova, Marianna ^[1]; Falschlunger, Christoph ^[2]; Krasheninina, Olga ^[2]; Egger, Michaela ^[2]; Ren, Aiming ^[3]; Patel, Dinshaw J. ^[1]; ^[2]

Memorial Sloan-Kettering Cancer Center, New York, NY (United States)
Leopold-Franzens Univ., Innsbruck (Austria)
Zhejiang Univ., Hangzhou (China)

Pistol ribozymes constitute a new class of small self-cleaving RNAs. Crystal structures have been solved, providing three-dimensional snapshots along the reaction coordinate of pistol phosphodiester cleavage, corresponding to the pre-catalytic state, a vanadate mimic of the transition state, and the product. The results led to the proposed underlying chemical mechanism. Importantly, a hydrated Mg²⁺ ion remains innersphere-coordinated to N7 of G33 in all three states, and is consistent with its likely role as acid in general acid base catalysis (δ and β catalysis). Strikingly, the new structures shed light on a second hydrated Mg²⁺ ion that approaches the scissile phosphate from its binding site in the pre-cleavage state to reach out for water-mediated hydrogen bonding in the cyclophosphate product. The major role of the second Mg²⁺ ion appears to be the stabilization of product conformation. This study delivers a mechanistic understanding of ribozyme-catalyzed backbone cleavage.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: Austrian Science Fund (FWF); National Institutes of Health (NIH); National Natural Science Foundation of China (NSFC); The Austrian Research Promotion Agency (FFG)

OSTI ID:: 1598035

Journal Information:: Angewandte Chemie (International Edition), Journal Name: Angewandte Chemie (International Edition) Journal Issue: 7 Vol. 59; ISSN 1433-7851

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (40)

A Mini-Twister Variant and Impact of Residues/Cations on the Phosphodiester Cleavage of this Ribozyme Class Košutić, Marija; Neuner, Sandro; Ren, Aiming Angewandte Chemie, Vol. 127, Issue 50 https://doi.org/10.1002/ange.201506601	journal	October 2015
Atom-Specific Mutagenesis Reveals Structural and Catalytic Roles for an Active-Site Adenosine and Hydrated Mg ²⁺ in Pistol Ribozymes Neuner, Sandro; Falschlunger, Christoph; Fuchs, Elisabeth Angewandte Chemie, Vol. 129, Issue 50 https://doi.org/10.1002/ange.201708679	journal	November 2017
A Mini-Twister Variant and Impact of Residues/Cations on the Phosphodiester Cleavage of this Ribozyme Class Košutić, Marija; Neuner, Sandro; Ren, Aiming Angewandte Chemie International Edition, Vol. 54, Issue 50 https://doi.org/10.1002/anie.201506601	journal	October 2015
Atom-Specific Mutagenesis Reveals Structural and Catalytic Roles for an Active-Site Adenosine and Hydrated Mg ²⁺ in Pistol Ribozymes Neuner, Sandro; Falschlunger, Christoph; Fuchs, Elisabeth Angewandte Chemie International Edition, Vol. 56, Issue 50 https://doi.org/10.1002/anie.201708679	journal	November 2017
Ligand-dependent ribozymes: Ligand-dependent ribozymes Felletti, Michele; Hartig, Jörg S. Wiley Interdisciplinary Reviews: RNA, Vol. 8, Issue 2 https://doi.org/10.1002/wrna.1395	journal	September 2016
Unwinding the twister ribozyme: from structure to mechanism: Unwinding the twister ribozyme Gebetsberger, Jennifer; Micura, Ronald Wiley Interdisciplinary Reviews: RNA, Vol. 8, Issue 3 https://doi.org/10.1002/wrna.1402	journal	November 2016
Modulating RNA structure and catalysis: lessons from small cleaving ribozymes Reymond, Cedric; Beaudoin, Jean-Denis; Perreault, Jean-Pierre Cellular and Molecular Life Sciences, Vol. 66, Issue 24 https://doi.org/10.1007/s00018-009-0124-1	journal	August 2009
Efficient access to N-trifluoroacetylated 2′-amino-2′-deoxyadenosine phosphoramidite for RNA solid-phase synthesis Falschlunger, Christoph; Micura, Ronald Monatshefte für Chemie - Chemical Monthly, Vol. 150, Issue 5 https://doi.org/10.1007/s00706-019-02390-x	journal	April 2019
Nucleobase catalysis in ribozyme mechanism Bevilacqua, P.; Yajima, R. Current Opinion in Chemical Biology, Vol. 10, Issue 5 https://doi.org/10.1016/j.cbpa.2006.08.014	journal	October 2006
Structure-based mechanistic insights into catalysis by small self-cleaving ribozymes Ren, Aiming; Micura, Ronald; Patel, Dinshaw J. Current Opinion in Chemical Biology, Vol. 41 https://doi.org/10.1016/j.cbpa.2017.09.017	journal	December 2017
Chemistry and Biology of Self-Cleaving Ribozymes Jimenez, Randi M.; Polanco, Julio A.; Lupták, Andrej Trends in Biochemical Sciences, Vol. 40, Issue 11 https://doi.org/10.1016/j.tibs.2015.09.001	journal	November 2015
Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue Mir, Aamir; Golden, Barbara L. Biochemistry, Vol. 55, Issue 4 https://doi.org/10.1021/acs.biochem.5b01139	journal	January 2016
Mechanistic Debris Generated by Twister Ribozymes Breaker, Ronald R. ACS Chemical Biology, Vol. 12, Issue 4 https://doi.org/10.1021/acschembio.7b00010	journal	February 2017
An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes Bevilacqua, Philip C.; Harris, Michael E.; Piccirilli, Joseph A. ACS Chemical Biology, Vol. 14, Issue 6 https://doi.org/10.1021/acschembio.9b00202	journal	May 2019
Catalytic Strategies of Self-Cleaving Ribozymes Cochrane, Jesse C.; Strobel, Scott A. Accounts of Chemical Research, Vol. 41, Issue 8 https://doi.org/10.1021/ar800050c	journal	August 2008
Model for General Acid−Base Catalysis by the Hammerhead Ribozyme: pH−Activity Relationships of G8 and G12 Variants at the Putative Active Site ^† Han, Joonhee; Burke, John M. Biochemistry, Vol. 44, Issue 21 https://doi.org/10.1021/bi047941z	journal	May 2005
Thio Effects and an Unconventional Metal Ion Rescue in the Genomic Hepatitis Delta Virus Ribozyme Thaplyal, Pallavi; Ganguly, Abir; Golden, Barbara L. Biochemistry, Vol. 52, Issue 37 https://doi.org/10.1021/bi4000673	journal	September 2013
General Acid–Base Catalysis Mediated by Nucleobases in the Hairpin Ribozyme Kath-Schorr, Stephanie; Wilson, Timothy J.; Li, Nan-Sheng Journal of the American Chemical Society, Vol. 134, Issue 40 https://doi.org/10.1021/ja3067429	journal	September 2012
Pseudoknot Formation Seeds the Twister Ribozyme Cleavage Reaction Coordinate Vušurović, Nikola; Altman, Roger B.; Terry, Daniel S. Journal of the American Chemical Society, Vol. 139, Issue 24 https://doi.org/10.1021/jacs.7b01549	journal	June 2017
Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes Wilson, Timothy J.; Liu, Yijin; Li, Nan-Sheng Journal of the American Chemical Society, Vol. 141, Issue 19 https://doi.org/10.1021/jacs.9b02141	journal	April 2019
A widespread self-cleaving ribozyme class is revealed by bioinformatics Roth, Adam; Weinberg, Zasha; Chen, Andy G. Y. Nature Chemical Biology, Vol. 10, Issue 1 https://doi.org/10.1038/nchembio.1386	journal	November 2013
Crystal structure and mechanistic investigation of the twister ribozyme Liu, Yijin; Wilson, Timothy J.; McPhee, Scott A. Nature Chemical Biology, Vol. 10, Issue 9 https://doi.org/10.1038/nchembio.1587	journal	July 2014
New classes of self-cleaving ribozymes revealed by comparative genomics analysis Weinberg, Zasha; Kim, Peter B.; Chen, Tony H. Nature Chemical Biology, Vol. 11, Issue 8 https://doi.org/10.1038/nchembio.1846	journal	July 2015
Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage Ren, Aiming; Vušurović, Nikola; Gebetsberger, Jennifer Nature Chemical Biology, Vol. 12, Issue 9 https://doi.org/10.1038/nchembio.2125	journal	July 2016
The structure of a nucleolytic ribozyme that employs a catalytic metal ion Liu, Yijin; Wilson, Timothy J.; Lilley, David M. J. Nature Chemical Biology, Vol. 13, Issue 5 https://doi.org/10.1038/nchembio.2333	journal	March 2017
In-line alignment and Mg2+ coordination at the cleavage site of the env22 twister ribozyme Ren, Aiming; Košutić, Marija; Rajashankar, Kanagalaghatta R. Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms6534	journal	November 2014
Structure-based insights into self-cleavage by a four-way junctional twister-sister ribozyme Zheng, Luqian; Mairhofer, Elisabeth; Teplova, Marianna Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-01276-y	journal	October 2017
Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme Eiler, D.; Wang, J.; Steitz, T. A. Proceedings of the National Academy of Sciences, Vol. 111, Issue 36 https://doi.org/10.1073/pnas.1414571111	journal	August 2014
Crystal structure of Pistol, a class of self-cleaving ribozyme Nguyen, Laura A.; Wang, Jimin; Steitz, Thomas A. Proceedings of the National Academy of Sciences, Vol. 114, Issue 5 https://doi.org/10.1073/pnas.1611191114	journal	January 2017
Hatchet ribozyme structure and implications for cleavage mechanism Zheng, Luqian; Falschlunger, Christoph; Huang, Kaiyi Proceedings of the National Academy of Sciences, Vol. 116, Issue 22 https://doi.org/10.1073/pnas.1902413116	journal	May 2019
Mg ²⁺ ions: do they bind to nucleobase nitrogens? Leonarski, Filip; D'Ascenzo, Luigi; Auffinger, Pascal Nucleic Acids Research, Vol. 45, Issue 2 https://doi.org/10.1093/nar/gkw1175	journal	December 2016
Small Self-cleaving Ribozymes Ferre-D'Amare, A. R.; Scott, W. G. Cold Spring Harbor Perspectives in Biology, Vol. 2, Issue 10 https://doi.org/10.1101/cshperspect.a003574	journal	September 2010
Engineering of hairpin ribozyme variants for RNA recombination and splicing Hieronymus, Robert; Müller, Sabine Annals of the New York Academy of Sciences, Vol. 1447, Issue 1 https://doi.org/10.1111/nyas.14052	journal	April 2019
Transition State Stabilization by a Catalytic RNA Rupert, P. B. Science, Vol. 298, Issue 5597 https://doi.org/10.1126/science.1076093	journal	October 2002
Comparative Enzymology and Structural Biology of RNA Self-Cleavage Fedor, Martha J. Annual Review of Biophysics, Vol. 38, Issue 1 https://doi.org/10.1146/annurev.biophys.050708.133710	journal	June 2009
The amazing world of bacterial structured RNAs Westhof, Eric Genome Biology, Vol. 11, Issue 3 https://doi.org/10.1186/gb-2010-11-3-108	journal	January 2010
Biochemical analysis of pistol self-cleaving ribozymes Harris, Kimberly A.; Lünse, Christina E.; Li, Sanshu RNA, Vol. 21, Issue 11 https://doi.org/10.1261/rna.052514.115	journal	September 2015
Molecular simulations of the pistol ribozyme: unifying the interpretation of experimental data and establishing functional links with the hammerhead ribozyme Kostenbader, Ken; York, Darrin M. RNA, Vol. 25, Issue 11 https://doi.org/10.1261/rna.071944.119	journal	July 2019
A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization Torelli, A. T.; Krucinska, J.; Wedekind, J. E. RNA, Vol. 13, Issue 7 https://doi.org/10.1261/rna.510807	journal	July 2007
A common speed limit for RNA-cleaving ribozymes and deoxyribozymes Breaker, R. R. RNA, Vol. 9, Issue 8 https://doi.org/10.1261/rna.5670703	journal	August 2003

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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
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oligonucleotides
reaction mechanisms
structure–function relationships

Crucial Roles of Two Hydrated Mg2+ Ions in Reaction Catalysis of the Pistol Ribozyme

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Crucial Roles of Two Hydrated Mg²⁺ Ions in Reaction Catalysis of the Pistol Ribozyme