Structural basis for substrate binding and catalysis by a self-alkylating ribozyme

Krochmal, Daniel; Shao, Yaming; Li, Nan-Sheng; DasGupta, Saurja; Shelke, Sandip A.; Koirala, Deepak; Piccirilli, Joseph A.

doi:10.1038/s41589-021-00950-z

Structural basis for substrate binding and catalysis by a self-alkylating ribozyme

Journal Article · 01 January 2022 · Nat. Chem. Biol.

DOI:https://doi.org/10.1038/s41589-021-00950-z· OSTI ID:1867492

Krochmal, Daniel; Shao, Yaming; Li, Nan-Sheng; DasGupta, Saurja; Shelke, Sandip A.; Koirala, Deepak; Piccirilli, Joseph A.

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

Sponsoring Organization:: DOE - Office Of Science; National Institutes of Health (NIH)

OSTI ID:: 1867492

Journal Information:: Nat. Chem. Biol., Vol. 18

Country of Publication:: United States

Language:: ENGLISH

References (39)

The Mechanism of Peptidyl Transfer Catalysis by the Ribosome Leung, Edward Ki Yun; Suslov, Nikolai; Tuttle, Nicole Annual Review of Biochemistry, Vol. 80, Issue 1 https://doi.org/10.1146/annurev-biochem-082108-165150	journal	July 2011
Biological Phosphoryl-Transfer Reactions: Understanding Mechanism and Catalysis Lassila, Jonathan K.; Zalatan, Jesse G.; Herschlag, Daniel Annual Review of Biochemistry, Vol. 80, Issue 1 https://doi.org/10.1146/annurev-biochem-060409-092741	journal	July 2011
Structurally complex and highly active RNA ligases derived from random RNA sequences Ekland, E.; Szostak, J.; Bartel, D. Science, Vol. 269, Issue 5222 https://doi.org/10.1126/science.7618102	journal	July 1995
Isolation of new ribozymes from a large pool of random sequences [see comment] Bartel, D.; Szostak, J. Science, Vol. 261, Issue 5127, p. 1411-1418 https://doi.org/10.1126/science.7690155	journal	September 1993
Aminoacyl esterase activity of the Tetrahymena ribozyme Piccirilli, J.; McConnell, T.; Zaug, A. Science, Vol. 256, Issue 5062 https://doi.org/10.1126/science.1604316	journal	June 1992
Catalytic Nucleic Acids: Biochemistry, Chemical Biology, Biosensors, and Nanotechnology Ma, Lingzi; Liu, Juewen iScience, Vol. 23, Issue 1 https://doi.org/10.1016/j.isci.2019.100815	journal	January 2020
In vitro evolution of a self-alkylatlng ribozyme Wilson, Charles; Szostak, Jack W. Nature, Vol. 374, Issue 6525 https://doi.org/10.1038/374777a0	journal	April 1995
An RNA catalyst that reacts with a mechanistic inhibitor of serine proteases Ameta, Sandeep; Jäschke, Andres Chem. Sci., Vol. 4, Issue 3 https://doi.org/10.1039/C2SC21588H	journal	January 2013
Fluorescent RNA Labeling Using Self-Alkylating Ribozymes Sharma, Ashwani K.; Plant, Joshua J.; Rangel, Alexandra E. ACS Chemical Biology, Vol. 9, Issue 8 https://doi.org/10.1021/cb5002119	journal	June 2014
Site-specific RNA methylation by a methyltransferase ribozyme Scheitl, Carolin P. M.; Ghaem Maghami, Mohammad; Lenz, Ann-Kathrin Nature, Vol. 587, Issue 7835 https://doi.org/10.1038/s41586-020-2854-z	journal	October 2020
Electrophilic activity-based RNA probes reveal a self-alkylating RNA for RNA labeling McDonald, Richard I.; Guilinger, John P.; Mukherji, Shankar Nature Chemical Biology, Vol. 10, Issue 12 https://doi.org/10.1038/nchembio.1655	journal	October 2014
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
The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design Gaines, Colin S.; Piccirilli, Joseph A.; York, Darrin M. RNA, Vol. 26, Issue 2 https://doi.org/10.1261/rna.071894.119	journal	November 2019
A G-quadruplex–containing RNA activates fluorescence in a GFP-like fluorophore Huang, Hao; Suslov, Nikolai B.; Li, Nan-Sheng Nature Chemical Biology, Vol. 10, Issue 8 https://doi.org/10.1038/nchembio.1561	journal	June 2014
Affinity maturation of a portable Fab–RNA module for chaperone-assisted RNA crystallography Koirala, Deepak; Shelke, Sandip A.; Dupont, Marcel Nucleic Acids Research, Vol. 46, Issue 5 https://doi.org/10.1093/nar/gkx1292	journal	January 2018
Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif Shelke, Sandip A.; Shao, Yaming; Laski, Artur Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-06942-3	journal	October 2018
A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination Koldobskaya, Yelena; Duguid, Erica M.; Shechner, David M. Nature Structural & Molecular Biology, Vol. 18, Issue 1 https://doi.org/10.1038/nsmb.1945	journal	December 2010
Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein U1A as a crystallization module 1 1Edited by D. C. Rees Ferré-D’Amaré, Adrian R.; Doudna, Jennifer A. Journal of Molecular Biology, Vol. 295, Issue 3 https://doi.org/10.1006/jmbi.1999.3398	journal	January 2000
A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites Koirala, Deepak; Shao, Yaming; Koldobskaya, Yelena Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-11585-z	journal	August 2019
The hydrolysis of epoxides catalyzed by inorganic ammonium salts in water: kinetic evidence for hydrogen bond catalysis Nozière, B.; Fache, F.; Maxut, A. Physical Chemistry Chemical Physics, Vol. 20, Issue 3 https://doi.org/10.1039/C7CP06790A	journal	January 2018
The HDOCK server for integrated protein–protein docking Yan, Yumeng; Tao, Huanyu; He, Jiahua Nature Protocols https://doi.org/10.1038/s41596-020-0312-x	journal	April 2020
Imidazole Rescue of a Cytosine Mutation in a Self-Cleaving Ribozyme Perrotta, Anne T.; Shih, I-hung; Been, Michael D. Science, Vol. 286, Issue 5437 https://doi.org/10.1126/science.286.5437.123	journal	October 1999
A computational study of acid catalyzed aerosol reactions of atmospherically relevant epoxides Piletic, Ivan R.; Edney, Edward O.; Bartolotti, Libero J. Physical Chemistry Chemical Physics, Vol. 15, Issue 41 https://doi.org/10.1039/c3cp52851k	journal	January 2013
Catalytic roles for proton transfer and protonation in ribozymes Bevilacqua, Philip C.; Brown, Trevor S.; Nakano, Shu-ichi Biopolymers, Vol. 73, Issue 1 https://doi.org/10.1002/bip.10519	journal	January 2003
General acid catalysis by the hepatitis delta virus ribozyme Das, Subha R.; Piccirilli, Joseph A. Nature Chemical Biology, Vol. 1, Issue 1 https://doi.org/10.1038/nchembio703	journal	May 2005
Ribozymes and Riboswitches: Modulation of RNA Function by Small Molecules Zhang, Jinwei; Lau, Matthew W.; Ferré-D’Amaré, Adrian R. Biochemistry, Vol. 49, Issue 43 https://doi.org/10.1021/bi1012645	journal	November 2010
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
The glmS Ribozyme Cofactor is a General Acid–Base Catalyst Viladoms, Júlia; Fedor, Martha J. Journal of the American Chemical Society, Vol. 134, Issue 46 https://doi.org/10.1021/ja307021f	journal	November 2012
Ribozymes and the mechanisms that underlie RNA catalysis Wilson, Timothy J.; Liu, Yijin; Lilley, David M. J. Frontiers of Chemical Science and Engineering, Vol. 10, Issue 2 https://doi.org/10.1007/s11705-016-1558-2	journal	February 2016
Synthetic antibodies for specific recognition and crystallization of structured RNA Ye, J. -D.; Tereshko, V.; Frederiksen, J. K. Proceedings of the National Academy of Sciences, Vol. 105, Issue 1 https://doi.org/10.1073/pnas.0709082105	journal	December 2007
Specific Recognition of a Single-Stranded RNA Sequence by a Synthetic Antibody Fragment Shao, Yaming; Huang, Hao; Qin, Daoming Journal of Molecular Biology, Vol. 428, Issue 20 https://doi.org/10.1016/j.jmb.2016.08.029	journal	October 2016
A Simple and Efficient Method to Transcribe RNAs with Reduced 3′ Heterogeneity Kao, Cheng; Rüdisser, Simon; Zheng, Minxue Methods, Vol. 23, Issue 3 https://doi.org/10.1006/meth.2000.1131	journal	March 2001
Expression and Purification of Active Recombinant T7 RNA Polymerase from E. coli Rio, D. C. Cold Spring Harbor Protocols, Vol. 2013, Issue 11 https://doi.org/10.1101/pdb.prot078527	journal	November 2013
In Vitro Selection of RNA Aptamers to a Protein Target by Filter Immobilization Hall, Bradley; Arshad, Seyed; Seo, Kyunghyun Current Protocols in Nucleic Acid Chemistry https://doi.org/10.1002/0471142700.nc0903s40	book	March 2010
WebLogo: A Sequence Logo Generator Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc Genome Research, Vol. 14, Issue 6, p. 1188-1190 https://doi.org/10.1101/gr.849004	journal	May 2004
MEME SUITE: tools for motif discovery and searching Bailey, T. L.; Boden, M.; Buske, F. A. Nucleic Acids Research, Vol. 37, Issue Web Server https://doi.org/10.1093/nar/gkp335	journal	May 2009
A new bioinformatics analysis tools framework at EMBL-EBI Goujon, M.; McWilliam, H.; Li, W. Nucleic Acids Research, Vol. 38, Issue Web Server https://doi.org/10.1093/nar/gkq313	journal	May 2010
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010

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