Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase
Abstract
Abstract Replicative DNA polymerases are highly efficient enzymes that maintain stringent geometric control over shape and orientation of the template and incoming nucleoside triphosphate. In a surprising twist to this paradigm, a naturally occurring bacterial DNA polymerase I member isolated from Geobacillus stearothermophilus (Bst) exhibits an innate ability to reverse transcribe RNA and other synthetic congeners (XNAs) into DNA. This observation raises the interesting question of how a replicative DNA polymerase is able to recognize templates of diverse chemical composition. Here, we present crystal structures of natural Bst DNA polymerase that capture the post-translocated product of DNA synthesis on templates composed entirely of 2′-deoxy-2′-fluoro-β-d-arabino nucleic acid (FANA) and α-l-threofuranosyl nucleic acid (TNA). Analysis of the enzyme active site reveals the importance of structural plasticity as a possible mechanism for XNA-dependent DNA synthesis and provides insights into the construction of variants with improved activity.
- Authors:
-
[1];
[1];
[2]
- Departments of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
- Departments of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA, Department of Chemistry, University of California, Irvine, CA 92697-3958, USA, Department of Molecular Biology and Biochemistry, University of California, CA 92697-3958, USA
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1525514
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- Nucleic Acids Research
- Additional Journal Information:
- Journal Name: Nucleic Acids Research Journal Volume: 47 Journal Issue: 13; Journal ID: ISSN 0305-1048
- Publisher:
- Oxford University Press
- Country of Publication:
- United Kingdom
- Language:
- English
Citation Formats
Jackson, Lynnette N., Chim, Nicholas, Shi, Changhua, and Chaput, John C. Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase. United Kingdom: N. p., 2019.
Web. doi:10.1093/nar/gkz513.
Jackson, Lynnette N., Chim, Nicholas, Shi, Changhua, & Chaput, John C. Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase. United Kingdom. https://doi.org/10.1093/nar/gkz513
Jackson, Lynnette N., Chim, Nicholas, Shi, Changhua, and Chaput, John C. Thu .
"Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase". United Kingdom. https://doi.org/10.1093/nar/gkz513.
@article{osti_1525514,
title = {Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase},
author = {Jackson, Lynnette N. and Chim, Nicholas and Shi, Changhua and Chaput, John C.},
abstractNote = {Abstract Replicative DNA polymerases are highly efficient enzymes that maintain stringent geometric control over shape and orientation of the template and incoming nucleoside triphosphate. In a surprising twist to this paradigm, a naturally occurring bacterial DNA polymerase I member isolated from Geobacillus stearothermophilus (Bst) exhibits an innate ability to reverse transcribe RNA and other synthetic congeners (XNAs) into DNA. This observation raises the interesting question of how a replicative DNA polymerase is able to recognize templates of diverse chemical composition. Here, we present crystal structures of natural Bst DNA polymerase that capture the post-translocated product of DNA synthesis on templates composed entirely of 2′-deoxy-2′-fluoro-β-d-arabino nucleic acid (FANA) and α-l-threofuranosyl nucleic acid (TNA). Analysis of the enzyme active site reveals the importance of structural plasticity as a possible mechanism for XNA-dependent DNA synthesis and provides insights into the construction of variants with improved activity.},
doi = {10.1093/nar/gkz513},
journal = {Nucleic Acids Research},
number = 13,
volume = 47,
place = {United Kingdom},
year = {2019},
month = {6}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1093/nar/gkz513
https://doi.org/10.1093/nar/gkz513
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 4 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Structural Insights into the Processing of Nucleobase-Modified Nucleotides by DNA Polymerases
journal, February 2016
- Hottin, Audrey; Marx, Andreas
- Accounts of Chemical Research, Vol. 49, Issue 3
TM-align: a protein structure alignment algorithm based on the TM-score
journal, April 2005
- Zhang, Y.
- Nucleic Acids Research, Vol. 33, Issue 7
Synthesis and Evolution of a Threose Nucleic Acid Aptamer Bearing 7-Deaza-7-Substituted Guanosine Residues
journal, April 2018
- Mei, Hui; Liao, Jen-Yu; Jimenez, Randi M.
- Journal of the American Chemical Society, Vol. 140, Issue 17
Chemical discrimination between dC and 5Me dC via their hydroxylamine adducts
journal, September 2010
- Münzel, Martin; Lercher, Lukas; Müller, Markus
- Nucleic Acids Research, Vol. 38, Issue 21
Synthesis and polymerase activity of a fluorescent cytidine TNA triphosphate analogue
journal, May 2017
- Mei, Hui; Shi, Changhua; Jimenez, Randi M.
- Nucleic Acids Research, Vol. 45, Issue 10
Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures
journal, May 2009
- Zheng, G.; Lu, X. -J.; Olson, W. K.
- Nucleic Acids Research, Vol. 37, Issue Web Server
Structures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates
journal, April 2012
- Bergen, Konrad; Steck, Anna-Lena; Strütt, Stefan
- Journal of the American Chemical Society, Vol. 134, Issue 29
Synthetic Genetic Polymers Capable of Heredity and Evolution
journal, April 2012
- Pinheiro, V. B.; Taylor, A. I.; Cozens, C.
- Science, Vol. 336, Issue 6079
Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP
journal, June 1994
- Pelletier, H.; Sawaya, M.; Kumar, A.
- Science, Vol. 264, Issue 5167
DNA Polymerase-Mediated DNA Synthesis on a TNA Template
journal, January 2003
- Chaput, John C.; Ichida, Justin K.; Szostak, Jack W.
- Journal of the American Chemical Society, Vol. 125, Issue 4
Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution
journal, January 1998
- Doublié, Sylvie; Tabor, Stanley; Long, Alexander M.
- Nature, Vol. 391, Issue 6664
Characterization of the aes gene of Escherichia coli encoding an enzyme with esterase activity.
journal, December 1997
- Peist, R.; Koch, A.; Bolek, P.
- Journal of Bacteriology, Vol. 179, Issue 24
Reverse Transcription of Threose Nucleic Acid by a Naturally Occurring DNA Polymerase
journal, August 2016
- Dunn, Matthew R.; Chaput, John C.
- ChemBioChem, Vol. 17, Issue 19
Replicative DNA Polymerases
journal, June 2013
- Johansson, E.; Dixon, N.
- Cold Spring Harbor Perspectives in Biology, Vol. 5, Issue 6
Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations
journal, March 2003
- Johnson, S. J.; Taylor, J. S.; Beese, L. S.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 7
Active Site Tightness and Substrate Fit in DNA Replication
journal, June 2002
- Kool, Eric T.
- Annual Review of Biochemistry, Vol. 71, Issue 1
Towards automated crystallographic structure refinement with phenix.refine
journal, March 2012
- Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel
- Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4
Structure of a Covalently Trapped Catalytic Complex of HIV-1 Reverse Transcriptase: Implications for Drug Resistance
journal, November 1998
- Huang, H.
- Science, Vol. 282, Issue 5394
Reverse transcription and direct amplification of cellular RNA transcripts by Taq polymerase
journal, April 1990
- Tse, William T.; Forget, Bernard G.
- Gene, Vol. 88, Issue 2
Investigation of the DNA-dependent cyclohexenyl nucleic acid polymerization and the cyclohexenyl nucleic acid-dependent DNA polymerization
journal, July 2005
- Kempeneers, V.
- Nucleic Acids Research, Vol. 33, Issue 12
Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation
journal, December 1998
- Li, Y.
- The EMBO Journal, Vol. 17, Issue 24
The solution structure of double helical arabino nucleic acids (ANA and 2′F-ANA): effect of arabinoses in duplex-hairpin interconversion
journal, July 2012
- Martín-Pintado, Nerea; Yahyaee-Anzahaee, Maryam; Campos-Olivas, Ramón
- Nucleic Acids Research, Vol. 40, Issue 18
Crystal structure of a thermostable Bacillus DNA polymerase l large fragment at 2.1 Å resolution
journal, January 1997
- Kiefer, James R.; Mao, Chen; Hansen, Connie J.
- Structure, Vol. 5, Issue 1
XDS
journal, January 2010
- Kabsch, Wolfgang
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
A unified polymerase mechanism for nonhomologous DNA and RNA polymerases
journal, December 1994
- Steitz, T.; Smerdon, S.; Jager, J.
- Science, Vol. 266, Issue 5193
UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004
- Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
- Journal of Computational Chemistry, Vol. 25, Issue 13
Structural Insights into Conformation Differences between DNA/TNA and RNA/TNA Chimeric Duplexes
journal, July 2016
- Anosova, Irina; Kowal, Ewa A.; Sisco, Nicholas J.
- ChemBioChem, Vol. 17, Issue 18
The structural diversity of artificial genetic polymers
journal, December 2015
- Anosova, Irina; Kowal, Ewa A.; Dunn, Matthew R.
- Nucleic Acids Research, Vol. 44, Issue 3
Why Does TNA Cross-Pair More Strongly with RNA Than with DNA? An Answer From X-ray Analysis
journal, December 2003
- Pallan, Pradeep S.; Wilds, Christopher J.; Wawrzak, Zdzislaw
- Angewandte Chemie International Edition, Vol. 42, Issue 47
A mutant of DNA polymerase I (Klenow fragment) with reduced fidelity
journal, January 1991
- Carroll, Steven S.; Cowart, Marlon; Benkovic, Stephen J.
- Biochemistry, Vol. 30, Issue 3
Snapshots of a modified nucleotide moving through the confines of a DNA polymerase
journal, September 2018
- Kropp, Heike Maria; Dürr, Simon Leonard; Peter, Christine
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 40
The Structure of a TNA−TNA Complex in Solution: NMR Study of the Octamer Duplex Derived from α-( l )-Threofuranosyl-(3′-2′)-CGAATTCG
journal, November 2008
- Ebert, Marc-Olivier; Mang, Christian; Krishnamurthy, Ramanarayanan
- Journal of the American Chemical Society, Vol. 130, Issue 45
Efficient Reverse Transcription Using Locked Nucleic Acid Nucleotides towards the Evolution of Nuclease Resistant RNA Aptamers
journal, April 2012
- Crouzier, Lucile; Dubois, Camille; Edwards, Stacey L.
- PLoS ONE, Vol. 7, Issue 4
iMOSFLM : a new graphical interface for diffraction-image processing with MOSFLM
journal, March 2011
- Battye, T. Geoff G.; Kontogiannis, Luke; Johnson, Owen
- Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
Capture of a third Mg2+ is essential for catalyzing DNA synthesis
journal, June 2016
- Gao, Y.; Yang, W.
- Science, Vol. 352, Issue 6291
Structures of Mismatch Replication Errors Observed in a DNA Polymerase
journal, March 2004
- Johnson, Sean J.; Beese, Lorena S.
- Cell, Vol. 116, Issue 6
Analysis of aptamer discovery and technology
journal, October 2017
- Dunn, Matthew R.; Jimenez, Randi M.; Chaput, John C.
- Nature Reviews Chemistry, Vol. 1, Issue 10
Structures of KOD and 9°N DNA Polymerases Complexed with Primer Template Duplex
journal, June 2013
- Bergen, Konrad; Betz, Karin; Welte, Wolfram
- ChemBioChem, Vol. 14, Issue 9
Evolution of a General RNA-Cleaving FANA Enzyme
journal, November 2018
- Wang, Yajun; Ngor, Arlene K.; Nikoomanzar, Ali
- Nature Communications, Vol. 9, Issue 1
“Skinny” and “Fat” DNA: Two New Double Helices
journal, August 2018
- Hoshika, Shuichi; Singh, Isha; Switzer, Christopher
- Journal of the American Chemical Society, Vol. 140, Issue 37
Replication of hexitol oligonucleotides as a prelude to the propagation of a third type of nucleic acid in vivo
journal, December 2003
- Pochet, Sylvie; Kaminski, P. Alexandre; Van Aerschot, Arthur
- Comptes Rendus Biologies, Vol. 326, Issue 12
MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009
- Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
Base Miscoding and Strand Misalignment Errors by Mutator Klenow Polymerases with Amino Acid Substitutions at Tyrosine 766 in the O Helix of the Fingers Subdomain
journal, March 1997
- Bell, Juliette B.; Eckert, Kristin A.; Joyce, Catherine M.
- Journal of Biological Chemistry, Vol. 272, Issue 11
Features and development of Coot
journal, March 2010
- Emsley, P.; Lohkamp, B.; Scott, W. G.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
Crystal Structure of a B-Form DNA Duplex Containing ( l )-α-Threofuranosyl (3‘→2‘) Nucleosides: A Four-Carbon Sugar Is Easily Accommodated into the Backbone of DNA
journal, November 2002
- Wilds, Christopher J.; Wawrzak, Zdzislaw; Krishnamurthy, Ramanarayanan
- Journal of the American Chemical Society, Vol. 124, Issue 46
DNA polymerases and biotechnological applications
journal, December 2017
- Aschenbrenner, Joos; Marx, Andreas
- Current Opinion in Biotechnology, Vol. 48
Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal
journal, January 1998
- Kiefer, James R.; Mao, Chen; Braman, Jeffrey C.
- Nature, Vol. 391, Issue 6664
Engineering and application of polymerases for synthetic genetics
journal, December 2017
- Houlihan, Gillian; Arangundy-Franklin, Sebastian; Holliger, Philipp
- Current Opinion in Biotechnology, Vol. 48
2‘,5‘-Linked DNA Is a Template for Polymerase-Directed DNA Synthesis
journal, January 2004
- Sinha, Surajit; Kim, Paul H.; Switzer, Christopher
- Journal of the American Chemical Society, Vol. 126, Issue 1
Innate Reverse Transcriptase Activity of DNA Polymerase for Isothermal RNA Direct Detection
journal, October 2015
- Shi, Chao; Shen, Xiaotong; Niu, Shuyan
- Journal of the American Chemical Society, Vol. 137, Issue 43
A Scalable Synthesis of α- l -Threose Nucleic Acid Monomers
journal, February 2016
- Sau, Sujay P.; Fahmi, Nour Eddine; Liao, Jen-Yu.
- The Journal of Organic Chemistry, Vol. 81, Issue 6
Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway
journal, October 2018
- Chim, Nicholas; Jackson, Lynnette N.; Trinh, Anh M.
- eLife, Vol. 7
Thermostable Bst DNA polymerase I lacks a 3′ → 5′ proofreading exonuclease activity
journal, March 1996
- Aliotta, Jason M.; Pelletier, John J.; Ware, Jennifer L.
- Genetic Analysis: Biomolecular Engineering, Vol. 12, Issue 5-6
Unlocking the Sugar “Steric Gate” of DNA Polymerases
journal, February 2011
- Brown, Jessica A.; Suo, Zucai
- Biochemistry, Vol. 50, Issue 7
Enzymatic synthesis of DNA on glycerol nucleic acid templates without stable duplex formation between product and template
journal, September 2007
- Tsai, C. -H.; Chen, J.; Szostak, J. W.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 37
Chemical Etiology of Nucleic Acid Structure: The alpha -Threofuranosyl-(3'rightarrow 2') Oligonucleotide System
journal, November 2000
- Schoning, K. -U.
- Science, Vol. 290, Issue 5495
A general strategy for expanding polymerase function by droplet microfluidics
journal, April 2016
- Larsen, Andrew C.; Dunn, Matthew R.; Hatch, Andrew
- Nature Communications, Vol. 7, Issue 1
Nucleoside Triphosphates — Building Blocks for the Modification of Nucleic Acids
journal, November 2012
- Hollenstein, Marcel
- Molecules, Vol. 17, Issue 11
The Emerging World of Synthetic Genetics
journal, November 2012
- Chaput, John C.; Yu, Hanyang; Zhang, Su
- Chemistry & Biology, Vol. 19, Issue 11
Phaser crystallographic software
journal, July 2007
- McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Journal of Applied Crystallography, Vol. 40, Issue 4
Evaluating TNA stability under simulated physiological conditions
journal, May 2016
- Culbertson, Michelle C.; Temburnikar, Kartik W.; Sau, Sujay P.
- Bioorganic & Medicinal Chemistry Letters, Vol. 26, Issue 10