Improving the kinetic parameters of nicotine oxidizing enzymes by homologous structure comparison an

Deay III, Dwight O.; Seibold, Steve; Battaile, Kevin P.; Lovell, Scott; Richter, Mark L.; Petillo, Peter A.

doi:10.1016/j.abb.2022.109122

Improving the kinetic parameters of nicotine oxidizing enzymes by homologous structure comparison an

Journal Article · 28 February 2022 · Arch. Biochem. Biophys.

DOI:https://doi.org/10.1016/j.abb.2022.109122· OSTI ID:1845483

Deay III, Dwight O.; Seibold, Steve; Battaile, Kevin P.; Lovell, Scott; Richter, Mark L.; Petillo, Peter A.

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: DOE - Office Of Science; DOE - BASIC ENERGY SCIENCES

OSTI ID:: 1845483

Journal Information:: Arch. Biochem. Biophys., Journal Name: Arch. Biochem. Biophys. Vol. 718

Country of Publication:: United States

Language:: ENGLISH

References (48)

Crystallographic snapshots of the complete reaction cycle of nicotine degradation by an amine oxidase of the monoamine oxidase (MAO) family Kachalova, G.; Decker, K.; Holt, A. Proceedings of the National Academy of Sciences, Vol. 108, Issue 12 https://doi.org/10.1073/pnas.1016684108	journal	March 2011
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
Integration, scaling, space-group assignment and post-refinement Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 133-144 https://doi.org/10.1107/S0907444909047374	journal	January 2010
Mechanism of the Flavoprotein l -Hydroxynicotine Oxidase: Kinetic Mechanism, Substrate Specificity, Reaction Product, and Roles of Active-Site Residues Fitzpatrick, Paul F.; Chadegani, Fatemeh; Zhang, Shengnan Biochemistry, Vol. 55, Issue 4 https://doi.org/10.1021/acs.biochem.5b01325	journal	January 2016
Data processing and analysis with the autoPROC toolbox Vonrhein, Clemens; Flensburg, Claus; Keller, Peter Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911007773	journal	March 2011
To be or not to be an oxidase: challenging the oxygen reactivity of flavoenzymes Mattevi, Andrea Trends in Biochemical Sciences, Vol. 31, Issue 5 https://doi.org/10.1016/j.tibs.2006.03.003	journal	May 2006
Scaling and assessment of data quality Evans, Philip Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 1, p. 72-82 https://doi.org/10.1107/S0907444905036693	journal	December 2005
Biodegradation of tobacco waste by composting: Genetic identification of nicotine-degrading bacteria and kinetic analysis of transformations in leachate Briški, Felicita; Kopčić, Nina; Ćosić, Ivana Chemical Papers, Vol. 66, Issue 12 https://doi.org/10.2478/s11696-012-0234-3	journal	January 2012
An enzymatic approach reverses nicotine dependence, decreases compulsive-like intake, and prevents relapse Kallupi, Marsida; Xue, Song; Zhou, Bin Science Advances, Vol. 4, Issue 10 https://doi.org/10.1126/sciadv.aat4751	journal	October 2018
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Computational insights for the hydride transfer and distinctive roles of key residues in cholesterol oxidase Yu, Li-Juan; Golden, Emily; Chen, Nanhao Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-17503-x	journal	December 2017
A Stable Nonfluorescent Derivative of Resorufin for the Fluorometric Determination of Trace Hydrogen Peroxide: Applications in Detecting the Activity of Phagocyte NADPH Oxidase and Other Oxidases Zhou, Mingjie; Diwu, Zhenjun; Panchuk-Voloshina, Nataliya Analytical Biochemistry, Vol. 253, Issue 2 https://doi.org/10.1006/abio.1997.2391	journal	November 1997
Optimization of a nicotine degrading enzyme for potential use in treatment of nicotine addiction Thisted, Thomas; Biesova, Zuzana; Walmacq, Celine BMC Biotechnology, Vol. 19, Issue 1 https://doi.org/10.1186/s12896-019-0551-5	journal	August 2019
An introduction to data reduction: space-group determination, scaling and intensity statistics Evans, Philip R. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S090744491003982X	journal	March 2011
Global indicators of X-ray data quality Weiss, Manfred S. Journal of Applied Crystallography, Vol. 34, Issue 2 https://doi.org/10.1107/S0021889800018227	journal	April 2001
Novel Nicotine Oxidoreductase-Encoding Gene Involved in Nicotine Degradation by Pseudomonas putida Strain S16 Tang, Hongzhi; Wang, Lijuan; Meng, Xiangzhou Applied and Environmental Microbiology, Vol. 75, Issue 3 https://doi.org/10.1128/AEM.02300-08	journal	February 2009
Linking Crystallographic Model and Data Quality Karplus, P. A.; Diederichs, K. Science, Vol. 336, Issue 6084 https://doi.org/10.1126/science.1218231	journal	May 2012
The nicotine-degrading enzyme NicA2 reduces nicotine levels in blood, nicotine distribution to brain, and nicotine discrimination and reinforcement in rats Pentel, Paul R.; Raleigh, Michael D.; LeSage, Mark G. BMC Biotechnology, Vol. 18, Issue 1 https://doi.org/10.1186/s12896-018-0457-7	journal	July 2018
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility Morris, Garrett M.; Huey, Ruth; Lindstrom, William Journal of Computational Chemistry, Vol. 30, Issue 16 https://doi.org/10.1002/jcc.21256	journal	December 2009
On the Oxygen Reactivity of Flavoprotein Oxidases Piubelli, Luciano; Pedotti, Mattia; Molla, Gianluca Journal of Biological Chemistry, Vol. 283, Issue 36 https://doi.org/10.1074/jbc.M802321200	journal	September 2008
Solvent content of protein crystals Matthews, B. W. Journal of Molecular Biology, Vol. 33, Issue 2 https://doi.org/10.1016/0022-2836(68)90205-2	journal	April 1968
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/S2059798319011471	journal	October 2019
Expression and Purification of Soluble His6-Tagged TEV Protease Tropea, Joseph E.; Cherry, Scott; Waugh, David S. Methods in Molecular Biology https://doi.org/10.1007/978-1-59745-196-3_19	book	January 2009
An active site mutation in 6-hydroxy-l-Nicotine oxidase from Arthrobacter nicotinovorans changes the substrate specificity in favor of (S)-nicotine Deay, Dwight O.; Colvert, Kim K.; Gao, Fei Archives of Biochemistry and Biophysics, Vol. 692 https://doi.org/10.1016/j.abb.2020.108520	journal	October 2020
A Novel ( S )-6-Hydroxynicotine Oxidase Gene from Shinella sp. Strain HZN7 Qiu, Jiguo; Wei, Yin; Ma, Yun Applied and Environmental Microbiology, Vol. 80, Issue 18 https://doi.org/10.1128/AEM.01312-14	journal	July 2014
Mechanism of Flavoprotein l -6-Hydroxynicotine Oxidase: pH and Solvent Isotope Effects and Identification of Key Active Site Residues Fitzpatrick, Paul F.; Chadegani, Fatemeh; Zhang, Shengnan Biochemistry, Vol. 56, Issue 6 https://doi.org/10.1021/acs.biochem.6b01160	journal	January 2017
Oxidation of amines by flavoproteins Fitzpatrick, Paul F. Archives of Biochemistry and Biophysics, Vol. 493, Issue 1 https://doi.org/10.1016/j.abb.2009.07.019	journal	January 2010
Flavogenomics - a genomic and structural view of flavin-dependent proteins: Flavin-dependent proteins Macheroux, Peter; Kappes, Barbara; Ealick, Steven E. FEBS Journal, Vol. 278, Issue 15 https://doi.org/10.1111/j.1742-4658.2011.08202.x	journal	July 2011
Resolving Some Old Problems in Protein Crystallography Evans, P. Science, Vol. 336, Issue 6084 https://doi.org/10.1126/science.1222162	journal	May 2012
The human flavoproteome Lienhart, Wolf-Dieter; Gudipati, Venugopal; Macheroux, Peter Archives of Biochemistry and Biophysics, Vol. 535, Issue 2 https://doi.org/10.1016/j.abb.2013.02.015	journal	July 2013
CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories Jurcik, Adam; Bednar, David; Byska, Jan Bioinformatics, Vol. 34, Issue 20 https://doi.org/10.1093/bioinformatics/bty386	journal	May 2018
Fast Kinetics Reveals Rate-Limiting Oxidation and the Role of the Aromatic Cage in the Mechanism of the Nicotine-Degrading Enzyme NicA2 Tararina, Margarita A.; Dam, Katie K.; Dhingra, Manaswni Biochemistry, Vol. 60, Issue 4 https://doi.org/10.1021/acs.biochem.0c00855	journal	January 2021
Distortion of flavin geometry is linked to ligand binding in cholesterol oxidase Lyubimov, Artem Y.; Heard, Kathryn; Tang, Hui Protein Science, Vol. 16, Issue 12 https://doi.org/10.1110/ps.073168207	journal	December 2007
Presenting your structures: the CCP 4 mg molecular-graphics software McNicholas, S.; Potterton, E.; Wilson, K. S. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911007281	journal	March 2011
Oxygen Isotope Effects on Electron Transfer to O ₂ Probed Using Chemically Modified Flavins Bound to Glucose Oxidase Roth, Justine P.; Wincek, Roseanne; Nodet, Gabrielle Journal of the American Chemical Society, Vol. 126, Issue 46 https://doi.org/10.1021/ja047050e	journal	November 2004
Nature of Oxygen Activation in Glucose Oxidase from Aspergillus niger : The Importance of Electrostatic Stabilization in Superoxide Formation Su, Qiaojuan; Klinman, Judith P. Biochemistry, Vol. 38, Issue 26 https://doi.org/10.1021/bi990044o	journal	June 1999
How good are my data and what is the resolution? Evans, Philip R.; Murshudov, Garib N. Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7 https://doi.org/10.1107/S0907444913000061	journal	June 2013
A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding Bradford, Marion M. Analytical Biochemistry, Vol. 72, Issue 1-2 https://doi.org/10.1016/0003-2697(76)90527-3	journal	May 1976
A new MR-SAD algorithm for the automatic building of protein models from low-resolution X-ray data and a poor starting model Skubák, Pavol; Araç, Demet; Bowler, Matthew W. IUCrJ, Vol. 5, Issue 2 https://doi.org/10.1107/S2052252517017961	journal	January 2018
Molecular Deceleration Regulates Toxicant Release to Prevent Cell Damage in Pseudomonas putida S16 (DSM 28022) Tang, Hongzhi; Zhang, Kunzhi; Hu, Haiyang mBio, Vol. 11, Issue 5 https://doi.org/10.1128/mBio.02012-20	journal	October 2020
Improved R-factors for diffraction data analysis in macromolecular crystallography Diederichs, Kay; Karplus, P. Andrew Nature Structural Biology, Vol. 4, Issue 4 https://doi.org/10.1038/nsb0497-269	journal	April 1997
Crystallography Coupled with Kinetic Analysis Provides Mechanistic Underpinnings of a Nicotine-Degrading Enzyme Tararina, Margarita A.; Xue, Song; Smith, Lauren C. Biochemistry, Vol. 57, Issue 26 https://doi.org/10.1021/acs.biochem.8b00384	journal	May 2018
Structural Analysis Provides Mechanistic Insight into Nicotine Oxidoreductase from Pseudomonas putida Tararina, Margarita A.; Janda, Kim D.; Allen, Karen N. Biochemistry, Vol. 55, Issue 48 https://doi.org/10.1021/acs.biochem.6b00963	journal	November 2016
Multiple pathways guide oxygen diffusion into flavoenzyme active sites Baron, R.; Riley, C.; Chenprakhon, P. Proceedings of the National Academy of Sciences, Vol. 106, Issue 26 https://doi.org/10.1073/pnas.0903809106	journal	June 2009
A cytochrome c is the natural electron acceptor for nicotine oxidoreductase Dulchavsky, Mark; Clark, Christopher T.; Bardwell, James C. A. Nature Chemical Biology, Vol. 17, Issue 3 https://doi.org/10.1038/s41589-020-00712-3	journal	January 2021
A New Strategy for Smoking Cessation: Characterization of a Bacterial Enzyme for the Degradation of Nicotine Xue, Song; Schlosburg, Joel E.; Janda, Kim D. Journal of the American Chemical Society, Vol. 137, Issue 32 https://doi.org/10.1021/jacs.5b06605	journal	August 2015
TM-align: a protein structure alignment algorithm based on the TM-score Zhang, Y. Nucleic Acids Research, Vol. 33, Issue 7 https://doi.org/10.1093/nar/gki524	journal	April 2005

Similar Records

Structural Characterization of Inhibitors with Selectivity against Members of a Homologous Enzyme Family

Journal Article · 2013 · Chem. Biol. Drug Des. · OSTI ID:1040641

Parameter estimation for models of ligninolytic and cellulolytic enzyme kinetics

Journal Article · 2011 · Soil Biology and Biochemistry · OSTI ID:1034679

UniKP: a unified framework for the prediction of enzyme kinetic parameters

Journal Article · 2023 · Nature Communications · OSTI ID:2470985

Improving the kinetic parameters of nicotine oxidizing enzymes by homologous structure comparison an

Citation Formats

References (48)

Similar Records

Related Subjects