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Clinger JA, Zhang Y, Liu Y, Miller MD, Hall RE, Van Lanen SG, Phillips Jr. GN, Thorson JS, Elshahawi SI. Structure and Function of a Dual Reductase-Dehydratase Enzyme System Involved in p-Terphenyl Biosynthesis. ACS Chem Biol 2021; 16:2816-2824. [PMID: 34763417 DOI: 10.1021/acschembio.1c00701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report the identification of the ter gene cluster responsible for the formation of the p-terphenyl derivatives terfestatins B and C and echoside B from the Appalachian Streptomyces strain RM-5-8. We characterize the function of TerB/C, catalysts that work together as a dual enzyme system in the biosynthesis of natural terphenyls. TerB acts as a reductase and TerC as a dehydratase to enable the conversion of polyporic acid to a terphenyl triol intermediate. X-ray crystallography of the apo and substrate-bound forms for both enzymes provides additional mechanistic insights. Validation of the TerC structural model via mutagenesis highlights a critical role of arginine 143 and aspartate 173 in catalysis. Cumulatively, this work highlights a set of enzymes acting in harmony to control and direct reactive intermediates and advances fundamental understanding of the previously unresolved early steps in terphenyl biosynthesis.
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Affiliation(s)
- Jonathan A. Clinger
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Yinan Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Yang Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Mitchell D. Miller
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Ronnie E. Hall
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Steven G. Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - George N. Phillips Jr.
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Jon S. Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Sherif I. Elshahawi
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
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2
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Engstrom T, Clinger JA, Spoth KA, Clarke OB, Closs DS, Jayne R, Apker BA, Thorne RE. High-resolution single-particle cryo-EM of samples vitrified in boiling nitro-gen. IUCrJ 2021; 8:867-877. [PMID: 34804541 PMCID: PMC8562666 DOI: 10.1107/s2052252521008095] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/05/2021] [Indexed: 05/24/2023]
Abstract
Based on work by Dubochet and others in the 1980s and 1990s, samples for single-particle cryo-electron microscopy (cryo-EM) have been vitrified using ethane, propane or ethane/propane mixtures. These liquid cryogens have a large difference between their melting and boiling temperatures and so can absorb substantial heat without formation of an insulating vapor layer adjacent to a cooling sample. However, ethane and propane are flammable, they must be liquified in liquid nitro-gen immediately before cryo-EM sample preparation, and cryocooled samples must be transferred to liquid nitro-gen for storage, complicating workflows and increasing the chance of sample damage during handling. Experiments over the last 15 years have shown that cooling rates required to vitrify pure water are only ∼250 000 K s-1, at the low end of earlier estimates, and that the dominant factor that has limited cooling rates of small samples in liquid nitro-gen is sample precooling in cold gas present above the liquid cryogen surface, not the Leidenfrost effect. Using an automated cryocooling instrument developed for cryocrystallography that combines high plunge speeds with efficient removal of cold gas, we show that single-particle cryo-EM samples on commercial grids can be routinely vitrified using only boiling nitro-gen and obtain apoferritin datasets and refined structures with 2.65 Å resolution. The use of liquid nitro-gen as the primary coolant may allow manual and automated workflows to be simplified and may reduce sample stresses that contribute to beam-induced motion.
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Affiliation(s)
| | | | - Katherine A. Spoth
- Cornell Center for Materials Research, Cornell University, Ithaca, NY 14853, USA
| | - Oliver B. Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
- Department of Anesthesiology, Columbia University, New York, NY 10032, USA
| | | | - Richard Jayne
- MiTeGen, LLC, PO Box 3867, Ithaca, NY 14850-3867, USA
| | | | - Robert E. Thorne
- MiTeGen, LLC, PO Box 3867, Ithaca, NY 14850-3867, USA
- Physics Department, Cornell University, Ithaca, NY 14853, USA
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5
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Clinger JA, Wang X, Cai W, Zhu Y, Miller MD, Zhan CG, Van Lanen SG, Thorson JS, Phillips GN. The crystal structure of AbsH3: A putative flavin adenine dinucleotide-dependent reductase in the abyssomicin biosynthesis pathway. Proteins 2020; 89:132-137. [PMID: 32852843 DOI: 10.1002/prot.25994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/01/2020] [Accepted: 07/26/2020] [Indexed: 11/06/2022]
Abstract
Natural products and natural product-derived compounds have been widely used for pharmaceuticals for many years, and the search for new natural products that may have interesting activity is ongoing. Abyssomicins are natural product molecules that have antibiotic activity via inhibition of the folate synthesis pathway in microbiota. These compounds also appear to undergo a required [4 + 2] cycloaddition in their biosynthetic pathway. Here we report the structure of an flavin adenine dinucleotide-dependent reductase, AbsH3, from the biosynthetic gene cluster of novel abyssomicins found in Streptomyces sp. LC-6-2.
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Affiliation(s)
| | - Xiachang Wang
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - Wenlong Cai
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - Yanyan Zhu
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | | | - Chang-Guo Zhan
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - Steven G Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - Jon S Thorson
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas, USA.,Department of Chemistry, Rice University, Houston, Texas, USA
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6
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Huber TD, Clinger JA, Liu Y, Xu W, Miller MD, Phillips GN, Thorson JS. Methionine Adenosyltransferase Engineering to Enable Bioorthogonal Platforms for AdoMet-Utilizing Enzymes. ACS Chem Biol 2020; 15:695-705. [PMID: 32091873 DOI: 10.1021/acschembio.9b00943] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The structural conservation among methyltransferases (MTs) and MT functional redundancy is a major challenge to the cellular study of individual MTs. As a first step toward the development of an alternative biorthogonal platform for MTs and other AdoMet-utilizing enzymes, we describe the evaluation of 38 human methionine adenosyltransferase II-α (hMAT2A) mutants in combination with 14 non-native methionine analogues to identify suitable bioorthogonal mutant/analogue pairings. Enabled by the development and implementation of a hMAT2A high-throughput (HT) assay, this study revealed hMAT2A K289L to afford a 160-fold inversion of the hMAT2A selectivity index for a non-native methionine analogue over the native substrate l-Met. Structure elucidation of K289L revealed the mutant to be folded normally with minor observed repacking within the modified substrate pocket. This study highlights the first example of exchanging l-Met terminal carboxylate/amine recognition elements within the hMAT2A active-site to enable non-native bioorthgonal substrate utilization. Additionally, several hMAT2A mutants and l-Met substrate analogues produced AdoMet analogue products with increased stability. As many AdoMet-producing (e.g., hMAT2A) and AdoMet-utlizing (e.g., MTs) enzymes adopt similar active-site strategies for substrate recognition, the proof of concept first generation hMAT2A engineering highlighted herein is expected to translate to a range of AdoMet-utilizing target enzymes.
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Affiliation(s)
- Tyler D. Huber
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
- Center for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | | | - Yang Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
- Center for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | | | | | | | - Jon S. Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
- Center for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
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9
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Fuller FD, Gul S, Chatterjee R, Burgie ES, Young ID, Lebrette H, Srinivas V, Brewster AS, Michels-Clark T, Clinger JA, Andi B, Ibrahim M, Pastor E, de Lichtenberg C, Hussein R, Pollock CJ, Zhang M, Stan CA, Kroll T, Fransson T, Weninger C, Kubin M, Aller P, Lassalle L, Bräuer P, Miller MD, Amin M, Koroidov S, Roessler CG, Allaire M, Sierra RG, Docker PT, Glownia JM, Nelson S, Koglin JE, Zhu D, Chollet M, Song S, Lemke H, Liang M, Sokaras D, Alonso-Mori R, Zouni A, Messinger J, Bergmann U, Boal AK, Bollinger JM, Krebs C, Högbom M, Phillips GN, Vierstra RD, Sauter NK, Orville AM, Kern J, Yachandra VK, Yano J. Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Nat Methods 2017; 14:443-449. [PMID: 28250468 DOI: 10.1038/nmeth.4195] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/18/2017] [Indexed: 12/22/2022]
Abstract
X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.
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Affiliation(s)
- Franklin D Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - E Sethe Burgie
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Iris D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Babak Andi
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ernest Pastor
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Rana Hussein
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christopher J Pollock
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Miao Zhang
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Claudiu A Stan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Thomas Kroll
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Clemens Weninger
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA.,LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Markus Kubin
- Institute for Methods and Instrumentation on Synchrotron Radiation Research, Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany
| | - Pierre Aller
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, UK
| | - Louise Lassalle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philipp Bräuer
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, UK.,Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Muhamed Amin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sergey Koroidov
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden.,Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Christian G Roessler
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, USA
| | - Marc Allaire
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Raymond G Sierra
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Peter T Docker
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, UK
| | - James M Glownia
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Silke Nelson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Jason E Koglin
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Diling Zhu
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Matthieu Chollet
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Sanghoon Song
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Henrik Lemke
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Mengning Liang
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | | | | | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden.,Department of Chemistry-Ångström, Molecular Biomimetics, Uppsala University, Uppsala, Sweden
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Amie K Boal
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - J Martin Bollinger
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Carsten Krebs
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Department of Chemistry, Stanford University, Stanford, California, USA
| | - George N Phillips
- Department of BioSciences, Rice University, Houston, Texas, USA.,Department of Chemistry, Rice University, Houston, Texas, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Allen M Orville
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, UK
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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