1
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Agbaglo DA, Summers TJ, Cheng Q, DeYonker NJ. The influence of model building schemes and molecular dynamics sampling on QM-cluster models: the chorismate mutase case study. Phys Chem Chem Phys 2024; 26:12467-12482. [PMID: 38618904 PMCID: PMC11090134 DOI: 10.1039/d3cp06100k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Most QM-cluster models of enzymes are constructed based on X-ray crystal structures, which limits comparison to in vivo structure and mechanism. The active site of chorismate mutase from Bacillus subtilis and the enzymatic transformation of chorismate to prephenate is used as a case study to guide construction of QM-cluster models built first from the X-ray crystal structure, then from molecular dynamics (MD) simulation snapshots. The Residue Interaction Network ResidUe Selector (RINRUS) software toolkit, developed by our group to simplify and automate the construction of QM-cluster models, is expanded to handle MD to QM-cluster model workflows. Several options, some employing novel topological clustering from residue interaction network (RIN) information, are evaluated for generating conformational clustering from MD simulation. RINRUS then generates a statistical thermodynamic framework for QM-cluster modeling of the chorismate mutase mechanism via refining 250 MD frames with density functional theory (DFT). The 250 QM-cluster models sampled provide a mean ΔG‡ of 10.3 ± 2.6 kcal mol-1 compared to the experimental value of 15.4 kcal mol-1 at 25 °C. While the difference between theory and experiment is consequential, the level of theory used is modest and therefore "chemical" accuracy is unexpected. More important are the comparisons made between QM-cluster models designed from the X-ray crystal structure versus those from MD frames. The large variations in kinetic and thermodynamic properties arise from geometric changes in the ensemble of QM-cluster models, rather from the composition of the QM-cluster models or from the active site-solvent interface. The findings open the way for further quantitative and reproducible calibration in the field of computational enzymology using the model construction framework afforded with the RINRUS software toolkit.
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Affiliation(s)
- Donatus A Agbaglo
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA.
| | - Thomas J Summers
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA.
| | - Qianyi Cheng
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA.
| | - Nathan J DeYonker
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA.
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2
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McFarlane NR, Harvey JN. Exploration of biochemical reactivity with a QM/MM growing string method. Phys Chem Chem Phys 2024; 26:5999-6007. [PMID: 38293892 DOI: 10.1039/d3cp05772k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
In this work, we have implemented the single-ended growing string method using a hybrid internal/Cartesian coordinate scheme within our in-house QM/MM package, QoMMMa, representing the first implementation of the growing string method in the QM/MM framework. The goal of the implementation was to facilitate generation of QM/MM reaction pathways with minimal user input, and also to improve the quality of the pathways generated as compared to the widely used adiabatic mapping approach. We have validated the algorithm against a reaction which has been studied extensively in previous computational investigations - the Claisen rearrangement catalysed by chorismate mutase. The nature of the transition state and the height of the barrier was predicted well using our algorithm, where more than 88% of the pathways generated were deemed to be of production quality. Directly compared to using adiabatic mapping, we found that while our QM/MM single-ended growing string method is slightly less efficient, it readily produces reaction pathways with fewer discontinuites and thus minimises the need for involved remapping of unsatisfactory energy profiles.
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Affiliation(s)
- Neil R McFarlane
- Department of Chemistry, KU Leuven, B-3001 Leuven, Celestijnenlaan 200f, 2404, Belgium.
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, B-3001 Leuven, Celestijnenlaan 200f, 2404, Belgium.
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3
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Das S, Pattanayakanahalli Henjarappa K, Mahanta N. Enzymatic reconstitution of salicylate formation in promysalin biosynthesis. Bioorg Med Chem Lett 2023; 94:129440. [PMID: 37567320 DOI: 10.1016/j.bmcl.2023.129440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Promysalin is an amphipathic antibiotic isolated from Pseudomonas promysalinigenes (previously Pseudomonas putida RW10S1) which shows potent antibacterial activities against Gram-negative pathogens by inactivating succinate dehydrogenase. Based on the in-vivo studies, promysalin is hypothesized to be assembled from three building blocks: salicylic acid, proline, and myristic acid via a proposed but uncharacterized hybrid NRPS-PKS biosynthetic pathway. So far, no in-vitro biosynthetic studies have been reported for this promising antibiotic. Here, we report the first in-vitro reconstitution and biochemical characterization of two early enzymes on the pathway: PpgH, an isochorismate synthase (IS), and PpgG, an isochorismate pyruvate lyase (IPL) which are involved in the biosynthesis of salicylic acid, the polar fragment of promysalin. We also report a secondary chorismate mutase (CM) activity for PpgG. Based on our biochemical experiments, preliminary mechanistic proposals have been postulated for PpgH and PpgG. We believe this study will lay a strong foundation for elucidating the functions and mechanisms of other intriguing enzymes of the promysalin biosynthesis pathway, which may potentially unravel interesting enzyme chemistries and promote pathway engineering in the future.
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Affiliation(s)
- Simita Das
- Department of Chemistry, Indian Institute of Technology Dharwad, Karnataka 580011, India
| | | | - Nilkamal Mahanta
- Department of Chemistry, Indian Institute of Technology Dharwad, Karnataka 580011, India.
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4
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Thorbjørnsrud H, Bressan L, Khatanbaatar T, Carrer M, Würth-Roderer K, Cordara G, Kast P, Cascella M, Krengel U. What Drives Chorismate Mutase to Top Performance? Insights from a Combined In Silico and In Vitro Study. Biochemistry 2023; 62:782-796. [PMID: 36705397 PMCID: PMC9910054 DOI: 10.1021/acs.biochem.2c00635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Unlike typical chorismate mutases, the enzyme from Mycobacterium tuberculosis (MtCM) has only low activity on its own. Remarkably, its catalytic efficiency kcat/Km can be boosted more than 100-fold by complex formation with a partner enzyme. Recently, an autonomously fully active MtCM variant was generated using directed evolution, and its structure was solved by X-ray crystallography. However, key residues were involved in crystal contacts, challenging the functional interpretation of the structural changes. Here, we address these challenges by microsecond molecular dynamics simulations, followed up by additional kinetic and structural analyses of selected sets of specifically engineered enzyme variants. A comparison of wild-type MtCM with naturally and artificially activated MtCMs revealed the overall dynamic profiles of these enzymes as well as key interactions between the C-terminus and the active site loop. In the artificially evolved variant of this model enzyme, this loop is preorganized and stabilized by Pro52 and Asp55, two highly conserved residues in typical, highly active chorismate mutases. Asp55 stretches across the active site and helps to appropriately position active site residues Arg18 and Arg46 for catalysis. The role of Asp55 can be taken over by another acidic residue, if introduced at position 88 close to the C-terminus of MtCM, as suggested by molecular dynamics simulations and confirmed by kinetic investigations of engineered variants.
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Affiliation(s)
- Helen
V. Thorbjørnsrud
- Department
of Chemistry, University of Oslo, Oslo 0315, NO, Norway,Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, Oslo 0315, NO, Norway
| | - Luca Bressan
- Laboratory
of Organic Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Tamjidmaa Khatanbaatar
- Department
of Chemistry, University of Oslo, Oslo 0315, NO, Norway,Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, Oslo 0315, NO, Norway
| | - Manuel Carrer
- Department
of Chemistry, University of Oslo, Oslo 0315, NO, Norway,Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, Oslo 0315, NO, Norway
| | | | - Gabriele Cordara
- Department
of Chemistry, University of Oslo, Oslo 0315, NO, Norway,Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, Oslo 0315, NO, Norway
| | - Peter Kast
- Laboratory
of Organic Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland,
| | - Michele Cascella
- Department
of Chemistry, University of Oslo, Oslo 0315, NO, Norway,Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, Oslo 0315, NO, Norway,
| | - Ute Krengel
- Department
of Chemistry, University of Oslo, Oslo 0315, NO, Norway,Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, Oslo 0315, NO, Norway,
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5
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Hubrich F, Müller M, Andexer JN. Chorismate- and isochorismate converting enzymes: versatile catalysts acting on an important metabolic node. Chem Commun (Camb) 2021; 57:2441-2463. [PMID: 33605953 DOI: 10.1039/d0cc08078k] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chorismate and isochorismate represent an important branching point connecting primary and secondary metabolism in bacteria, fungi, archaea and plants. Chorismate- and isochorismate-converting enzymes are potential targets for new bioactive compounds, as well as valuable biocatalysts for the in vivo and in vitro synthesis of fine chemicals. The diversity of the products of chorismate- and isochorismate-converting enzymes is reflected in the enzymatic three-dimensional structures and molecular mechanisms. Due to the high reactivity of chorismate and its derivatives, these enzymes have evolved to be accurately tailored to their respective reaction; at the same time, many of them exhibit a fascinating flexibility regarding side reactions and acceptance of alternative substrates. Here, we give an overview of the different (sub)families of chorismate- and isochorismate-converting enzymes, their molecular mechanisms, and three-dimensional structures. In addition, we highlight important results of mutagenetic approaches that generate a broader understanding of the influence of distinct active site residues for product formation and the conversion of one subfamily into another. Based on this, we discuss to what extent the recent advances in the field might influence the general mechanistic understanding of chorismate- and isochorismate-converting enzymes. Recent discoveries of new chorismate-derived products and pathways, as well as biocatalytic conversions of non-physiological substrates, highlight how this vast field is expected to continue developing in the future.
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Affiliation(s)
- Florian Hubrich
- ETH Zurich, Institute of Microbiology, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.
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6
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Rivilla I, Odriozola-Gimeno M, Aires A, Gimeno A, Jiménez-Barbero J, Torrent-Sucarrat M, Cortajarena AL, Cossío FP. Discovering Biomolecules with Huisgenase Activity: Designed Repeat Proteins as Biocatalysts for (3 + 2) Cycloadditions. J Am Chem Soc 2019; 142:762-776. [DOI: 10.1021/jacs.9b06823] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Iván Rivilla
- Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO−CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P° Manuel Lardizabal 3, E-20018 Donostia/San Sebastián, Spain
| | - Mikel Odriozola-Gimeno
- Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO−CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P° Manuel Lardizabal 3, E-20018 Donostia/San Sebastián, Spain
| | - Antonio Aires
- Parque Tecnológico de San Sebastián, CIC biomaGUNE, Paseo Miramón 182, 20014 Donostia/San Sebastián, Spain
| | - Ana Gimeno
- Molecular Recognition & Host−Pathogen Interactions Unit, CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170 Derio, Spain
| | - Jesús Jiménez-Barbero
- Molecular Recognition & Host−Pathogen Interactions Unit, CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170 Derio, Spain
- Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, Leioa 48940, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Ma Diaz de Haro 3, Bilbao 48013, Spain
| | - Miquel Torrent-Sucarrat
- Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO−CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P° Manuel Lardizabal 3, E-20018 Donostia/San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, Ma Diaz de Haro 3, Bilbao 48013, Spain
| | - Aitziber L. Cortajarena
- Parque Tecnológico de San Sebastián, CIC biomaGUNE, Paseo Miramón 182, 20014 Donostia/San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, Ma Diaz de Haro 3, Bilbao 48013, Spain
| | - Fernando P. Cossío
- Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO−CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P° Manuel Lardizabal 3, E-20018 Donostia/San Sebastián, Spain
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7
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Jamieson CS, Ohashi M, Liu F, Tang Y, Houk KN. The expanding world of biosynthetic pericyclases: cooperation of experiment and theory for discovery. Nat Prod Rep 2019; 36:698-713. [PMID: 30311924 DOI: 10.1039/c8np00075a] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: 2000 to 2018 Pericyclic reactions are a distinct class of reactions that have wide synthetic utility. Before the recent discoveries described in this review, enzyme-catalyzed pericyclic reactions were not widely known to be involved in biosynthesis. This situation is changing rapidly. We define the scope of pericyclic reactions, give a historical account of their discoveries as biosynthetic reactions, and provide evidence that there are many enzymes in nature that catalyze pericyclic reactions. These enzymes, the "pericyclases," are the subject of this review.
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Affiliation(s)
- Cooper S Jamieson
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, USA.
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8
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9
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Grüninger MJ, Buchholz PCF, Mordhorst S, Strack P, Müller M, Hubrich F, Pleiss J, Andexer JN. Chorismatases – the family is growing. Org Biomol Chem 2019; 17:2092-2098. [DOI: 10.1039/c8ob03038c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A newly discovered subfamily of chorismatases catalyses the same reaction as chorismate lyases (cleavage of chorismate to 4-hydroxybenzoate), but does not suffer from product inhibition.
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Affiliation(s)
- Mads J. Grüninger
- Institute of Pharmaceutical Sciences
- University of Freiburg
- 79104 Freiburg
- Germany
| | - Patrick C. F. Buchholz
- Institute of Biochemistry and Technical Biochemistry
- University of Stuttgart
- 70569 Stuttgart
- Germany
| | - Silja Mordhorst
- Institute of Pharmaceutical Sciences
- University of Freiburg
- 79104 Freiburg
- Germany
| | - Patrick Strack
- Institute of Pharmaceutical Sciences
- University of Freiburg
- 79104 Freiburg
- Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences
- University of Freiburg
- 79104 Freiburg
- Germany
| | - Florian Hubrich
- Institute of Pharmaceutical Sciences
- University of Freiburg
- 79104 Freiburg
- Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry
- University of Stuttgart
- 70569 Stuttgart
- Germany
| | - Jennifer N. Andexer
- Institute of Pharmaceutical Sciences
- University of Freiburg
- 79104 Freiburg
- Germany
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10
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Freindorf M, Tao Y, Sethio D, Cremer D, Kraka E. New mechanistic insights into the Claisen rearrangement of chorismate – a Unified Reaction Valley Approach study. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1530464] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Yunwen Tao
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Daniel Sethio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
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11
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Abstract
Enzymes in biosynthetic pathways, especially in plant and microbial metabolism, generate structural and functional group complexity in small molecules by conversion of acyclic frameworks to cyclic scaffolds via short, efficient routes. The distinct chemical logic used by several distinct classes of cyclases, oxidative and non-oxidative, has recently been elucidated by genome mining, heterologous expression, and genetic and mechanistic analyses. These include enzymes performing pericyclic transformations, pyran synthases, tandem acting epoxygenases, and epoxide "hydrolases", as well as oxygenases and radical S-adenosylmethionine enzymes that involve rearrangements of substrate radicals under aerobic or anaerobic conditions.
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Affiliation(s)
- Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA
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12
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Shelton CL, Lamb AL. Unraveling the Structure and Mechanism of the MST(ery) Enzymes. Trends Biochem Sci 2018; 43:342-357. [PMID: 29573882 DOI: 10.1016/j.tibs.2018.02.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 02/23/2018] [Accepted: 02/27/2018] [Indexed: 01/06/2023]
Abstract
The menaquinone, siderophore, and tryptophan (MST) enzymes transform chorismate to generate precursor molecules for the biosynthetic pathways defined in their name. Kinetic data, both steady-state and transient-state, and X-ray crystal structures indicate that these enzymes are highly conserved both in mechanism and in structure. Because these enzymes are found in pathogens but not in humans, there is considerable interest in these enzymes as drug design targets. While great progress has been made in defining enzyme structure and mechanism, inhibitor design has lagged behind. This review provides a detailed description of the evidence that begins to unravel the mystery of how the MST enzymes work, and how that information has been used in inhibitor design.
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Affiliation(s)
- Catherine L Shelton
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA.
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13
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Nonribosomal peptides for iron acquisition: pyochelin biosynthesis as a case study. Curr Opin Struct Biol 2018; 53:1-11. [PMID: 29455106 DOI: 10.1016/j.sbi.2018.01.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 01/03/2023]
Abstract
Microbes synthesize small, iron-chelating molecules known as siderophores to acquire iron from the environment. One way siderophores are generated is by nonribosomal peptide synthetases (NRPSs). The bioactive peptides generated by NRPS enzymes have unique chemical features, which are incorporated by accessory and tailoring domains or proteins. The first part of this review summarizes recent progress in NRPS structural biology. The second part uses the biosynthesis of pyochelin, a siderophore from Pseudomonas aeruginosa, as a case study to examine enzymatic methods for generating the observed diversity in NRPS-derived natural products.
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14
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Dong L, Liu Y. Comparative studies of the catalytic mechanisms of two chorismatases: CH-fkbo and CH-Hyg5. Proteins 2017; 85:1146-1158. [DOI: 10.1002/prot.25279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 02/13/2017] [Accepted: 02/21/2017] [Indexed: 01/11/2023]
Affiliation(s)
- Lihua Dong
- School of Chemistry and Chemical Engineering; Shandong University; Jinan Shandong 250100 China
- School of Chemistry and Chemical Engineering; Qilu Normal University; Jinan Shandong 250013 China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering; Shandong University; Jinan Shandong 250100 China
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15
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Tantillo DJ. Does Nature Know Best? Pericyclic Reactions in the Daphniphyllum Alkaloid-Forming Cation Cascade. Org Lett 2016; 18:4482-4. [PMID: 27559932 DOI: 10.1021/acs.orglett.6b01919] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heathcock's classic cyclization/rearrangement cascade for formation of Daphniphyllum alkaloids is subjected to analysis using density functional theory calculations. The results of these calculations are consistent with a two-step pathway involving two pericyclic reactions, a Diels-Alder cycloaddition and an ene reaction.
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Affiliation(s)
- Dean J Tantillo
- Department of Chemistry, University of California-Davis , Davis, California 95616, United States
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16
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Meneely KM, Sundlov JA, Gulick AM, Moran GR, Lamb AL. An Open and Shut Case: The Interaction of Magnesium with MST Enzymes. J Am Chem Soc 2016; 138:9277-93. [PMID: 27373320 PMCID: PMC5029964 DOI: 10.1021/jacs.6b05134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
![]()
The shikimate pathway of bacteria,
fungi, and plants generates
chorismate, which is drawn into biosynthetic pathways that form aromatic
amino acids and other important metabolites, including folates, menaquinone,
and siderophores. Many of the pathways initiated at this branch point
transform chorismate using an MST enzyme. The MST enzymes (menaquinone, siderophore, and tryptophan biosynthetic enzymes) are structurally homologous and magnesium-dependent,
and all perform similar chemical permutations to chorismate by nucleophilic
addition (hydroxyl or amine) at the 2-position of the ring, inducing
displacement of the 4-hydroxyl. The isomerase enzymes release isochorismate
or aminodeoxychorismate as the product, while the synthase enzymes
also have lyase activity that displaces pyruvate to form either salicylate
or anthranilate. This has led to the hypothesis that the isomerase
and lyase activities performed by the MST enzymes are functionally
conserved. Here we have developed tailored pre-steady-state approaches
to establish the kinetic mechanisms of the isochorismate and salicylate
synthase enzymes of siderophore biosynthesis. Our data are centered
on the role of magnesium ions, which inhibit the isochorismate synthase
enzymes but not the salicylate synthase enzymes. Prior structural
data have suggested that binding of the metal ion occludes access
or egress of substrates. Our kinetic data indicate that for the production
of isochorismate, a high magnesium ion concentration suppresses the
rate of release of product, accounting for the observed inhibition
and establishing the basis of the ordered-addition kinetic mechanism.
Moreover, we show that isochorismate is channeled through the synthase
reaction as an intermediate that is retained in the active site by
the magnesium ion. Indeed, the lyase-active enzyme has 3 orders of
magnitude higher affinity for the isochorismate complex relative to
the chorismate complex. Apparent negative-feedback inhibition by ferrous
ions is documented at nanomolar concentrations, which is a potentially
physiologically relevant mode of regulation for siderophore biosynthesis
in vivo.
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Affiliation(s)
- Kathleen M Meneely
- Department of Molecular Biosciences, University of Kansas , Lawrence, Kansas 66045, United States
| | - Jesse A Sundlov
- Hauptman-Woodward Medical Research Institute , 700 Ellicott Street, Buffalo, New York 14203, United States
| | - Andrew M Gulick
- Hauptman-Woodward Medical Research Institute , 700 Ellicott Street, Buffalo, New York 14203, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee , Milwaukee, Wisconsin 53201, United States
| | - Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas , Lawrence, Kansas 66045, United States
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17
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Thompson B, Machas M, Nielsen DR. Engineering and comparison of non‐natural pathways for microbial phenol production. Biotechnol Bioeng 2016; 113:1745-54. [DOI: 10.1002/bit.25942] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/23/2015] [Accepted: 01/18/2016] [Indexed: 01/14/2023]
Affiliation(s)
- Brian Thompson
- Chemical Engineering, School for Engineering of Matter, Transport, and EnergyUniversity of Arizona StateTempeArizona
| | - Michael Machas
- Chemical Engineering, School for Engineering of Matter, Transport, and EnergyUniversity of Arizona StateTempeArizona
| | - David R. Nielsen
- Chemical Engineering, School for Engineering of Matter, Transport, and EnergyUniversity of Arizona StateTempeArizona
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18
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Culbertson JE, Chung DH, Ziebart KT, Espiritu E, Toney MD. Conversion of aminodeoxychorismate synthase into anthranilate synthase with Janus mutations: mechanism of pyruvate elimination catalyzed by chorismate enzymes. Biochemistry 2015; 54:2372-84. [PMID: 25710100 DOI: 10.1021/acs.biochem.5b00013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The central importance of chorismate enzymes in bacteria, fungi, parasites, and plants combined with their absence in mammals makes them attractive targets for antimicrobials and herbicides. Two of these enzymes, anthranilate synthase (AS) and aminodeoxychorismate synthase (ADCS), are structurally and mechanistically similar. The first catalytic step, amination at C2, is common between them, but AS additionally catalyzes pyruvate elimination, aromatizing the aminated intermediate to anthranilate. Despite prior attempts, the conversion of a pyruvate elimination-deficient enzyme into an elimination-proficient one has not been reported. Janus, a bioinformatics method for predicting mutations required to functionally interconvert homologous enzymes, was employed to predict mutations to convert ADCS into AS. A genetic selection on a library of Janus-predicted mutations was performed. Complementation of an AS-deficient strain of Escherichia coli grown on minimal medium led to several ADCS mutants that allow growth in 6 days compared to 2 days for wild-type AS. The purified mutant enzymes catalyze the conversion of chorismate to anthranilate at rates that are ∼50% of the rate of wild-type ADCS-catalyzed conversion of chorismate to aminodeoxychorismate. The residues mutated do not contact the substrate. Molecular dynamics studies suggest that pyruvate elimination is controlled by the conformation of the C2-aminated intermediate. Enzymes that catalyze elimination favor the equatorial conformation, which presents the C2-H to a conserved active site lysine (Lys424) for deprotonation and maximizes stereoelectronic activation. Acid/base catalysis of pyruvate elimination was confirmed in AS and salicylate synthase by showing incorporation of a solvent-derived proton into the pyruvate methyl group and by solvent kinetic isotope effects on pyruvate elimination catalyzed by AS.
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Affiliation(s)
- Justin E Culbertson
- †Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Dong hee Chung
- †Department of Chemistry, University of California, Davis, Davis, California 95616, United States
| | - Kristin T Ziebart
- ‡Department of Chemistry, Oregon State University, Corvallis, Oregon 97331-4003, United States
| | - Eduardo Espiritu
- §Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Michael D Toney
- †Department of Chemistry, University of California, Davis, Davis, California 95616, United States
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Meneely KM, Luo Q, Riley AP, Taylor B, Roy A, Stein RL, Prisinzano TE, Lamb AL. Expanding the results of a high throughput screen against an isochorismate-pyruvate lyase to enzymes of a similar scaffold or mechanism. Bioorg Med Chem 2014; 22:5961-9. [PMID: 25282647 DOI: 10.1016/j.bmc.2014.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 08/27/2014] [Accepted: 09/05/2014] [Indexed: 01/31/2023]
Abstract
Antibiotic resistance is a growing health concern, and new avenues of antimicrobial drug design are being actively sought. One suggested pathway to be targeted for inhibitor design is that of iron scavenging through siderophores. Here we present a high throughput screen to the isochorismate-pyruvate lyase of Pseudomonas aeruginosa, an enzyme required for the production of the siderophore pyochelin. Compounds identified in the screen are high nanomolar to low micromolar inhibitors of the enzyme and produce growth inhibition in PAO1 P. aeruginosa in the millimolar range under iron-limiting conditions. The identified compounds were also tested for enzymatic inhibition of Escherichia coli chorismate mutase, a protein of similar fold and similar chemistry, and of Yersinia enterocolitica salicylate synthase, a protein of differing fold but catalyzing the same lyase reaction. In both cases, subsets of the inhibitors from the screen were found to be inhibitory to enzymatic activity (mutase or synthase) in the micromolar range and capable of growth inhibition in their respective organisms (E. coli or Y. enterocolitica).
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Affiliation(s)
- Kathleen M Meneely
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66045, United States
| | - Qianyi Luo
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66045, United States
| | - Andrew P Riley
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr, Lawrence, KS 66045, United States
| | - Byron Taylor
- High Throughput Screening Facility, University of Kansas, 2034 Becker Dr, Lawrence, KS 66047, United States
| | - Anuradha Roy
- High Throughput Screening Facility, University of Kansas, 2034 Becker Dr, Lawrence, KS 66047, United States
| | - Ross L Stein
- High Throughput Screening Facility, University of Kansas, 2034 Becker Dr, Lawrence, KS 66047, United States
| | - Thomas E Prisinzano
- Department of Medicinal Chemistry, University of Kansas, 1251 Wescoe Hall Dr, Lawrence, KS 66045, United States
| | - Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66045, United States.
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Juneja P, Hubrich F, Diederichs K, Welte W, Andexer JN. Mechanistic Implications for the Chorismatase FkbO Based on the Crystal Structure. J Mol Biol 2014; 426:105-15. [DOI: 10.1016/j.jmb.2013.09.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/06/2013] [Accepted: 09/09/2013] [Indexed: 11/29/2022]
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21
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Choutko A, Eichenberger AP, van Gunsteren WF, Dolenc J. Exploration of swapping enzymatic function between two proteins: a simulation study of chorismate mutase and isochorismate pyruvate lyase. Protein Sci 2013; 22:809-22. [PMID: 23595942 DOI: 10.1002/pro.2264] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 03/31/2013] [Indexed: 01/09/2023]
Abstract
The enzyme chorismate mutase EcCM from Escherichia coli catalyzes one of the few pericyclic reactions in biology, the transformation of chorismate to prephenate. The isochorismate pyruvate lyase PchB from Pseudomonas aeroginosa catalyzes another pericyclic reaction, the isochorismate to salicylate transformation. Interestingly, PchB possesses weak chorismate mutase activity as well thus being able to catalyze two distinct pericyclic reactions in a single active site. EcCM and PchB possess very similar folds, despite their low sequence identity. Using molecular dynamics simulations of four combinations of the two enzymes (EcCM and PchB) with the two substrates (chorismate and isochorismate) we show that the electrostatic field due to EcCM at atoms of chorismate favors the chorismate to prephenate transition and that, analogously, the electrostatic field due to PchB at atoms of isochorismate favors the isochorismate to salicylate transition. The largest differences between EcCM and PchB in electrostatic field strengths at atoms of the substrates are found to be due to residue side chains at distances between 0.6 and 0.8 nm from particular substrate atoms. Both enzymes tend to bring their non-native substrate in the same conformation as their native substrate. EcCM and to a lower extent PchB fail in influencing the forces on and conformations of the substrate such as to favor the other chemical reaction (isochorismate pyruvate lyase activity for EcCM and chorismate mutase activity for PchB). These observations might explain the difficulty of engineering isochorismate pyruvate lyase activity in EcCM by solely mutating active site residues.
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Affiliation(s)
- Alexandra Choutko
- Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zürich, Switzerland
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22
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Direct evidence for a covalent ene adduct intermediate in NAD(P)H-dependent enzymes. Nat Chem Biol 2013; 10:50-5. [PMID: 24240506 DOI: 10.1038/nchembio.1385] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 10/01/2013] [Indexed: 11/08/2022]
Abstract
The pyridine nucleotides NADH and NADPH (NAD(P)H) are ubiquitous redox coenzymes that are present in all living cells. Although about 16% of all characterized enzymes use pyridine nucleotides as hydride donors or acceptors during catalysis, a detailed understanding of how the hydride is transferred between NAD(P)H and the corresponding substrate is lacking for many enzymes. Here we present evidence for a new mechanism that operates during enzymatic hydride transfers using crotonyl-CoA carboxylase/reductase (Ccr) as a case study. We observed a covalent ene intermediate between NADPH and the substrate, crotonyl-CoA, using NMR, high-resolution MS and stopped-flow spectroscopy. Preparation of the ene intermediate further allowed direct access to the catalytic cycle of other NADPH-dependent enzymes-including those from type II fatty acid biosynthesis-in an unprecedented way, suggesting that formation of NAD(P)H ene intermediates is a more general principle in catalysis.
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Meneely KM, Luo Q, Lamb AL. Redesign of MST enzymes to target lyase activity instead promotes mutase and dehydratase activities. Arch Biochem Biophys 2013; 539:70-80. [PMID: 24055536 DOI: 10.1016/j.abb.2013.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/10/2013] [Accepted: 09/11/2013] [Indexed: 11/20/2022]
Abstract
The isochorismate and salicylate synthases are members of the MST family of enzymes. The isochorismate synthases establish an equilibrium for the conversion chorismate to isochorismate and the reverse reaction. The salicylate synthases convert chorismate to salicylate with an isochorismate intermediate; therefore, the salicylate synthases perform isochorismate synthase and isochorismate-pyruvate lyase activities sequentially. While the active site residues are highly conserved, there are two sites that show trends for lyase-activity and lyase-deficiency. Using steady state kinetics and HPLC progress curves, we tested the "interchange" hypothesis that interconversion of the amino acids at these sites would promote lyase activity in the isochorismate synthases and remove lyase activity from the salicylate synthases. An alternative, "permute" hypothesis, that chorismate-utilizing enzymes are designed to permute the substrate into a variety of products and tampering with the active site may lead to identification of adventitious activities, is tested by more sensitive NMR time course experiments. The latter hypothesis held true. The variant enzymes predominantly catalyzed chorismate mutase-prephenate dehydratase activities, sequentially generating prephenate and phenylpyruvate, augmenting previously debated (mutase) or undocumented (dehydratase) adventitious activities.
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Affiliation(s)
- Kathleen M Meneely
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, United States
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Meneely KM, Luo Q, Dhar P, Lamb AL. Lysine221 is the general base residue of the isochorismate synthase from Pseudomonas aeruginosa (PchA) in a reaction that is diffusion limited. Arch Biochem Biophys 2013; 538:49-56. [PMID: 23942051 DOI: 10.1016/j.abb.2013.07.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 07/25/2013] [Accepted: 07/28/2013] [Indexed: 01/30/2023]
Abstract
The isochorismate synthase from Pseudomonas aeruginosa (PchA) catalyzes the conversion of chorismate to isochorismate, which is subsequently converted by a second enzyme (PchB) to salicylate for incorporation into the salicylate-capped siderophore pyochelin. PchA is a member of the MST family of enzymes, which includes the structurally homologous isochorismate synthases from Escherichia coli (EntC and MenF) and salicylate synthases from Yersinia enterocolitica (Irp9) and Mycobacterium tuberculosis (MbtI). The latter enzymes generate isochorismate as an intermediate before generating salicylate and pyruvate. General acid-general base catalysis has been proposed for isochorismate synthesis in all five enzymes, but the residues required for the isomerization are a matter of debate, with both lysine221 and glutamate313 proposed as the general base (PchA numbering). This work includes a classical characterization of PchA with steady state kinetic analysis, solvent kinetic isotope effect analysis and by measuring the effect of viscosogens on catalysis. The results suggest that isochorismate production from chorismate by the MST enzymes is the result of general acid-general base catalysis with a lysine as the base and a glutamic acid as the acid, in reverse protonation states. Chemistry is determined to not be rate limiting, favoring the hypothesis of a conformational or binding step as the slow step.
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Affiliation(s)
- Kathleen M Meneely
- Molecular Biosciences, University of Kansas, Lawrence, KS 66045, United States
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25
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Kim HJ, Ruszczycky MW, Liu HW. Current developments and challenges in the search for a naturally selected Diels-Alderase. Curr Opin Chem Biol 2012; 16:124-31. [PMID: 22260931 DOI: 10.1016/j.cbpa.2011.12.017] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 12/21/2011] [Accepted: 12/23/2011] [Indexed: 11/27/2022]
Abstract
Only a very few examples of enzymes known to catalyze pericyclic reactions have been reported, and presently no enzyme has been demonstrated unequivocally to catalyze a Diels-Alder reaction. Nevertheless, research into secondary metabolism has led to the discovery of numerous natural products exhibiting the structural hallmarks of [4+2] cycloadditions, prompting efforts to characterize the responsible enzymatic processes. These efforts have resulted in a growing collection of enzymes believed to catalyze pericyclic [4+2] cycloaddition reactions; however, in each case the complexity of the substrates and catalytic properties of these enzymes poses significant challenges in substantiating these hypotheses. Herein we consider the principles motivating these efforts and the enzymological systems currently under investigation.
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Affiliation(s)
- Hak Joong Kim
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, United States
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