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Rocchi R, Zwinkels J, Kooijman M, Garre A, Smid EJ. Development of novel natto using legumes produced in Europe. Heliyon 2024; 10:e26849. [PMID: 38463896 PMCID: PMC10923668 DOI: 10.1016/j.heliyon.2024.e26849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/12/2024] Open
Abstract
Natto is a traditional Japanese fermented product consisting of cooked soybeans fermented with Bacillus subtilis var. natto. We assessed three different B. subtilis strains and investigated their impact on product quality aspects, such as microbial quality, textural quality (poly-γ-glutamate strand formation), free amino acids (FAA), and volatile organic compounds (VOCs), but also the vitamin K1, K2 and B1 content, and presence of nattokinase. Using Bayesian contrast analysis, we conclude that the quality attributes were influenced by both the substrate and strain used, without significant differences in bacterial growth between strain or substrate. Overall, all the tested European legumes, except for brown beans, are adequate substrates to produce natto, with comparable or higher qualities compared to the traditional soy. Out of all the tested legumes, red lentils were the most optimal fermentation substrate. They were fermented most consistently, with high concentrations of vitamin K2, VOCs, FAA.
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Affiliation(s)
- Rebecca Rocchi
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Jasper Zwinkels
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Merit Kooijman
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Alberto Garre
- Department of Agricultural Engineering & Institute of Plant Biotechnology, Universidad Politécnica de Cartagena, Spain
| | - Eddy J. Smid
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
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2
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Stanborough T, Ho NAT, Bulloch EMM, Bashiri G, Dawes SS, Akazong EW, Titterington J, Allison TM, Jiao W, Johnston JM. Allosteric inhibition of Staphylococcus aureus MenD by 1,4-dihydroxy naphthoic acid: a feedback inhibition mechanism of the menaquinone biosynthesis pathway. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220035. [PMID: 36633276 PMCID: PMC9835592 DOI: 10.1098/rstb.2022.0035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Menaquinones (MKs) are electron carriers in bacterial respiratory chains. In Staphylococcus aureus (Sau), MKs are essential for aerobic and anaerobic respiration. As MKs are redox-active, their biosynthesis likely requires tight regulation to prevent disruption of cellular redox balance. We recently found that the Mycobacterium tuberculosis MenD, the first committed enzyme of the MK biosynthesis pathway, is allosterically inhibited by the downstream metabolite 1,4-dihydroxy-2-naphthoic acid (DHNA). To understand if this is a conserved mechanism in phylogenetically distant genera that also use MK, we investigated whether the Sau-MenD is allosterically inhibited by DHNA. Our results show that DHNA binds to and inhibits the SEPHCHC synthase activity of Sau-MenD enzymes. We identified residues in the DHNA binding pocket that are important for catalysis (Arg98, Lys283, Lys309) and inhibition (Arg98, Lys283). Furthermore, we showed that exogenous DHNA inhibits the growth of Sau, an effect that can be rescued by supplementing the growth medium with MK-4. Our results demonstrate that, despite a lack of strict conservation of the DHNA binding pocket between Mtb-MenD and Sau-MenD, feedback inhibition by DHNA is a conserved mechanism in Sau-MenD and hence the Sau MK biosynthesis pathway. These findings may have implications for the development of anti-staphylococcal agents targeting MK biosynthesis. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Tamsyn Stanborough
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre (BIC), University of Canterbury, Christchurch 8041, New Zealand
| | - Ngoc Anh Thu Ho
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre (BIC), University of Canterbury, Christchurch 8041, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, c/o The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Esther M. M. Bulloch
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, c/o The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Ghader Bashiri
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, c/o The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Stephanie S. Dawes
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, c/o The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Etheline W. Akazong
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre (BIC), University of Canterbury, Christchurch 8041, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, c/o The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - James Titterington
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre (BIC), University of Canterbury, Christchurch 8041, New Zealand
| | - Timothy M. Allison
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre (BIC), University of Canterbury, Christchurch 8041, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, c/o The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Wanting Jiao
- Ferrier Research Institute, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, c/o The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Jodie M. Johnston
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre (BIC), University of Canterbury, Christchurch 8041, New Zealand,Maurice Wilkins Centre for Molecular Biodiscovery, c/o The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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3
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Abstract
Compensatory substitutions happen when one mutation is advantageously selected because it restores the loss of fitness induced by a previous deleterious mutation. How frequent such mutations occur in evolution and what is the structural and functional context permitting their emergence remain open questions. We built an atlas of intra-protein compensatory substitutions using a phylogenetic approach and a dataset of 1,630 bacterial protein families for which high-quality sequence alignments and experimentally derived protein structures were available. We identified more than 51,000 positions coevolving by the mean of predicted compensatory mutations. Using the evolutionary and structural properties of the analyzed positions, we demonstrate that compensatory mutations are scarce (typically only a few in the protein history) but widespread (the majority of proteins experienced at least one). Typical coevolving residues are evolving slowly, are located in the protein core outside secondary structure motifs, and are more often in contact than expected by chance, even after accounting for their evolutionary rate and solvent exposure. An exception to this general scheme is residues coevolving for charge compensation, which are evolving faster than noncoevolving sites, in contradiction with predictions from simple coevolutionary models, but similar to stem pairs in RNA. While sites with a significant pattern of coevolution by compensatory mutations are rare, the comparative analysis of hundreds of structures ultimately permits a better understanding of the link between the three-dimensional structure of a protein and its fitness landscape.
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Affiliation(s)
- Shilpi Chaurasia
- RG Molecular Systems Evolution, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany.,Excelra Knowledge Solutions Pvt Ltd, Hyderabad, India
| | - Julien Y Dutheil
- RG Molecular Systems Evolution, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany.,Institute of Evolution Sciences of Montpellier (ISEM), CNRS, University of Montpellier, IRD, EPHE, 34095 Montpellier, France
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4
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Planas F, McLeish MJ, Himo F. Enzymatic Stetter Reaction: Computational Study of the Reaction Mechanism of MenD. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Ferran Planas
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-10691, Sweden
| | - Michael J. McLeish
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-10691, Sweden
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5
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Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea. Genes (Basel) 2021; 12:genes12070963. [PMID: 34202810 PMCID: PMC8305020 DOI: 10.3390/genes12070963] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.
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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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7
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Johnston JM, Bulloch EM. Advances in menaquinone biosynthesis: sublocalisation and allosteric regulation. Curr Opin Struct Biol 2020; 65:33-41. [PMID: 32634692 DOI: 10.1016/j.sbi.2020.05.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 12/31/2022]
Abstract
Menaquinones (vitamin K2) are a family of redox-active small molecules with critical functions across all domains of life, including energy generation in bacteria and bone health in humans. The enzymes involved in menaquinone biosynthesis also have bioengineering applications and are potential antimicrobial drug targets. New insights into the essential roles of menaquinones, and their potential to cause redox-related toxicity, have highlighted the need for this pathway to be tightly controlled. Here, we provide an overview of our current understanding of the classical menaquinone biosynthesis pathway in bacteria. We also review recent discoveries on protein-level allostery and sublocalisation of membrane-bound enzymes that have provided insight into the regulation of flux through this biosynthetic pathway.
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Affiliation(s)
- Jodie M Johnston
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre, and Maurice Wilkins Centre for MolecularBiodiscovery, University of Canterbury, Christchurch 8041, New Zealand.
| | - Esther Mm Bulloch
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for MolecularBiodiscovery, University of Auckland, Private Bag 92019, Auckland, New Zealand
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8
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Bashiri G, Nigon LV, Jirgis ENM, Ho NAT, Stanborough T, Dawes SS, Baker EN, Bulloch EMM, Johnston JM. Allosteric regulation of menaquinone (vitamin K 2) biosynthesis in the human pathogen Mycobacterium tuberculosis. J Biol Chem 2020; 295:3759-3770. [PMID: 32029475 DOI: 10.1074/jbc.ra119.012158] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/01/2020] [Indexed: 11/06/2022] Open
Abstract
Menaquinone (vitamin K2) plays a vital role in energy generation and environmental adaptation in many bacteria, including the human pathogen Mycobacterium tuberculosis (Mtb). Although menaquinone levels are known to be tightly linked to the cellular redox/energy status of the cell, the regulatory mechanisms underpinning this phenomenon are unclear. The first committed step in menaquinone biosynthesis is catalyzed by MenD, a thiamine diphosphate-dependent enzyme comprising three domains. Domains I and III form the MenD active site, but no function has yet been ascribed to domain II. Here, we show that the last cytosolic metabolite in the menaquinone biosynthesis pathway, 1,4-dihydroxy-2-naphthoic acid (DHNA), binds to domain II of Mtb-MenD and inhibits its activity. Using X-ray crystallography of four apo- and cofactor-bound Mtb-MenD structures, along with several spectroscopy assays, we identified three arginine residues (Arg-97, Arg-277, and Arg-303) that are important for both enzyme activity and the feedback inhibition by DHNA. Among these residues, Arg-277 appeared to be particularly important for signal propagation from the allosteric site to the active site. This is the first evidence of feedback regulation of the menaquinone biosynthesis pathway in bacteria, identifying a protein-level regulatory mechanism that controls menaquinone levels within the cell and may therefore represent a good target for disrupting menaquinone biosynthesis in M. tuberculosis.
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Affiliation(s)
- Ghader Bashiri
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Laura V Nigon
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Ehab N M Jirgis
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Ngoc Anh Thu Ho
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre (BIC), and Maurice Wilkins Centre for Molecular Biodiscovery, University of Canterbury, Christchurch 8041, New Zealand
| | - Tamsyn Stanborough
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre (BIC), and Maurice Wilkins Centre for Molecular Biodiscovery, University of Canterbury, Christchurch 8041, New Zealand
| | - Stephanie S Dawes
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Edward N Baker
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Esther M M Bulloch
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Jodie M Johnston
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre (BIC), and Maurice Wilkins Centre for Molecular Biodiscovery, University of Canterbury, Christchurch 8041, New Zealand
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9
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Fries A, Mazzaferro LS, Grüning B, Bisel P, Stibal K, Buchholz PCF, Pleiss J, Sprenger GA, Müller M. Alteration of the Route to Menaquinone towards Isochorismate-Derived Metabolites. Chembiochem 2019; 20:1672-1677. [PMID: 30866142 PMCID: PMC6618250 DOI: 10.1002/cbic.201900050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Indexed: 12/29/2022]
Abstract
Chorismate and isochorismate constitute branch-point intermediates in the biosynthesis of many aromatic metabolites in microorganisms and plants. To obtain unnatural compounds, we modified the route to menaquinone in Escherichia coli. We propose a model for the binding of isochorismate to the active site of MenD ((1R,2S, 5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxycyclohex-3-ene-1-carboxylate (SEPHCHC) synthase) that explains the outcome of the native reaction with α-ketoglutarate. We have rationally designed variants of MenD for the conversion of several isochorismate analogues. The double-variant Asn117Arg-Leu478Thr preferentially converts (5S,6S)-5,6-dihydroxycyclohexa-1,3-diene-1-carboxylate (2,3-trans-CHD), the hydrolysis product of isochorismate, with a >70-fold higher ratio than that for the wild type. The single-variant Arg107Ile uses (5S,6S)-6-amino-5-hydroxycyclohexa-1,3-diene-1-carboxylate (2,3-trans-CHA) as substrate with >6-fold conversion compared to wild-type MenD. The novel compounds have been made accessible in vivo (up to 5.3 g L-1 ). Unexpectedly, as the identified residues such as Arg107 are highly conserved (>94 %), some of the designed variations can be found in wild-type SEPHCHC synthases from other bacteria (Arg107Lys, 0.3 %). This raises the question for the possible natural occurrence of as yet unexplored branches of the shikimate pathway.
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Affiliation(s)
- Alexander Fries
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
- INCITAP-CONICET, Departamento de QuímicaFacultad de Ciencias Exactas y NaturalesUniversidad Nacional de La PampaAvenida Uruguay 1516300Santa RosaLa PampaArgentina
| | - Laura S. Mazzaferro
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
- INCITAP-CONICET, Departamento de QuímicaFacultad de Ciencias Exactas y NaturalesUniversidad Nacional de La PampaAvenida Uruguay 1516300Santa RosaLa PampaArgentina
| | - Björn Grüning
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Philippe Bisel
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Karin Stibal
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Patrick C. F. Buchholz
- Institute of Biochemistry and Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical BiochemistryUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Georg A. Sprenger
- Institute of MicrobiologyUniversity of StuttgartAllmandring 3170569StuttgartGermany
| | - Michael Müller
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
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10
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Massaiu I, Pasotti L, Sonnenschein N, Rama E, Cavaletti M, Magni P, Calvio C, Herrgård MJ. Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains. Microb Cell Fact 2019; 18:3. [PMID: 30626384 PMCID: PMC6325765 DOI: 10.1186/s12934-018-1052-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/29/2018] [Indexed: 12/15/2022] Open
Abstract
Background Genome-scale metabolic models (GEMs) allow predicting metabolic phenotypes from limited data on uptake and secretion fluxes by defining the space of all the feasible solutions and excluding physio-chemically and biologically unfeasible behaviors. The integration of additional biological information in genome-scale models, e.g., transcriptomic or proteomic profiles, has the potential to improve phenotype prediction accuracy. This is particularly important for metabolic engineering applications where more accurate model predictions can translate to more reliable model-based strain design. Results Here we present a GEM with Enzymatic Constraints using Kinetic and Omics data (GECKO) model of Bacillus subtilis, which uses publicly available proteomic data and enzyme kinetic parameters for central carbon (CC) metabolic reactions to constrain the flux solution space. This model allows more accurate prediction of the flux distribution and growth rate of wild-type and single-gene/operon deletion strains compared to a standard genome-scale metabolic model. The flux prediction error decreased by 43% and 36% for wild-type and mutants respectively. The model additionally increased the number of correctly predicted essential genes in CC pathways by 2.5-fold and significantly decreased flux variability in more than 80% of the reactions with variable flux. Finally, the model was used to find new gene deletion targets to optimize the flux toward the biosynthesis of poly-γ-glutamic acid (γ-PGA) polymer in engineered B. subtilis. We implemented the single-reaction deletion targets identified by the model experimentally and showed that the new strains have a twofold higher γ-PGA concentration and production rate compared to the ancestral strain. Conclusions This work confirms that integration of enzyme constraints is a powerful tool to improve existing genome-scale models, and demonstrates the successful use of enzyme-constrained models in B. subtilis metabolic engineering. We expect that the new model can be used to guide future metabolic engineering efforts in the important industrial production host B. subtilis.
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Affiliation(s)
- Ilaria Massaiu
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Dep. Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy.,Centre for Health Technologies, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
| | - Lorenzo Pasotti
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Dep. Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy.,Centre for Health Technologies, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
| | - Nikolaus Sonnenschein
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Erlinda Rama
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Matteo Cavaletti
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Paolo Magni
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Dep. Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy.,Centre for Health Technologies, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
| | - Cinzia Calvio
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
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11
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Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis. Biochem J 2018; 475:3651-3667. [DOI: 10.1042/bcj20180548] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/10/2018] [Accepted: 10/17/2018] [Indexed: 11/17/2022]
Abstract
The bacterial enzyme MenD, or 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) synthase, catalyzes an essential Stetter reaction in menaquinone (vitamin K2) biosynthesis via thiamine diphosphate (ThDP)-bound tetrahedral post-decarboxylation intermediates. The detailed mechanism of this intermediate chemistry, however, is still poorly understood, but of significant interest given that menaquinone is an essential electron transporter in many pathogenic bacteria. Here, we used site-directed mutagenesis, enzyme kinetic assays, and protein crystallography to reveal an active–inactive intermediate equilibrium in MenD catalysis and its modulation by two conserved active site arginine residues. We observed that these conserved residues play a key role in shifting the equilibrium to the active intermediate by orienting the C2-succinyl group of the intermediates through strong ionic hydrogen bonding. We found that when this interaction is moderately weakened by amino acid substitutions, the resulting proteins are catalytically competent with the C2-succinyl group taking either the active or the inactive orientation in the post-decarboxylation intermediate. When this hydrogen-bonding interaction was strongly weakened, the succinyl group was re-oriented by 180° relative to the native intermediate, resulting in the reversal of the stereochemistry at the reaction center that disabled catalysis. Interestingly, this inactive intermediate was formed with a distinct kinetic behavior, likely as a result of a non-native mode of enzyme–substrate interaction. The mechanistic insights gained from these findings improve our understanding of the new ThDP-dependent catalysis. More importantly, the non-native-binding site of the inactive MenD intermediate uncovered here provides a new target for the development of antibiotics.
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12
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Qin M, Song H, Dai X, Chan C, Chan W, Guo Z. Single‐Turnover Kinetics Reveal a Distinct Mode of Thiamine Diphosphate‐Dependent Catalysis in Vitamin K Biosynthesis. Chembiochem 2018; 19:1514-1522. [DOI: 10.1002/cbic.201800143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Mingming Qin
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Haigang Song
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Present address: Division of Structural BiologyWellcome Trust Centre of Human GenomicsUniversity of Oxford Roosevelt Drive Oxford OX3 7BN UK
| | - Xin Dai
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Chi‐Kong Chan
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Environmental Science ProgramThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Wan Chan
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Environmental Science ProgramThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Zhihong Guo
- Department of ChemistryThe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
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13
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Zhang J, Liu Y. Theoretical study of the catalytic mechanism of glyoxylate carboligase and its mutant V51E. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2079-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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Xu JZ, Yan WL, Zhang WG. Enhancing menaquinone-7 production in recombinant Bacillus amyloliquefaciens by metabolic pathway engineering. RSC Adv 2017. [DOI: 10.1039/c7ra03388e] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Six key enzymes are vital for MK-7 production, but the same enzyme has different effect on MK-7 production in different cultivating methods. Thus, the high enzyme activity and high-traffic biosynthetic pathway are beneficial to synthesize MK-7.
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Affiliation(s)
- Jian-Zhong Xu
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Wei-Liu Yan
- The Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
| | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology
- Ministry of Education
- School of Biotechnology
- Jiangnan University
- Wuxi 214122
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15
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Jirgis ENM, Bashiri G, Bulloch EMM, Johnston JM, Baker EN. Structural Views along the Mycobacterium tuberculosis MenD Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms. Structure 2016; 24:1167-77. [PMID: 27291649 DOI: 10.1016/j.str.2016.04.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/19/2016] [Accepted: 04/27/2016] [Indexed: 01/19/2023]
Abstract
Menaquinone (MQ) is an essential component of the respiratory chains of many pathogenic organisms, including Mycobacterium tuberculosis (Mtb). The first committed step in MQ biosynthesis is catalyzed by 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase (MenD), a thiamin diphosphate (ThDP)-dependent enzyme. Catalysis proceeds through two covalent intermediates as the substrates 2-oxoglutarate and isochorismate are successively added to the cofactor before final cleavage of the product. We have determined a series of crystal structures of Mtb-MenD that map the binding of both substrates, visualizing each step in the MenD catalytic cycle, including both intermediates. ThDP binding induces a marked asymmetry between the coupled active sites of each dimer, and possible mechanisms of communication can be identified. The crystal structures also reveal conformational features of the two intermediates that facilitate reaction but prevent premature product release. These data fully map chemical space to inform early-stage drug discovery targeting MenD.
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Affiliation(s)
- Ehab N M Jirgis
- Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Ghader Bashiri
- Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Esther M M Bulloch
- Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Jodie M Johnston
- Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand.
| | - Edward N Baker
- Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand.
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16
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Song H, Dong C, Qin M, Chen Y, Sun Y, Liu J, Chan W, Guo Z. A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis. J Am Chem Soc 2016; 138:7244-7. [PMID: 27213829 DOI: 10.1021/jacs.6b03437] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Enamine is a well-known reactive intermediate mediating essential thiamine-dependent catalysis in central metabolic pathways. However, this intermediate is not found in the thiamine-dependent catalysis of the vitamin K biosynthetic enzyme MenD. Instead, an active tetrahedral post-decarboxylation intermediate is stably formed in the enzyme and was structurally determined at 1.34 Å resolution in crystal. This intermediate takes a unique conformation that allows only one proton between its tetrahedral reaction center and the exo-ring nitrogen atom of the aminopyrimidine moiety in the cofactor with a short distance of 3.0 Å. It is readily convertible to the final product of the enzymic reaction with a solvent-exchangeable proton at its reaction center. These results show that the thiamine-dependent enzyme utilizes a tetrahedral intermediate in a mechanism distinct from the enamine catalytic chemistry.
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Affiliation(s)
- Haigang Song
- Department of Chemistry, ‡State Key Laboratory for Molecular Neuroscience, and §Environmental Science Program, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Chen Dong
- Department of Chemistry, ‡State Key Laboratory for Molecular Neuroscience, and §Environmental Science Program, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Mingming Qin
- Department of Chemistry, ‡State Key Laboratory for Molecular Neuroscience, and §Environmental Science Program, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Yaozong Chen
- Department of Chemistry, ‡State Key Laboratory for Molecular Neuroscience, and §Environmental Science Program, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Yueru Sun
- Department of Chemistry, ‡State Key Laboratory for Molecular Neuroscience, and §Environmental Science Program, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Jingjing Liu
- Department of Chemistry, ‡State Key Laboratory for Molecular Neuroscience, and §Environmental Science Program, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Wan Chan
- Department of Chemistry, ‡State Key Laboratory for Molecular Neuroscience, and §Environmental Science Program, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Zhihong Guo
- Department of Chemistry, ‡State Key Laboratory for Molecular Neuroscience, and §Environmental Science Program, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, China
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17
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Paudel A, Hamamoto H, Panthee S, Sekimizu K. Menaquinone as a potential target of antibacterial agents. Drug Discov Ther 2016; 10:123-8. [DOI: 10.5582/ddt.2016.01041] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | | | | | - Kazuhisa Sekimizu
- Teikyo University Institute of Medical Mycology
- Genome Pharmaceuticals Institute Co., Ltd
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18
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Sun W, Wei X, Niu A, Ma X, Li JJ, Gao D. Enhanced anti-colon cancer immune responses with modified eEF2-derived peptides. Cancer Lett 2015; 369:112-23. [PMID: 26304717 DOI: 10.1016/j.canlet.2015.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/31/2015] [Accepted: 08/05/2015] [Indexed: 12/22/2022]
Abstract
Eukaryotic elongation factor-2 (eEF2) is overexpressed in many human cancers and is an attractive target for cancer immunotherapy. The eEF2 derived polypeptides have been shown to be able to induce cytotoxic T lymphocytes from healthy donor. Here, we demonstrate the evidence indicating that modification of a segment of peptides from wild type eEF2-derived immunogenic peptides is able to further enhance its capacity of inducing antigen-specific cytotoxic T lymphocytes (CTLs) against colon cancer cells. Using peptide-MHC binding algorithms, potential HLA-A2.1-restricted epitopes capable of inducing specific CD8(+) CTLs were identified. By analyzing HLA-A2.1 affinity and immunogenicity, we further identified one novel immunogenic peptide, P739-747 (RLMEPIYLV), that elicited specific CTL responses in HLA-A2.1/K(b) transgenic mice and culture with peripheral blood lymphocytes from colon cancer patients. Furthermore, replacing certain amino acids (at positions 1, 3, 7) within the P739-747 sequence improved the immunogenicity against eEF2. Several analogs containing the auxiliary HLA-A*0201 anchor residues were able to stably bind to HLA-A*0201 and enhance CTL responses compared with the native sequence; two of them showed increased anti-tumor effects during the adoptive immunotherapy in vivo. Thus, these results support that modified immunogenic analogs are promising candidates for peptide-based cancer vaccination and immunotherapy.
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Affiliation(s)
- Weihong Sun
- Biotherapy Center, The Second Affiliated Hospital, Qingdao University Medical College, Qingdao 266042, China.
| | - Xiaofang Wei
- Biotherapy Center, The Second Affiliated Hospital, Qingdao University Medical College, Qingdao 266042, China
| | - Airong Niu
- Department of Clinical Laboratory, The Second Affiliated Hospital, Qingdao University Medical College, Qingdao 266042, China
| | - Xuezhen Ma
- Department of Oncology, The Second Affiliated Hospital, Qingdao University Medical College, Qingdao 266042, China
| | - Jian Jian Li
- Department of Radiation Oncology, NCI-designated Compressive Cancer Center, University of California Davis, Sacramento, CA 95817, USA.
| | - Daiqing Gao
- Biotherapy Center, The Second Affiliated Hospital, Qingdao University Medical College, Qingdao 266042, China
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19
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Beigi M, Waltzer S, Zarei M, Müller M. New Stetter reactions catalyzed by thiamine diphosphate dependent MenD from E. coli. J Biotechnol 2014; 191:64-8. [DOI: 10.1016/j.jbiotec.2014.07.451] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/18/2014] [Accepted: 07/25/2014] [Indexed: 02/01/2023]
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20
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21
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Westphal R, Jansen S, Vogel C, Pleiss J, Müller M, Rother D, Pohl M. MenD from Bacillus subtilis
: A Potent Catalyst for the Enantiocomplementary Asymmetric Synthesis of Functionalized α-Hydroxy Ketones. ChemCatChem 2013. [DOI: 10.1002/cctc.201300690] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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22
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Hailes HC, Rother D, Müller M, Westphal R, Ward JM, Pleiss J, Vogel C, Pohl M. Engineering stereoselectivity of ThDP-dependent enzymes. FEBS J 2013; 280:6374-94. [DOI: 10.1111/febs.12496] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/16/2013] [Accepted: 08/21/2013] [Indexed: 01/12/2023]
Affiliation(s)
- Helen C. Hailes
- Department of Chemistry; Christopher Ingold Laboratories; University College London; UK
| | - Dörte Rother
- IBG-1: Biotechnology; Forschungszentrum Jülich Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences; University of Freiburg; Germany
| | | | - John M. Ward
- Department of Biochemical Engineering; University College London; UK
| | - Jürgen Pleiss
- Institute of Technical Biochemistry; University of Stuttgart; Germany
| | - Constantin Vogel
- Institute of Technical Biochemistry; University of Stuttgart; Germany
| | - Martina Pohl
- IBG-1: Biotechnology; Forschungszentrum Jülich Germany
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23
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Westphal R, Hahn D, Mackfeld U, Waltzer S, Beigi M, Widmann M, Vogel C, Pleiss J, Müller M, Rother D, Pohl M. Tailoring theS-Selectivity of 2-Succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate Synthase (MenD) fromEscherichia coli. ChemCatChem 2013. [DOI: 10.1002/cctc.201300318] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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24
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A differential fluorescence-based genetic screen identifies Listeria monocytogenes determinants required for intracellular replication. J Bacteriol 2013; 195:3331-40. [PMID: 23687268 DOI: 10.1128/jb.00210-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Listeria monocytogenes is a Gram-positive, facultative intracellular pathogen capable of causing severe invasive disease with high mortality rates in humans. While previous studies have largely elucidated the bacterial and host cell mechanisms necessary for invasion, vacuolar escape, and subsequent cell-to-cell spread, the L. monocytogenes factors required for rapid replication within the restrictive environment of the host cell cytosol are poorly understood. In this report, we describe a differential fluorescence-based genetic screen utilizing fluorescence-activated cell sorting (FACS) and high-throughput microscopy to identify L. monocytogenes mutants defective in optimal intracellular replication. Bacteria harboring deletions within the identified gene menD or pepP were defective for growth in primary murine macrophages and plaque formation in monolayers of L2 fibroblasts, thus validating the ability of the screening method to identify intracellular replication-defective mutants. Genetic complementation of the menD and pepP deletion strains rescued the in vitro intracellular infection defects. Furthermore, the menD deletion strain displayed a general extracellular replication defect that could be complemented by growth under anaerobic conditions, while the intracellular growth defect of this strain could be complemented by the addition of exogenous menaquinone. As prior studies have indicated the importance of aerobic metabolism for L. monocytogenes infection, these findings provide further evidence for the importance of menaquinone and aerobic metabolism for L. monocytogenes pathogenesis. Lastly, both the menD and pepP deletion strains were attenuated during in vivo infection of mice. These findings demonstrate that the differential fluorescence-based screening approach provides a powerful tool for the identification of intracellular replication determinants in multiple bacterial systems.
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25
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The thiamine-dependent enzyme of the vitamin K biosynthesis catalyzes reductive C-N bond ligation between nitroarenes and α-ketoacids. Sci China Chem 2012. [DOI: 10.1007/s11426-012-4792-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Song H, Guo Z. Characterization of 1,4-dihydroxy-2-naphthoyl-coenzyme A synthase (MenB) in phylloquinone biosynthesis of Synechocystis sp. PCC 6803. Sci China Chem 2011. [DOI: 10.1007/s11426-011-4448-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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27
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Fang M, Macova A, Hanson KL, Kos J, Palmer DRJ. Using substrate analogues to probe the kinetic mechanism and active site of Escherichia coli MenD. Biochemistry 2011; 50:8712-21. [PMID: 21928762 DOI: 10.1021/bi201202n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
MenD catalyzes the thiamin diphosphate-dependent decarboxylative carboligation of α-ketoglutarate and isochorismate. The enzyme is essential for menaquinone biosynthesis in many bacteria and has been proposed to be an antibiotic target. The kinetic mechanism of this enzyme has not previously been demonstrated because of the limitations of the UV-based kinetic assay. We have reported the synthesis of an isochorismate analogue that acts as a substrate for MenD. The apparent weaker binding of this analogue is advantageous in that it allows accurate kinetic experiments at substrate concentrations near K(m). Using this substrate in concert with the dead-end inhibitor methyl succinylphosphonate, an analogue of α-ketoglutarate, we show that MenD follows a ping-pong kinetic mechanism. Using both the natural and synthetic substrates, we have measured the effects of 12 mutations of residues at the active site. The results give experimental support to previous models and hypotheses and allow observations unavailable using only the natural substrate.
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Affiliation(s)
- Maohai Fang
- Department of Chemistry, University of Saskatchewan, Saskatoon, SK S7N 5C9, Canada
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28
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Dawson A, Fyfe PK, Gillet F, Hunter WN. Exploiting the high-resolution crystal structure of Staphylococcus aureus MenH to gain insight into enzyme activity. BMC STRUCTURAL BIOLOGY 2011; 11:19. [PMID: 21513522 PMCID: PMC3097144 DOI: 10.1186/1472-6807-11-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 04/22/2011] [Indexed: 11/23/2022]
Abstract
Background MenH (2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase) is a key enzyme in the biosynthesis of menaquinone, catalyzing an unusual 2,5-elimination of pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate. Results The crystal structure of Staphylococcus aureus MenH has been determined at 2 Å resolution. In the absence of a complex to inform on aspects of specificity a model of the enzyme-substrate complex has been used in conjunction with previously published kinetic analyses, site-directed mutagenesis studies and comparisons with orthologues to investigate the structure and reactivity of MenH. Conclusions The overall basic active site displays pronounced hydrophobic character on one side and these properties complement those of the substrate. A complex network of hydrogen bonds involving well-ordered water molecules serves to position key residues participating in the recognition of substrate and subsequent catalysis. We propose a proton shuttle mechanism, reliant on a catalytic triad consisting of Ser89, Asp216 and His243. The reaction is initiated by proton abstraction from the substrate by an activated Ser89. The propensity to form a conjugated system provides the driving force for pyruvate elimination. During the elimination, a methylene group is converted to a methyl and we judge it likely that His243 provides a proton, previously acquired from Ser89 for that reduction. A conformational change of the protonated His243 may be encouraged by the presence of an anionic intermediate in the active site.
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Affiliation(s)
- Alice Dawson
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
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