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Bin X, Pawelek PD. Evidence of isochorismate channeling between the Escherichia coli enterobactin biosynthetic enzymes EntC and EntB. Protein Sci 2024; 33:e5122. [PMID: 39031458 PMCID: PMC11258883 DOI: 10.1002/pro.5122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/21/2024] [Accepted: 07/10/2024] [Indexed: 07/22/2024]
Abstract
Enterobactin is a high-affinity iron chelator produced and secreted by Escherichia coli and Salmonella typhimurium to scavenge scarce extracellular Fe3+ as a micronutrient. EntC and EntB are the first two enzymes in the enterobactin biosynthetic pathway. Isochorismate, produced by EntC, is a substrate for EntB isochorismatase. By using a competing isochorismate-consuming enzyme (the E. coli SEPHCHC synthase MenD), we found in a coupled assay that residual EntB isochorismatase activity decreased as a function of increasing MenD concentration. In the presence of excess MenD, EntB isochorismatase activity was observed to decrease by 84%, indicative of partial EntC-EntB channeling (16%) of isochorismate. Furthermore, addition of glycerol to the assay resulted in an increase of residual EntB isochorismatase activity to approximately 25% while in the presence of excess MenD. These experimental outcomes supported the existence of a substrate channeling surface identified in a previously reported protein-docking model of the EntC-EntB complex. Two positively charged EntB residues (K21 and R196) that were predicted to electrostatically guide negatively charged isochorismate between the EntC and EntB active sites were mutagenized to determine their effects on substrate channeling. The EntB variants K21D and R196D exhibited a near complete loss of isochorismatase activity, likely due to electrostatic repulsion of the negatively charged isochorismate substrate. Variants K21A, R196A, and K21A/R196A retained partial EntB isochorismatase activity in the absence of EntC; in the presence of EntC, isochorismatase activity in all variants increased to near wild-type levels. The MenD competition assay of the variants revealed that while K21A channeled isochorismate as efficiently as wild-type EntB (~ 15%), the variants K21A/R196A and R196A exhibited an approximately 5-fold loss in observed channeling efficiency (~3%). Taken together, these results demonstrate that partial substrate channeling occurs between EntC and EntB via a leaky electrostatic tunnel formed upon dynamic EntC-EntB complex formation and that EntB R196 plays an essential role in isochorismate channeling.
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Affiliation(s)
- Xue Bin
- Department of Chemistry and BiochemistryConcordia UniversityMontrealQuebecCanada
| | - Peter D. Pawelek
- Department of Chemistry and BiochemistryConcordia UniversityMontrealQuebecCanada
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Fries A, Mazzaferro LS, Bisel P, Hubrich F, Andexer JN, Müller M. Biosynthesis of Menaquinone in E. coli: Identification of an Elusive Isomer of SEPHCHC. Chembiochem 2022; 23:e202200181. [PMID: 35901288 PMCID: PMC9544450 DOI: 10.1002/cbic.202200181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/10/2022] [Indexed: 11/10/2022]
Abstract
In the biosynthesis of menaquinone in bacteria, the thiamine diphosphate-dependent enzyme MenD catalyzes the decarboxylative carboligation of α-ketoglutarate and isochorismate to (1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxycyclohex-3-ene-1-carboxylate (SEPHCHC). The regioisomer of SEPHCHC, namely (1R,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxycyclohex-2-ene-1-carboxylate (iso-SEPHCHC), has been considered as a possible product, however, its existence has been doubtful due to a spontaneous elimination of pyruvate from SEPHCHC to 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC). In this work, the regioisomer iso-SEPHCHC was distinguished from SEPHCHC by liquid chromatography-tandem mass spectrometry. Iso-SEPHCHC was purified and identified by NMR spectroscopy. Just as SEPHCHC remained hidden as a MenD product for more than two decades, its regioisomer iso-SEPHCHC has remained until now.
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Affiliation(s)
- Alexander Fries
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany.,Present address: INCITAP-CONICET, Departamento de Química, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de La Pampa, Av. Uruguay 151, 6300, Santa Rosa, La Pampa, Argentina
| | - Laura S Mazzaferro
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany.,Present address: INCITAP-CONICET, Departamento de Química, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de La Pampa, Av. Uruguay 151, 6300, Santa Rosa, La Pampa, Argentina
| | - Philippe Bisel
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Florian Hubrich
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany.,Present address: ETH Zurich, Institute of Microbiology, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Jennifer N Andexer
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104, Freiburg, Germany
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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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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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5
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Extended substrate range of thiamine diphosphate-dependent MenD enzyme by coupling of two C–C-bonding reactions. Appl Microbiol Biotechnol 2018; 102:8359-8372. [DOI: 10.1007/s00253-018-9259-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 07/17/2018] [Accepted: 07/18/2018] [Indexed: 01/29/2023]
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Bitok JK, Lemetre C, Ternei MA, Brady SF. Identification of biosynthetic gene clusters from metagenomic libraries using PPTase complementation in a Streptomyces host. FEMS Microbiol Lett 2018; 364:3983257. [PMID: 28817927 DOI: 10.1093/femsle/fnx155] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/19/2017] [Indexed: 01/08/2023] Open
Abstract
The majority of environmental bacteria are not readily cultured in the lab, leaving the natural products they make inaccessible using culture-dependent discovery methods. Cloning and heterologous expression of DNA extracted from environmental samples (environmental DNA, eDNA) provides a means of circumventing this discovery bottleneck. To facilitate the identification of clones containing biosynthetic gene clusters, we developed a model heterologous expression reporter strain Streptomyces albus::bpsA ΔPPTase. This strain carries a 4΄-phosphopantetheinyl transferase (PPTase)-dependent blue pigment synthase A gene, bpsA, in a PPTase deletion background. eDNA clones that express a functional PPTase restore production of the blue pigment, indigoidine. As PPTase genes often occur in biosynthetic gene clusters (BGCs), indigoidine production can be used to identify eDNA clones containing BGCs. We screened a soil eDNA library hosted in S. albus::bpsA ΔPPTase and identified clones containing non-ribosomal peptide synthetase (NRPS), polyketide synthase (PKS) and mixed NRPS/PKS biosynthetic gene clusters. One NRPS gene cluster was shown to confer the production of myxochelin A to S. albus::bpsA ΔPPTase.
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Affiliation(s)
- J Kipchirchir Bitok
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Christophe Lemetre
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Melinda A Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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Aleku GA, Nowicka B, Turner NJ. Biocatalytic Potential of Enzymes Involved in the Biosynthesis of Isoprenoid Quinones. ChemCatChem 2017. [DOI: 10.1002/cctc.201700685] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Godwin A. Aleku
- School of Chemistry and Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Beatrycze Nowicka
- Department of Plant Physiology and Biochemistry; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Gronostajowa 7 30-387 Krakow Poland
| | - Nicholas J. Turner
- School of Chemistry and Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
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Quin MB, Wallin KK, Zhang G, Schmidt-Dannert C. Spatial organization of multi-enzyme biocatalytic cascades. Org Biomol Chem 2017; 15:4260-4271. [DOI: 10.1039/c7ob00391a] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multi-enzyme cascades provide a wealth of valuable chemicals. Efficiency of reaction schemes can be improved by spatial organization of biocatalysts. This review will highlight various methods of spatial organization of biocatalysts: fusion, immobilization, scaffolding and encapsulation.
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Affiliation(s)
- M. B. Quin
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - K. K. Wallin
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - G. Zhang
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - C. Schmidt-Dannert
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
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Hubrich F, Juneja P, Müller M, Diederichs K, Welte W, Andexer JN. Chorismatase Mechanisms Reveal Fundamentally Different Types of Reaction in a Single Conserved Protein Fold. J Am Chem Soc 2015; 137:11032-7. [DOI: 10.1021/jacs.5b05559] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Florian Hubrich
- Institute
of Pharmaceutical Sciences, University of Freiburg, Albertstr.
25, 79104 Freiburg, Germany
| | - Puneet Juneja
- Department
of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Michael Müller
- Institute
of Pharmaceutical Sciences, University of Freiburg, Albertstr.
25, 79104 Freiburg, Germany
| | - Kay Diederichs
- Department
of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Wolfram Welte
- Department
of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Jennifer N. Andexer
- Institute
of Pharmaceutical Sciences, University of Freiburg, Albertstr.
25, 79104 Freiburg, Germany
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