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Mori M, Stelitano G, Gelain A, Pini E, Chiarelli LR, Sammartino JC, Poli G, Tuccinardi T, Beretta G, Porta A, Bellinzoni M, Villa S, Meneghetti F. Shedding X-ray Light on the Role of Magnesium in the Activity of Mycobacterium tuberculosis Salicylate Synthase (MbtI) for Drug Design. J Med Chem 2020; 63:7066-7080. [PMID: 32530281 PMCID: PMC8008425 DOI: 10.1021/acs.jmedchem.0c00373] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
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The
Mg2+-dependent Mycobacterium tuberculosis salicylate synthase (MbtI) is a key enzyme involved in the biosynthesis
of siderophores. Because iron is essential for the survival and pathogenicity
of the microorganism, this protein constitutes an attractive target
for antitubercular therapy, also considering the absence of homologous
enzymes in mammals. An extension of the structure–activity
relationships of our furan-based candidates allowed us to disclose
the most potent competitive inhibitor known to date (10, Ki = 4 μM), which also proved
effective on mycobacterial cultures. By structural studies, we characterized
its unexpected Mg2+-independent binding mode. We also investigated
the role of the Mg2+ cofactor in catalysis, analyzing the
first crystal structure of the MbtI–Mg2+–salicylate
ternary complex. Overall, these results pave the way for the development
of novel antituberculars through the rational design of improved MbtI
inhibitors.
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Affiliation(s)
- Matteo Mori
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Giovanni Stelitano
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via A. Ferrata 9, 27100 Pavia, Italy
| | - Arianna Gelain
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Elena Pini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Laurent R Chiarelli
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via A. Ferrata 9, 27100 Pavia, Italy
| | - José C Sammartino
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via A. Ferrata 9, 27100 Pavia, Italy
| | - Giulio Poli
- Dipartimento di Farmacia, Università di Pisa, via Bonanno Pisano 6, 56126 Pisa, Italy
| | - Tiziano Tuccinardi
- Dipartimento di Farmacia, Università di Pisa, via Bonanno Pisano 6, 56126 Pisa, Italy.,Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Giangiacomo Beretta
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, via G. Celoria 2, 20133 Milano, Italy
| | - Alessio Porta
- Dipartimento di Chimica, Università degli Studi di Pavia, via T. Taramelli 12, 27100 Pavia, Italy
| | - Marco Bellinzoni
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, F-75015 Paris, France
| | - Stefania Villa
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Fiorella Meneghetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
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2
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Frati F, de Groot F, Cerezo J, Santoro F, Cheng L, Faber R, Coriani S. Coupled cluster study of the x-ray absorption spectra of formaldehyde derivatives at the oxygen, carbon, and fluorine K-edges. J Chem Phys 2019. [DOI: 10.1063/1.5097650] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Federica Frati
- Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584 GC Utrecht, The Netherlands
| | - Frank de Groot
- Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584 GC Utrecht, The Netherlands
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM–CNR), Area della Ricerca del CNR, Via Moruzzi 1, I-56124 Pisa, Italy
| | - Lan Cheng
- Department of Chemistry, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rasmus Faber
- DTU Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
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3
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Theoretical study of the inhibition mechanism of human 20S proteasome by dihydroeponemycin. Eur J Med Chem 2019; 164:399-407. [DOI: 10.1016/j.ejmech.2018.12.062] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/12/2018] [Accepted: 12/24/2018] [Indexed: 01/10/2023]
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4
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von Cosel J, Cerezo J, Kern-Michler D, Neumann C, van Wilderen LJGW, Bredenbeck J, Santoro F, Burghardt I. Vibrationally resolved electronic spectra including vibrational pre-excitation: Theory and application to VIPER spectroscopy. J Chem Phys 2017; 147:164116. [DOI: 10.1063/1.4999455] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Jan von Cosel
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Javier Cerezo
- Departamento de Química Física, Universidad de Murcia, E-30071 Murcia, Spain
| | - Daniela Kern-Michler
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany
| | - Carsten Neumann
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany
| | | | - Jens Bredenbeck
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche–CNR, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), UOS di Pisa, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Irene Burghardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
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5
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Bordes I, Ruiz-Pernía JJ, Castillo R, Moliner V. A computational study of the phosphoryl transfer reaction between ATP and Dha in aqueous solution. Org Biomol Chem 2015; 13:10179-90. [PMID: 26303076 DOI: 10.1039/c5ob01079a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phosphoryl transfer reactions are ubiquitous in biology, being involved in processes ranging from energy and signal transduction to the replication genetic material. Dihydroxyacetone phosphate (Dha-P), an intermediate of the synthesis of pyruvate and a very important building block in nature, can be generated by converting free dihydroxyacetone (Dha) through the action of the dihydroxyacetone kinase enzyme. In this paper the reference uncatalyzed reaction in solution has been studied in order to define the foundations of the chemical reaction and to determine the most adequate computational method to describe this electronically complex reaction. In particular, the phosphorylation reaction mechanism between adenosine triphosphate (ATP) and Dha in aqueous solution has been studied by means of quantum mechanics/molecular mechanics (QM/MM) Molecular Dynamics (MD) simulations with the QM subset of atoms described with semi-empirical and DFT methods. The results appear to be strongly dependent on the level of calculation, which will have to be taken into account for future studies of the reaction catalyzed by enzymes. In particular, PM3/MM renders lower free energy barriers and a less endergonic process than AM1d/MM and PM6/MM methods. Nevertheless, the concerted pathway was not located with the former combination of potentials.
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Affiliation(s)
- I Bordes
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
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6
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Liu Z, Liu F, Aldrich CC. Stereocontrolled Synthesis of a Potential Transition-State Inhibitor of the Salicylate Synthase MbtI from Mycobacterium tuberculosis. J Org Chem 2015; 80:6545-52. [PMID: 26035083 DOI: 10.1021/acs.joc.5b00455] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mycobactins are small-molecule iron chelators (siderophores) produced by Mycobacterium tuberculosis (Mtb) for iron mobilization. The bifunctional salicylate synthase MbtI catalyzes the first step of mycobactin biosynthesis through the conversion of the primary metabolite chorismate into salicylic acid via isochorismate. We report the design, synthesis, and biochemical evaluation of an inhibitor based on the putative transition state (TS) for the isochorismatase partial reaction of MbtI. The inhibitor mimics the hypothesized charge buildup at C-4 of chorismate in the TS as well as C-O bond formation at C-6. Another important design element of the inhibitor is replacement of the labile pyruvate side chain in chorismate with a stable C-linked propionate isostere. We developed a stereocontrolled synthesis of the highly functionalized cyclohexene inhibitor that features an asymmetric aldol reaction using a titanium enolate, diastereoselective Grignard addition to a tert-butanesulfinyl aldimine, and ring closing olefin metathesis as key steps.
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Affiliation(s)
- Zheng Liu
- †Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Feng Liu
- †Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Courtney C Aldrich
- †Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, Minnesota 55455, United States
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7
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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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8
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Świderek K, Tuñón I, Moliner V, Bertran J. Protein Flexibility and Preorganization in the Design of Enzymes. The Kemp Elimination Catalyzed by HG3.17. ACS Catal 2015. [DOI: 10.1021/cs501904w] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Katarzyna Świderek
- Departament
de Química Física, Universitat de València, 46100 Burjasot, Spain
- Institute
of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - Iñaki Tuñón
- Departament
de Química Física, Universitat de València, 46100 Burjasot, Spain
| | - Vicent Moliner
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Joan Bertran
- Departament
de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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9
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Janata J, Kadlcik S, Koberska M, Ulanova D, Kamenik Z, Novak P, Kopecky J, Novotna J, Radojevic B, Plhackova K, Gazak R, Najmanova L. Lincosamide synthetase--a unique condensation system combining elements of nonribosomal peptide synthetase and mycothiol metabolism. PLoS One 2015; 10:e0118850. [PMID: 25741696 PMCID: PMC4351081 DOI: 10.1371/journal.pone.0118850] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 01/19/2015] [Indexed: 12/19/2022] Open
Abstract
In the biosynthesis of lincosamide antibiotics lincomycin and celesticetin, the amino acid and amino sugar units are linked by an amide bond. The respective condensing enzyme lincosamide synthetase (LS) is expected to be an unusual system combining nonribosomal peptide synthetase (NRPS) components with so far unknown amino sugar related activities. The biosynthetic gene cluster of celesticetin was sequenced and compared to the lincomycin one revealing putative LS coding ORFs shared in both clusters. Based on a bioassay and production profiles of S. lincolnensis strains with individually deleted putative LS coding genes, the proteins LmbC, D, E, F and V were assigned to LS function. Moreover, the newly recognized N-terminal domain of LmbN (LmbN-CP) was also assigned to LS as a NRPS carrier protein (CP). Surprisingly, the homologous CP coding sequence in celesticetin cluster is part of ccbZ gene adjacent to ccbN, the counterpart of lmbN, suggesting the gene rearrangement, evident also from still active internal translation start in lmbN, and indicating the direction of lincosamide biosynthesis evolution. The in vitro test with LmbN-CP, LmbC and the newly identified S. lincolnensis phosphopantetheinyl transferase Slp, confirmed the cooperation of the previously characterized NRPS A-domain LmbC with a holo-LmbN-CP in activation of a 4-propyl-L-proline precursor of lincomycin. This result completed the functional characterization of LS subunits resembling NRPS initiation module. Two of the four remaining putative LS subunits, LmbE/CcbE and LmbV/CcbV, exhibit low but significant homology to enzymes from the metabolism of mycothiol, the NRPS-independent system processing the amino sugar and amino acid units. The functions of particular LS subunits as well as cooperation of both NRPS-based and NRPS-independent LS blocks are discussed. The described condensing enzyme represents a unique hybrid system with overall composition quite dissimilar to any other known enzyme system.
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Affiliation(s)
- Jiri Janata
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Prague, Czech Republic
- * E-mail:
| | - Stanislav Kadlcik
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Prague, Czech Republic
| | - Marketa Koberska
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Prague, Czech Republic
| | - Dana Ulanova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Prague, Czech Republic
- Oceanography Section, Science Research Center, Kochi University, IMT-MEXT, Kohasu, Oko-cho, Nankoku, Kochi, 783–8505, Japan
| | - Zdenek Kamenik
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Prague, Czech Republic
| | - Petr Novak
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Prague, Czech Republic
| | - Jan Kopecky
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Prague, Czech Republic
| | - Jitka Novotna
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Prague, Czech Republic
| | - Bojana Radojevic
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Prague, Czech Republic
| | - Kamila Plhackova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Prague, Czech Republic
| | - Radek Gazak
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Prague, Czech Republic
| | - Lucie Najmanova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Prague, Czech Republic
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10
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Theoretical studies of the hydrolysis of antibiotics catalyzed by a metallo-β-lactamase. Arch Biochem Biophys 2015; 582:116-26. [PMID: 25622886 DOI: 10.1016/j.abb.2015.01.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 01/13/2015] [Accepted: 01/14/2015] [Indexed: 12/27/2022]
Abstract
In this paper, hybrid QM/MM molecular dynamics (MD) simulations have been performed to explore the mechanisms of hydrolysis of two antibiotics, Imipenen (IMI), an antibiotic belonging to the subgroup of carbapenems, and the Cefotaxime (CEF), a third-generation cephalosporin antibiotic, in the active site of a mono-nuclear β-lactamase, CphA from Aeromonas hydrophila. Significant different transition state structures are obtained for the hydrolysis of both antibiotics: while the TS of the CEF is an ionic species with negative charge on nitrogen, the IMI TS presents a tetrahedral-like character with negative charge on oxygen atom of the carbonyl group of the lactam ring. Thus, dramatic conformational changes can take place in the cavity of CphA to accommodate different substrates, which would be the origin of its substrate promiscuity. Since CphA shows only activity against carbapenem antibiotic, this study sheds some light into the origin of the selectivity of the different MbL and, as a consequence, into the discovery of specific and potent MβL inhibitors against a broad spectrum of bacterial pathogens. We have finally probed that a re-parametrization of semiempirical methods should be done to properly describe the behavior the metal cation in active site, Zn(2+), when used in QM/MM calculations.
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11
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Świderek K, Martí S, Moliner V. Theoretical Study of Primary Reaction of Pseudozyma antarctica Lipase B as the Starting Point To Understand Its Promiscuity. ACS Catal 2014. [DOI: 10.1021/cs401047k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Katarzyna Świderek
- Departament
de Química Física, Universitat de València, 46100 Burjassot, Spain
- Institute
of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - Sergio Martí
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
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12
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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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13
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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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14
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Duarte F, Amrein BA, Kamerlin SCL. Modeling catalytic promiscuity in the alkaline phosphatase superfamily. Phys Chem Chem Phys 2013; 15:11160-77. [PMID: 23728154 PMCID: PMC3693508 DOI: 10.1039/c3cp51179k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 05/02/2013] [Indexed: 12/19/2022]
Abstract
In recent years, it has become increasingly clear that promiscuity plays a key role in the evolution of new enzyme function. This finding has helped to elucidate fundamental aspects of molecular evolution. While there has been extensive experimental work on enzyme promiscuity, computational modeling of the chemical details of such promiscuity has traditionally fallen behind the advances in experimental studies, not least due to the nearly prohibitive computational cost involved in examining multiple substrates with multiple potential mechanisms and binding modes in atomic detail with a reasonable degree of accuracy. However, recent advances in both computational methodologies and power have allowed us to reach a stage in the field where we can start to overcome this problem, and molecular simulations can now provide accurate and efficient descriptions of complex biological systems with substantially less computational cost. This has led to significant advances in our understanding of enzyme function and evolution in a broader sense. Here, we will discuss currently available computational approaches that can allow us to probe the underlying molecular basis for enzyme specificity and selectivity, discussing the inherent strengths and weaknesses of each approach. As a case study, we will discuss recent computational work on different members of the alkaline phosphatase superfamily (AP) using a range of different approaches, showing the complementary insights they have provided. We have selected this particular superfamily, as it poses a number of significant challenges for theory, ranging from the complexity of the actual reaction mechanisms involved to the reliable modeling of the catalytic metal centers, as well as the very large system sizes. We will demonstrate that, through current advances in methodologies, computational tools can provide significant insight into the molecular basis for catalytic promiscuity, and, therefore, in turn, the mechanisms of protein functional evolution.
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Affiliation(s)
- Fernanda Duarte
- Uppsala University, Science for Life Laboratory (SciLifeLab), Cell and Molecular Biology, Uppsala, Sweden. ; ;
| | - Beat Anton Amrein
- Uppsala University, Science for Life Laboratory (SciLifeLab), Cell and Molecular Biology, Uppsala, Sweden. ; ;
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15
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Culbertson JE, Toney MD. Expression and characterization of PhzE from P. aeruginosa PAO1: aminodeoxyisochorismate synthase involved in pyocyanin and phenazine-1-carboxylate production. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:240-6. [PMID: 23099261 DOI: 10.1016/j.bbapap.2012.10.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Revised: 10/04/2012] [Accepted: 10/15/2012] [Indexed: 12/21/2022]
Abstract
PhzE from Pseudomonas aeruginosa catalyzes the first step in the biosynthesis of phenazine-1-carboxylic acid, pyocyanin, and other phenazines, which are virulence factors for Pseudomonas species. The reaction catalyzed converts chorismate into aminodeoxyisochorismate using ammonia supplied by a glutamine amidotransferase domain. It has structural and sequence homology to other chorismate-utilizing enzymes such as anthranilate synthase, isochorismate synthase, aminodeoxychorismate synthase, and salicylate synthase. Like these enzymes, it is Mg(2+) dependent and catalyzes a similar S(N)2" nucleophilic substitution reaction. PhzE catalyzes the addition of ammonia to C2 of chorismate, as does anthranilate synthase, yet unlike anthranilate synthase it does not catalyze elimination of pyruvate from enzyme-bound aminodeoxyisochorismate. Herein, the cloning of the phzE gene, high level expression of active enzyme in E. coli, purification, and kinetic characterization of the enzyme is presented, including temperature and pH dependence. Steady-state kinetics give K(chorismate)=20±4μM, K(Mg)(2+)=294±22μM, K(L-gln)=11±1mM, and k(cat)=2.2±0.2s(-1) for a random kinetic mechanism. PhzE can use NH(4)(+) as an alternative nucleophile, while Co(2+) and Mn(2+) are alternative divalent metals.
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Affiliation(s)
- Justin E Culbertson
- Department of Chemistry, University of California, Davis, Davis, CA 95616, USA
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