1
|
Machado TFG, da Silva RG. Employing deuterium kinetic isotope effects to uncover the mechanism of (R)-3-hydroxybutyrate dehydrogenase. Methods Enzymol 2023; 685:225-240. [PMID: 37245903 DOI: 10.1016/bs.mie.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Short-chain dehydrogenases/reductases (SDR) form a large enzyme superfamily playing important roles in health and disease. Furthermore, they are useful tools in biocatalysis. Unveiling the nature of the transition state for hydride transfer is a crucial undertaking toward defining the physicochemical underpinnings of catalysis by SDR enzymes, including possible contributions from quantum mechanical tunneling. Primary deuterium kinetic isotope effects can uncover the contribution from chemistry to the rate-limiting step and potentially provide detailed information on the hydride-transfer transition state in SDR-catalyzed reactions. For the latter, however, one needs to determine the intrinsic isotope effect: that which would be measured if hydride transfer were rate determining. Alas, as is the case for many other enzymatic reactions, those catalyzed by SDRs are often limited by the rate of isotope-insensitive steps, such as product release and conformational changes, which masks the expression of the intrinsic isotope effect. This can be overcome by the powerful yet underexplored method of Palfey and Fagan via which intrinsic kinetic isotope effects can be extracted from pre-steady-state kinetics data. SDRs are ideal systems to which this method can be applied. We have employed this approach to elucidate the transition states for hydride transfer catalyzed by NADH-dependent cold- and warm-adapted (R)-3-hydroxybutyrate dehydrogenase. Experimental conditions which simplify the analysis are discussed.
Collapse
Affiliation(s)
- Teresa F G Machado
- School of Chemistry, Biomedical Sciences Research Complex, University of St Andrews, Fife, United Kingdom
| | - Rafael G da Silva
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, Fife, United Kingdom.
| |
Collapse
|
2
|
Aygün C, Kocer S, Danış Ö, Cubuk S, Mutlu O. Heterologous expression, purification, and partial characterisation of the apicoplast protein 3-oxoacyl-[acyl-carrier-protein] reductase from Toxoplasma gondii. Protein Expr Purif 2023; 202:106187. [PMID: 36216219 DOI: 10.1016/j.pep.2022.106187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/02/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022]
Abstract
Recombinant expression and purification of proteins have become a staple of modern drug discovery as it enables more precise in vitro analyses of drug targets, which may help obtain biochemical and biophysical parameters of a known enzyme and even uncover unknown characteristics indicative of novel enzymatic functions. Such information is often necessary to prepare adequate screening assays and drug-discovery experiments in general. Toxoplasma gondii is an obligate protozoan parasite that is a member of the phylum Apicomplexa, can develop several neuro-degenerative symptoms and, in specific cases, certain death for human hosts. Its relict non-photosynthetic plastid, the apicoplast, harbours a unique de novo long-chain fatty acid synthesis pathway of a prokaryotic character, FASII. The FASII pathway shows plasticity and, is essential for many intracellular and membranal components, along with fatty acid uptake via salvaging from the host, therefore, its disruption causes parasite death. TgFabG, a FASII enzyme responsible for a single reduction step in the pathway, was recombinantly expressed, purified and biochemically and biophysically characterised in this study. The bioengineering hurdle of expressing the recombinant gene of a eukaryotic, signal peptide-containing protein in a prokaryotic system was overcome for the apicomplexan enzyme TgFabG, by truncating the N-terminal signal peptide. TgFabG was ultimately recombinantly produced in a plasmid expression vector from its 1131 base pair gene, purified as 260 and 272 amino acid proteins using a hexahistidine (6 × Histag) affinity chromatography and its biochemical (enzyme activity and kinetics) and biophysical characteristics were analysed in vitro.
Collapse
Affiliation(s)
- Can Aygün
- Marmara University, Faculty of Arts and Sciences, Department of Biology, 34722, Istanbul, Turkey
| | - Sinem Kocer
- Istanbul Yeni Yüzyıl University, Faculty of Pharmacy, Department of Pharmaceutical Biotechnology, 34010, Istanbul, Turkey
| | - Özkan Danış
- Marmara University, Faculty of Arts and Sciences, Department of Chemistry, 34722, Istanbul, Turkey
| | - Soner Cubuk
- Marmara University, Faculty of Arts and Sciences, Department of Chemistry, 34722, Istanbul, Turkey
| | - Ozal Mutlu
- Marmara University, Faculty of Arts and Sciences, Department of Biology, 34722, Istanbul, Turkey.
| |
Collapse
|
3
|
Machado TFG, Purg M, Åqvist J, da Silva RG. Transition States for Psychrophilic and Mesophilic ( R)-3-Hydroxybutyrate Dehydrogenase-Catalyzed Hydride Transfer at Sub-zero Temperatures. Biochemistry 2021; 60:2186-2194. [PMID: 34190541 DOI: 10.1021/acs.biochem.1c00322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
(R)-3-Hydroxybutyrate dehydrogenase (HBDH) catalyzes the NADH-dependent reduction of 3-oxocarboxylates to (R)-3-hydroxycarboxylates. The active sites of a pair of cold- and warm-adapted HBDHs are identical except for a single residue, yet kinetics evaluated at -5, 0, and 5 °C show a much higher steady-state rate constant (kcat) for the cold-adapted than for the warm-adapted HBDH. Intriguingly, single-turnover rate constants (kSTO) are strikingly similar between the two orthologues. Psychrophilic HBDH primary deuterium kinetic isotope effects on kcat (Dkcat) and kSTO (DkSTO) decrease at lower temperatures, suggesting more efficient hydride transfer relative to other steps as the temperature decreases. However, mesophilic HBDH Dkcat and DkSTO are generally temperature-independent. The DkSTO data allowed calculation of intrinsic primary deuterium kinetic isotope effects. Intrinsic isotope effects of 4.2 and 3.9 for cold- and warm-adapted HBDH, respectively, at 5 °C, supported by quantum mechanics/molecular mechanics calculations, point to a late transition state for both orthologues. Conversely, intrinsic isotope effects of 5.7 and 3.1 for cold- and warm-adapted HBDH, respectively, at -5 °C indicate the transition state becomes nearly symmetric for the psychrophilic enzyme, but more asymmetric for the mesophilic enzyme. His-to-Asn and Asn-to-His mutations in the psychrophilic and mesophilic HBDH active sites, respectively, swap the single active-site position where these orthologues diverge. At 5 °C, the His-to-Asn mutation in psychrophilic HBDH decreases Dkcat to 3.1, suggesting a decrease in transition-state symmetry, while the His-to-Asn mutation in mesophilic HBDH increases Dkcat to 4.4, indicating an increase in transition-state symmetry. Hence, temperature adaptation and a single divergent active-site residue may influence transition-state geometry in HBDHs.
Collapse
Affiliation(s)
- Teresa F G Machado
- School of Chemistry, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Miha Purg
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Rafael G da Silva
- School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| |
Collapse
|
4
|
Machado TFG, Purg M, McMahon SA, Read BJ, Oehler V, Åqvist J, Gloster TM, da Silva RG. Dissecting the Mechanism of ( R)-3-Hydroxybutyrate Dehydrogenase by Kinetic Isotope Effects, Protein Crystallography, and Computational Chemistry. ACS Catal 2020; 10:15019-15032. [PMID: 33391858 PMCID: PMC7773212 DOI: 10.1021/acscatal.0c04736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/24/2020] [Indexed: 12/21/2022]
Abstract
The enzyme (R)-3-hydroxybutyrate dehydrogenase (HBDH) catalyzes the enantioselective reduction of 3-oxocarboxylates to (R)-3-hydroxycarboxylates, the monomeric precursors of biodegradable polyesters. Despite its application in asymmetric reduction, which prompted several engineering attempts of this enzyme, the order of chemical events in the active site, their contributions to limit the reaction rate, and interactions between the enzyme and non-native 3-oxocarboxylates have not been explored. Here, a combination of kinetic isotope effects, protein crystallography, and quantum mechanics/molecular mechanics (QM/MM) calculations were employed to dissect the HBDH mechanism. Initial velocity patterns and primary deuterium kinetic isotope effects establish a steady-state ordered kinetic mechanism for acetoacetate reduction by a psychrophilic and a mesophilic HBDH, where hydride transfer is not rate limiting. Primary deuterium kinetic isotope effects on the reduction of 3-oxovalerate indicate that hydride transfer becomes more rate limiting with this non-native substrate. Solvent and multiple deuterium kinetic isotope effects suggest hydride and proton transfers occur in the same transition state. Crystal structures were solved for both enzymes complexed to NAD+:acetoacetate and NAD+:3-oxovalerate, illustrating the structural basis for the stereochemistry of the 3-hydroxycarboxylate products. QM/MM calculations using the crystal structures as a starting point predicted a higher activation energy for 3-oxovalerate reduction catalyzed by the mesophilic HBDH, in agreement with the higher reaction rate observed experimentally for the psychrophilic orthologue. Both transition states show concerted, albeit not synchronous, proton and hydride transfers to 3-oxovalerate. Setting the MM partial charges to zero results in identical reaction activation energies with both orthologues, suggesting the difference in activation energy between the reactions catalyzed by cold- and warm-adapted HBDHs arises from differential electrostatic stabilization of the transition state. Mutagenesis and phylogenetic analysis reveal the catalytic importance of His150 and Asn145 in the respective orthologues.
Collapse
Affiliation(s)
- Teresa F G Machado
- School of Chemistry and School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom.,School of Chemistry and School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Miha Purg
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, Uppsala SE-751 24, Sweden
| | - Stephen A McMahon
- School of Chemistry and School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Benjamin J Read
- School of Chemistry and School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Verena Oehler
- School of Chemistry and School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, Uppsala SE-751 24, Sweden
| | - Tracey M Gloster
- School of Chemistry and School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Rafael G da Silva
- School of Chemistry and School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| |
Collapse
|
5
|
Faïon L, Djaout K, Frita R, Pintiala C, Cantrelle FX, Moune M, Vandeputte A, Bourbiaux K, Piveteau C, Herledan A, Biela A, Leroux F, Kremer L, Blaise M, Tanina A, Wintjens R, Hanoulle X, Déprez B, Willand N, Baulard AR, Flipo M. Discovery of the first Mycobacterium tuberculosis MabA (FabG1) inhibitors through a fragment-based screening. Eur J Med Chem 2020; 200:112440. [PMID: 32505086 DOI: 10.1016/j.ejmech.2020.112440] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 12/15/2022]
Abstract
Mycobacterium tuberculosis (M.tb), the etiologic agent of tuberculosis, remains the leading cause of death from a single infectious agent worldwide. The emergence of drug-resistant M.tb strains stresses the need for drugs acting on new targets. Mycolic acids are very long chain fatty acids playing an essential role in the architecture and permeability of the mycobacterial cell wall. Their biosynthesis involves two fatty acid synthase (FAS) systems. Among the four enzymes (MabA, HadAB/BC, InhA and KasA/B) of the FAS-II cycle, MabA (FabG1) remains the only one for which specific inhibitors have not been reported yet. The development of a new LC-MS/MS based enzymatic assay allowed the screening of a 1280 fragment-library and led to the discovery of the first small molecules that inhibit MabA activity. A fragment from the anthranilic acid series was optimized into more potent inhibitors and their binding to MabA was confirmed by 19F ligand-observed NMR experiments.
Collapse
Affiliation(s)
- Léo Faïon
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Kamel Djaout
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Rosangela Frita
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Catalin Pintiala
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Francois-Xavier Cantrelle
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000, Lille, France; CNRS, ERL9002 - Integrative Structural Biology, F-59000, Lille, France
| | - Martin Moune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Alexandre Vandeputte
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Kevin Bourbiaux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Alexandre Biela
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, 34293, Montpellier, France; INSERM, Institut de Recherche en Infectiologie de Montpellier, Montpellier, France
| | - Mickael Blaise
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, 34293, Montpellier, France
| | - Abdalkarim Tanina
- Unité Microbiologie, Chimie Bioorganique et Macromoléculaire (CP206/04), Département RD3, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050, Brussels, Belgium
| | - René Wintjens
- Unité Microbiologie, Chimie Bioorganique et Macromoléculaire (CP206/04), Département RD3, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050, Brussels, Belgium
| | - Xavier Hanoulle
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000, Lille, France; CNRS, ERL9002 - Integrative Structural Biology, F-59000, Lille, France
| | - Benoit Déprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Alain R Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France.
| |
Collapse
|
6
|
Inverse Solvent Isotope Effects in Enzyme-Catalyzed Reactions. Molecules 2020; 25:molecules25081933. [PMID: 32326332 PMCID: PMC7221790 DOI: 10.3390/molecules25081933] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/14/2020] [Accepted: 04/20/2020] [Indexed: 11/17/2022] Open
Abstract
Solvent isotope effects have long been used as a mechanistic tool for determining enzyme mechanisms. Most commonly, macroscopic rate constants such as kcat and kcat/Km are found to decrease when the reaction is performed in D2O for a variety of reasons including the transfer of protons. Under certain circumstances, these constants are found to increase, in what is termed an inverse solvent kinetic isotope effect (SKIE), which can be a diagnostic mechanistic feature. Generally, these phenomena can be attributed to an inverse solvent equilibrium isotope effect on a rapid equilibrium preceding the rate-limiting step(s). This review surveys inverse SKIEs in enzyme-catalyzed reactions by assessing their underlying origins in common mechanistic themes. Case studies for each category are presented, and the mechanistic implications are put into context. It is hoped that readers may find the illustrative examples valuable in planning and interpreting solvent isotope effect experiments.
Collapse
|
7
|
Machado TFG, Gloster TM, da Silva RG. Linear Eyring Plots Conceal a Change in the Rate-Limiting Step in an Enzyme Reaction. Biochemistry 2018; 57:6757-6761. [PMID: 30472832 PMCID: PMC6300308 DOI: 10.1021/acs.biochem.8b01099] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
The temperature dependence
of psychrophilic and mesophilic (R)-3-hydroxybutyrate
dehydrogenase steady-state rates yields
nonlinear and linear Eyring plots, respectively. Solvent viscosity
effects and multiple- and single-turnover pre-steady-state kinetics
demonstrate that while product release is rate-limiting at high temperatures
for the psychrophilic enzyme, either interconversion between enzyme–substrate
and enzyme–product complexes or a step prior to it limits the
rate at low temperatures. Unexpectedly, a similar change in the rate-limiting
step is observed with the mesophilic enzyme, where a step prior to
chemistry becomes rate-limiting at low temperatures. This observation
may have implications for past and future interpretations of temperature–rate
profiles.
Collapse
|
8
|
Dissecting the Structural Elements for the Activation of β-Ketoacyl-(Acyl Carrier Protein) Reductase from Vibrio cholerae. J Bacteriol 2015; 198:463-76. [PMID: 26553852 DOI: 10.1128/jb.00360-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 11/03/2015] [Indexed: 01/22/2023] Open
Abstract
UNLABELLED β-Ketoacyl-(acyl carrier protein) reductase (FabG) catalyzes the key reductive reaction in the elongation cycle of fatty acid synthesis (FAS), which is a vital metabolic pathway in bacteria and a promising target for new antibiotic development. The activation of the enzyme is usually linked to the formation of a catalytic triad and cofactor binding, and crystal structures of FabG from different organisms have been captured in either the active or inactive conformation. However, the structural elements which enable activation of FabG require further exploration. Here we report the findings of structural, enzymatic, and binding studies of the FabG protein found in the causative agent of cholera, Vibrio cholerae (vcFabG). vcFabG exists predominantly as a dimer in solution and is able to self-associate to form tetramers, which is the state seen in the crystal structure. The formation of the tetramer may be promoted by the presence of the cofactor NADP(H). The transition between the dimeric and tetrameric states of vcFabG is related to changes in the conformations of the α4/α5 helices on the dimer-dimer interface. Two glycine residues adjacent to the dimer interface (G92 and G141) are identified to be the hinge for the conformational changes, while the catalytic tyrosine (Y155) and a glutamine residue that forms hydrogen bonds to both loop β4-α4 and loop β5-α5 (Q152) stabilize the active conformation. The functions of the aforementioned residues were confirmed by binding and enzymatic assays for the corresponding mutants. IMPORTANCE This paper describes the results of structural, enzymatic, and binding studies of FabG from Vibrio cholerae (vcFabG). In this work, we dissected the structural elements responsible for the activation of vcFabG. The structural information provided here is essential for the development of antibiotics specifically targeting bacterial FabG, especially for the multidrug-resistant strains of V. cholerae.
Collapse
|
9
|
Patta PC, Martinelli LKB, Rotta M, Abbadi BL, Santos DS, Basso LA. Mode of action of recombinant hypoxanthine–guanine phosphoribosyltransferase from Mycobacterium tuberculosis. RSC Adv 2015. [DOI: 10.1039/c5ra14918e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Homodimeric Mycobacterium tuberculosis HGPRT follows a sequential compulsory ordered enzyme mechanism.
Collapse
Affiliation(s)
- Paulo C. Patta
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre
- Brazil
| | - Leonardo K. B. Martinelli
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre
- Brazil
| | - Mariane Rotta
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre
- Brazil
| | - Bruno L. Abbadi
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre
- Brazil
| | - Diogenes S. Santos
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre
- Brazil
| | - Luiz A. Basso
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre
- Brazil
| |
Collapse
|
10
|
3-oxoacyl-ACP reductase from Schistosoma japonicum: integrated in silico-in vitro strategy for discovering antischistosomal lead compounds. PLoS One 2013; 8:e64984. [PMID: 23762275 PMCID: PMC3676400 DOI: 10.1371/journal.pone.0064984] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 04/18/2013] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Schistosomiasis is a disease caused by parasitic worms and more than 200 million people are infected worldwide. The emergence of resistance to the most commonly used drug, praziquantel (PZQ), makes the development of novel drugs an urgent task. 3-oxoacyl-ACP reductase (OAR), a key enzyme involved in the fatty acid synthesis pathway, has been identified as a potential drug target against many pathogenic organisms. However, no research on Schistosoma japonicum OAR (SjOAR) has been reported. The characterization of the SjOAR protein will provide new strategies for screening antischistosomal drugs that target SjOAR. METHODOLOGY/PRINCIPAL FINDINGS After cloning the SjOAR gene, recombinant SjOAR protein was purified and assayed for enzymatic activity. The tertiary structure of SjOAR was obtained by homology modeling and 27 inhibitor candidates were identified from 14,400 compounds through molecular docking based on the structure. All of these compounds were confirmed to be able to bind to the SjOAR protein by BIAcore analysis. Two compounds exhibited strong antischistosomal activity and inhibitory effects on the enzymatic activity of SjOAR. In contrast, these two compounds showed relatively low toxicity towards host cells. CONCLUSIONS/SIGNIFICANCE The work presented here shows the feasibility of isolation of new antischistosomal compounds using a combination of virtual screening and experimental validation. Based on this strategy, we successfully identified 2 compounds that target SjOAR with strong antischistosomal activity but relatively low cytotoxicity to host cells.
Collapse
|
11
|
Crystal structure of hexanoyl-CoA bound to β-ketoacyl reductase FabG4 of Mycobacterium tuberculosis. Biochem J 2013; 450:127-39. [PMID: 23163771 DOI: 10.1042/bj20121107] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
FabGs, or β-oxoacyl reductases, are involved in fatty acid synthesis. The reaction entails NADPH/NADH-mediated conversion of β-oxoacyl-ACP (acyl-carrier protein) into β-hydroxyacyl-ACP. HMwFabGs (high-molecular-weight FabG) form a phylogenetically separate group of FabG enzymes. FabG4, an HMwFabG from Mycobacterium tuberculosis, contains two distinct domains, an N-terminal 'flavodoxintype' domain and a C-terminal oxoreductase domain. The catalytically active C-terminal domain utilizes NADH to reduce β-oxoacyl-CoA to β-hydroxyacyl-CoA. In the present study the crystal structures of the FabG4-NADH binary complex and the FabG4-NAD+-hexanoyl-CoA ternary complex have been determined to understand the substrate specificity and catalytic mechanism of FabG4. This is the first report to demonstrate how FabG4 interacts with its coenzyme NADH and hexanoyl-CoA that mimics an elongating fattyacyl chain covalently linked with CoA. Structural analysis shows that the binding of hexanoyl-CoA within the active site cavity of FabG significantly differs from that of the C16 fattyacyl substrate bound to mycobacterial FabI [InhA (enoyl-ACP reductase)]. The ternary complex reveals that both loop I and loop II interact with the phosphopantetheine moiety of CoA or ACP to align the covalently linked fattyacyl substrate near the active site. Structural data ACP inhibition studies indicate that FabG4 can accept both CoA- and ACP-based fattyacyl substrates. We have also shown that in the FabG4 dimer Arg146 and Arg445 of one monomer interact with the C-terminus of the second monomer to play pivotal role in substrate association and catalysis.
Collapse
|
12
|
Inhibitors of fatty acid synthesis in prokaryotes and eukaryotes as anti-infective, anticancer and anti-obesity drugs. Future Med Chem 2012; 4:1113-51. [PMID: 22709254 DOI: 10.4155/fmc.12.62] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
There is a large range of diseases, such diabetes and cancer, which are connected to abnormal fatty acid metabolism in human cells. Therefore, inhibitors of human fatty acid synthase have great potential to manage or treat these diseases. In prokaryotes, fatty acid synthesis is important for signaling, as well as providing starting materials for the synthesis of phospholipids, which are required for the formation of the cell membrane. Recently, there has been renewed interest in the development of new molecules that target bacterial fatty acid synthases for the treatment of bacterial diseases. In this review, we look at the differences and similarities between fatty acid synthesis in humans and bacteria and highlight various small molecules that have been shown to inhibit either the mammalian or bacterial fatty acid synthase or both.
Collapse
|
13
|
Rosado LA, Caceres RA, de Azevedo WF, Basso LA, Santos DS. Role of Serine140 in the mode of action of Mycobacterium tuberculosis β-ketoacyl-ACP Reductase (MabA). BMC Res Notes 2012; 5:526. [PMID: 23006410 PMCID: PMC3519566 DOI: 10.1186/1756-0500-5-526] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 09/14/2012] [Indexed: 11/10/2022] Open
Abstract
Background Tuberculosis (TB) still remains one of the most deadly infectious diseases in the world. Mycobacterium tuberculosis β-ketoacyl-ACP Reductase (MabA) is a member of the fatty acid elongation system type II, providing precursors of mycolic acids that are essential to the bacterial cell growth and survival. MabA has been shown to be essential for M. tuberculosis survival and to play a role in intracellular signal transduction of bacilli. Findings Here we describe site-directed mutagenesis, recombinant protein expression and purification, steady-state kinetics, fluorescence spectroscopy, and molecular modeling for S140T and S140A mutant MabA enzymes. No enzyme activity could be detected for S140T and S140A. Although the S140T protein showed impaired NADPH binding, the S140A mutant could bind to NADPH. Computational predictions for NADPH binding affinity to WT, S140T and S140A MabA proteins were consistent with fluorescence spectroscopy data. Conclusions The results suggest that the main role of the S140 side chain of MabA is in catalysis. The S140 side chain appears to also play an indirect role in NADPH binding. Interestingly, NADPH titrations curves shifted from sigmoidal for WT to hyperbolic for S140A, suggesting that the S140 residue may play a role in displacing the pre-existing equilibrium between two forms of MabA in solution. The results here reported provide a better understanding of the mode of action of MabA that should be useful to guide the rational (function-based) design of inhibitors of MabA enzyme activity which, hopefully, could be used as lead compounds with anti-TB action.
Collapse
Affiliation(s)
- Leonardo A Rosado
- Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Pontifícia Universidade Católica do Rio Grande do Sul, Av. Ipiranga 6681, Porto Alegre, RS 90619-900, Brazil
| | | | | | | | | |
Collapse
|
14
|
Hou J, Wojciechowska K, Zheng H, Chruszcz M, Cooper DR, Cymborowski M, Skarina T, Gordon E, Luo H, Savchenko A, Minor W. Structure of a short-chain dehydrogenase/reductase from Bacillus anthracis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:632-7. [PMID: 22684058 PMCID: PMC3370898 DOI: 10.1107/s1744309112017939] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 04/22/2012] [Indexed: 11/10/2022]
Abstract
The crystal structure of a short-chain dehydrogenase/reductase from Bacillus anthracis strain `Ames Ancestor' complexed with NADP has been determined and refined to 1.87 Å resolution. The structure of the enzyme consists of a Rossmann fold composed of seven parallel β-strands sandwiched by three α-helices on each side. An NADP molecule from an endogenous source is bound in the conserved binding pocket in the syn conformation. The loop region responsible for binding another substrate forms two perpendicular short helices connected by a sharp turn.
Collapse
Affiliation(s)
- Jing Hou
- Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - Kamila Wojciechowska
- Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA
| | - Heping Zheng
- Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - Maksymilian Chruszcz
- Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - David R. Cooper
- Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - Marcin Cymborowski
- Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - Tatiana Skarina
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario, Canada
| | - Elena Gordon
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario, Canada
| | - Haibin Luo
- Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| | - Alexei Savchenko
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario, Canada
| | - Wladek Minor
- Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Jordan Hall, Room 4223, Charlottesville, VA 22908, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), USA
| |
Collapse
|
15
|
Kinetic mechanism of 3-ketoacyl-(acyl-carrier-protein) reductase from Synechococcus sp. strain PCC 7942: A useful enzyme for the production of chiral alcohols. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.molcatb.2010.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
16
|
de Carvalho LPS, Ling Y, Shen C, Warren JD, Rhee KY. On the chemical mechanism of succinic semialdehyde dehydrogenase (GabD1) from Mycobacterium tuberculosis. Arch Biochem Biophys 2011; 509:90-9. [PMID: 21303655 DOI: 10.1016/j.abb.2011.01.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 01/30/2011] [Accepted: 01/31/2011] [Indexed: 02/06/2023]
Abstract
Succinic semialdehyde dehydrogenases (SSADHs) are ubiquitous enzymes that catalyze the NAD(P)+-coupled oxidation of succinic semialdehyde (SSA) to succinate, the last step of the γ-aminobutyrate shunt. Mycobacterium tuberculosis encodes two paralogous SSADHs (gabD1 and gabD2). Here, we describe the first mechanistic characterization of GabD1, using steady-state kinetics, pH-rate profiles, ¹H NMR, and kinetic isotope effects. Our results confirmed SSA and NADP+ as substrates and demonstrated that a divalent metal, such as Mg²+, linearizes the time course. pH-rate studies failed to identify any ionizable groups with pK(a) between 5.5 and 10 involved in substrate binding or rate-limiting chemistry. Primary deuterium, solvent and multiple kinetic isotope effects revealed that nucleophilic addition to SSA is very fast, followed by a modestly rate-limiting hydride transfer and fast thioester hydrolysis. Proton inventory studies revealed that a single proton is associated with the solvent-sensitive rate-limiting step. Together, these results suggest that product dissociation and/or conformational changes linked to it are rate-limiting. Using structural information for the human homolog enzyme and ¹H NMR, we further established that nucleophilic attack takes place at the Si face of SSA, generating a thiohemiacetal with S stereochemistry. Deuteride transfer to the Pro-R position in NADP+ generates the thioester intermediate and [4A-²H, 4B-¹H] NADPH. A chemical mechanism based on these data and the structural information available is proposed.
Collapse
Affiliation(s)
- Luiz Pedro S de Carvalho
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, 1300 York Ave. New York, NY 10065, USA.
| | | | | | | | | |
Collapse
|
17
|
Martinelli LKB, Ducati RG, Rosado LA, Breda A, Selbach BP, Santos DS, Basso LA. Recombinant Escherichia coli GMP reductase: kinetic, catalytic and chemical mechanisms, and thermodynamics of enzyme-ligand binary complex formation. MOLECULAR BIOSYSTEMS 2011; 7:1289-305. [PMID: 21298178 DOI: 10.1039/c0mb00245c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Guanosine monophosphate (GMP) reductase catalyzes the reductive deamination of GMP to inosine monophosphate (IMP). GMP reductase plays an important role in the conversion of nucleoside and nucleotide derivatives of guanine to adenine nucleotides. In addition, as a member of the purine salvage pathway, it also participates in the reutilization of free intracellular bases. Here we present cloning, expression and purification of Escherichia coli guaC-encoded GMP reductase to determine its kinetic mechanism, as well as chemical and thermodynamic features of this reaction. Initial velocity studies and isothermal titration calorimetry demonstrated that GMP reductase follows an ordered bi-bi kinetic mechanism, in which GMP binds first to the enzyme followed by NADPH binding, and NADP(+) dissociates first followed by IMP release. The isothermal titration calorimetry also showed that GMP and IMP binding are thermodynamically favorable processes. The pH-rate profiles showed groups with apparent pK values of 6.6 and 9.6 involved in catalysis, and pK values of 7.1 and 8.6 important to GMP binding, and a pK value of 6.2 important for NADPH binding. Primary deuterium kinetic isotope effects demonstrated that hydride transfer contributes to the rate-limiting step, whereas solvent kinetic isotope effects arise from a single protonic site that plays a modest role in catalysis. Multiple isotope effects suggest that protonation and hydride transfer steps take place in the same transition state, lending support to a concerted mechanism. Pre-steady-state kinetic data suggest that product release does not contribute to the rate-limiting step of the reaction catalyzed by E. coli GMP reductase.
Collapse
Affiliation(s)
- Leonardo Krás Borges Martinelli
- Centro de Pesquisas em Biologia Molecular e Funcional, Instituto Nacional de Ciência e Tecnologia em Tuberculose, Pontifícia Universidade Católica do Rio Grande do Sul, 6681/92-A Av Ipiranga, 90619-900 Porto Alegre, RS, Brazil
| | | | | | | | | | | | | |
Collapse
|
18
|
Czekster CM, Vandemeulebroucke A, Blanchard JS. Kinetic and chemical mechanism of the dihydrofolate reductase from Mycobacterium tuberculosis. Biochemistry 2010; 50:367-75. [PMID: 21138249 DOI: 10.1021/bi1016843] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Dihydrofolate reductase from Mycobacterium tuberculosis (MtDHFR) catalyzes the NAD(P)-dependent reduction of dihydrofolate, yielding NAD(P)(+) and tetrahydrofolate, the primary one-carbon unit carrier in biology. Tetrahydrofolate needs to be recycled so that reactions involved in dTMP synthesis and purine metabolism are maintained. In this work, we report the kinetic characterization of the MtDHFR. This enzyme has a sequential steady-state random kinetic mechanism, probably with a preferred pathway with NADPH binding first. A pK(a) value for an enzymic acid of approximately 7.0 was identified from the pH dependence of V, and the analysis of the primary kinetic isotope effects revealed that the hydride transfer step is at least partly rate-limiting throughout the pH range analyzed. Additionally, solvent and multiple kinetic isotope effects were determined and analyzed, and equilibrium isotope effects were measured on the equilibrium constant. (D(2)O)V and (D(2)O)V/K([4R-4-(2)H]NADH) were slightly inverse at pH 6.0, and inverse values for (D(2)O)V([4R-4-(2)H]NADH) and (D(2)O)V/K([4R-4-(2)H]NADH) suggested that a pre-equilibrium protonation is occurring before the hydride transfer step, indicating a stepwise mechanism for proton and hydride transfer. The same value was obtained for (D)k(H) at pH 5.5 and 7.5, reaffirming the rate-limiting nature of the hydride transfer step. A chemical mechanism is proposed on the basis of the results obtained here.
Collapse
Affiliation(s)
- Clarissa M Czekster
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | | | | |
Collapse
|
19
|
Slessor KE, Stok JE, Cavaignac SM, Hawkes DB, Ghasemi Y, De Voss JJ. Cineole biodegradation: molecular cloning, expression and characterisation of (1R)-6beta-hydroxycineole dehydrogenase from Citrobacter braakii. Bioorg Chem 2009; 38:81-6. [PMID: 20089292 DOI: 10.1016/j.bioorg.2009.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Revised: 12/04/2009] [Accepted: 12/04/2009] [Indexed: 11/16/2022]
Abstract
The first steps in the biodegradation of 1,8-cineole involve the introduction of an alcohol and its subsequent oxidation to a ketone. In Citrobacter braakii, cytochrome P450(cin) has previously been demonstrated to perform the first oxidation to produce (1R)-6beta-hydroxycineole. In this study, we have cloned cinD from C. braakii and expressed the gene product, which displays significant homology to a number of short-chain alcohol dehydrogenases. It was demonstrated that the gene product of cinD exhibits (1R)-6beta-hydroxycineole dehydrogenase activity, the second step in the degradation of 1,8-cineole. All four isomers of 6-hydroxycineole were examined but only (1R)-6beta-hydroxycineole was converted to (1R)-6-ketocineole. The (1R)-6beta-hydroxycineole dehydrogenase exhibited a strict requirement for NAD(H), with no reaction observed in the presence of NADP(H). The enzyme also catalyses the reverse reaction, reducing (1R)-6-ketocineole to (1R)-6beta-hydroxycineole. During this study the N-terminal His-tag used to assist protein purification was found to interfere with NAD(H) binding and lower enzyme activity. This could be recovered by the addition of Ni(2+) ions or proteolytic removal of the His-tag.
Collapse
Affiliation(s)
- Kate E Slessor
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Brisbane QLD 4072, Australia
| | | | | | | | | | | |
Collapse
|
20
|
Mycobacterium tuberculosis beta-ketoacyl-ACP reductase: alpha-secondary kinetic isotope effects and kinetic and equilibrium mechanisms of substrate binding. Arch Biochem Biophys 2007; 471:1-10. [PMID: 18155153 DOI: 10.1016/j.abb.2007.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Accepted: 12/05/2007] [Indexed: 11/22/2022]
Abstract
Beta-ketoacyl-ACP reductase catalyzes the NADPH-dependent reduction of beta-ketoacyl-acyl carrier protein to generate beta-hydroxyacyl-acyl carrier protein and NADP+, the second step of the fatty acid elongation system type II of bacteria, plants, and apicomplexan organisms. Here, a modified and more efficient purification protocol is reported for recombinant Mycobacterium tuberculosis beta-ketoacyl-ACP reductase (MabA). The increase in alpha-secondary deuterium kinetic isotope effect values measured at pH 10 as compared to those obtained at pH 7 points to isotope- and pH-sensitive steps occurring concomitantly. Equilibrium and kinetic fluorescence studies demonstrate positive cooperativity in binding of NADPH to MabA, with two forms of free enzyme in solution. Equilibrium dialysis shows no cooperativity in acetoacetyl-CoA binding to the enzyme. Moreover, modest affinity loss occurs when the substrates bind to the monomer as compared to the dimer of MabA. A mechanism of substrate binding to MabA is proposed on the basis of the experimental data.
Collapse
|