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Sastoque A, Triana S, Ehemann K, Suarez L, Restrepo S, Wösten H, de Cock H, Fernández-Niño M, González Barrios AF, Celis Ramírez AM. New Therapeutic Candidates for the Treatment of Malassezia pachydermatis -Associated Infections. Sci Rep 2020; 10:4860. [PMID: 32184419 PMCID: PMC7078309 DOI: 10.1038/s41598-020-61729-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/24/2020] [Indexed: 11/26/2022] Open
Abstract
The opportunistic pathogen Malassezia pachydermatis causes bloodstream infections in preterm infants or individuals with immunodeficiency disorders and has been associated with a broad spectrum of diseases in animals such as seborrheic dermatitis, external otitis and fungemia. The current approaches to treat these infections are failing as a consequence of their adverse effects, changes in susceptibility and antifungal resistance. Thus, the identification of novel therapeutic targets against M. pachydermatis infections are highly relevant. Here, Gene Essentiality Analysis and Flux Variability Analysis was applied to a previously reported M. pachydermatis metabolic network to identify enzymes that, when absent, negatively affect biomass production. Three novel therapeutic targets (i.e., homoserine dehydrogenase (MpHSD), homocitrate synthase (MpHCS) and saccharopine dehydrogenase (MpSDH)) were identified that are absent in humans. Notably, L-lysine was shown to be an inhibitor of the enzymatic activity of MpHCS and MpSDH at concentrations of 1 mM and 75 mM, respectively, while L-threonine (1 mM) inhibited MpHSD. Interestingly, L- lysine was also shown to inhibit M. pachydermatis growth during in vitro assays with reference strains and canine isolates, while it had a negligible cytotoxic activity on HEKa cells. Together, our findings form the bases for the development of novel treatments against M. pachydermatis infections.
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Affiliation(s)
- Angie Sastoque
- Instituto de Biotecnología (IBUN), Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, 11001, Colombia
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, 111711, Colombia
- Grupo de Diseño de Productos y Procesos (GDPP), Departamento de Ingeniería Química, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Sergio Triana
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, 111711, Colombia
- Grupo de Diseño de Productos y Procesos (GDPP), Departamento de Ingeniería Química, Universidad de los Andes, Bogotá, 111711, Colombia
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Kevin Ehemann
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Lina Suarez
- Grupo de Diseño de Productos y Procesos (GDPP), Departamento de Ingeniería Química, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Silvia Restrepo
- Laboratorio de Micología y Fitopatología (LAMFU), Departamento de Ingeniería Química, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Han Wösten
- Microbiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Hans de Cock
- Microbiology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Miguel Fernández-Niño
- Grupo de Diseño de Productos y Procesos (GDPP), Departamento de Ingeniería Química, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Andrés Fernando González Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), Departamento de Ingeniería Química, Universidad de los Andes, Bogotá, 111711, Colombia.
| | - Adriana Marcela Celis Ramírez
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, 111711, Colombia.
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Introduction of Glyoxylate Bypass Increases Hydrogen Gas Yield from Acetate and l-Glutamate in Rhodobacter sphaeroides. Appl Environ Microbiol 2019; 85:AEM.01873-18. [PMID: 30413472 DOI: 10.1128/aem.01873-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/05/2018] [Indexed: 11/20/2022] Open
Abstract
Rhodobacter sphaeroides produces hydrogen gas (H2) from organic compounds via nitrogenase under anaerobic-light conditions in the presence of poor nitrogen sources, such as l-glutamate. R. sphaeroides utilizes the ethylmalonyl-coenzyme A (EMC) pathway for acetate assimilation, but its H2 yield from acetate in the presence of l-glutamate has been reported to be low. In this study, the deletion of ccr encoding crotonyl-coenzyme A (crotonyl-CoA) carboxylase/reductase, a key enzyme for the EMC pathway in R. sphaeroides, revealed that the EMC pathway is essential for H2 production from acetate and l-glutamate but not for growth and acetate consumption in the presence of l-glutamate. We introduced a plasmid expressing aceBA from Rhodobacter capsulatus encoding two key enzymes for the glyoxylate bypass into R. sphaeroides, which resulted in a 64% increase in H2 production. However, compared with the wild-type strain expressing heterologous aceBA genes, the strain with aceBA introduced in the genetic background of an EMC pathway-disrupted mutant showed a lower H2 yield. These results indicate that a combination of the endogenous EMC pathway and a heterologously expressed glyoxylate bypass is beneficial for H2 production. In addition, introduction of the glyoxylate bypass into a polyhydroxybutyrate (PHB) biosynthesis-disrupted mutant resulted in a delay in growth along with H2 production, although its H2 yield was comparable to that of the wild-type strain expressing heterologous aceBA genes. These results suggest that PHB production is important for fitness to the culture during H2 production from acetate and l-glutamate when both acetate-assimilating pathways are present.IMPORTANCE As an alternative to fossil fuel, H2 is a promising renewable energy source. Although photofermentative H2 production from acetate is key to developing an efficient process of biohydrogen production from biomass-derived sugars, H2 yields from acetate and l-glutamate by R. sphaeroides have been reported to be low. In this study, we observed that in addition to the endogenous EMC pathway, heterologous expression of the glyoxylate bypass in R. sphaeroides markedly increased H2 yields from acetate and l-glutamate. Therefore, this study provides a novel strategy for improving H2 yields from acetate in the presence of l-glutamate and contributes to a clear understanding of acetate metabolism in R. sphaeroides during photofermentative H2 production.
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Gabriel I, Milewski S. Characterization of recombinant homocitrate synthase from Candida albicans. Protein Expr Purif 2015; 125:7-18. [PMID: 26363118 DOI: 10.1016/j.pep.2015.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/04/2015] [Accepted: 09/05/2015] [Indexed: 10/23/2022]
Abstract
LYS21 and LYS22 genes from Candida albicans encoding isoforms of homocitrate synthase (HCS), an enzyme catalyzing the first committed step in the l-lysine biosynthetic pathway, were cloned and expressed as N-oligoHistagged fusion proteins in Escherichia coli. The purified gene products revealed HCS activity, i.e. catalyzed the condensation of α-ketoglutarate with acetyl-coenzyme A to yield homocitrate. The recombinant enzymes were purified to homogeneity and characterized for their physical properties and substrate specificities. As determined by size-exclusion chromatography (SEC) and native page electrophoresis, both isoenzymes adopt multiple quaternary structures, with the homotetrameric one being the most abundant. The KM (acetyl-CoA)=0.8±0.15mM and KM (α-ketoglutarate)=0.113±0.02mM for His6CaLys21p and KM (acetyl-CoA)=0.48±0.09mM and KM (α-ketoglutarate)=0.152±0.03mM values for His6CaLys22p were determined. Both enzyme versions were inhibited by l-Lys, i.e. the end product of the α-aminoadipate pathway but Lys22p was more sensitive than Lys21p, with Ki (L-Lys)=128±8μM for His6CaLys21p and Ki (L-Lys)=4.37±0.68μM for His6CaLys22p. The isoforms of C. albicans HCS exhibited differential sensitivity to several l-Lys analogues. Most notably, dl-α-difluoromethyllysine strongly inhibited His6CaLys22p (IC50 32±3μM) but was not inhibitory at all towards His6CaLys21p. Differential sensitivity of recombinant C. albicans Δlys21/LYS22, LYS21/Δlys22 and Δlys21/Δlys22 mutant strains to lysine analog, 2-aminoethyl-l-cysteine and biochemical properties of homocitrate synthase isoforms suggest different roles of two HCS isoenzymes in α-aminoadipate pathway.
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Affiliation(s)
- Iwona Gabriel
- Department of Pharmaceutical Technology and Biochemistry, Gdansk University of Technology, 11/12 Narutowicza Str., 80-233 Gdansk, Poland.
| | - Sławomir Milewski
- Department of Pharmaceutical Technology and Biochemistry, Gdansk University of Technology, 11/12 Narutowicza Str., 80-233 Gdansk, Poland
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Zhang H, Ma H, Xie X, Ji J, Dong Y, Du Y, Tang W, Zheng X, Wang P, Zhang Z. Comparative proteomic analyses reveal that the regulators of G-protein signaling proteins regulate amino acid metabolism of the rice blast fungus Magnaporthe oryzae. Proteomics 2014; 14:2508-22. [DOI: 10.1002/pmic.201400173] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/22/2014] [Accepted: 09/15/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Haifeng Zhang
- Department of Plant Pathology; College of Plant Protection; Nanjing Agricultural University; Nanjing P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests; Ministry of Education; Nanjing P. R. China
| | - Hongyu Ma
- Department of Plant Pathology; College of Plant Protection; Nanjing Agricultural University; Nanjing P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests; Ministry of Education; Nanjing P. R. China
| | - Xin Xie
- Department of Plant Pathology; College of Plant Protection; Nanjing Agricultural University; Nanjing P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests; Ministry of Education; Nanjing P. R. China
| | - Jun Ji
- Department of Plant Pathology; College of Plant Protection; Nanjing Agricultural University; Nanjing P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests; Ministry of Education; Nanjing P. R. China
| | - Yanhan Dong
- Department of Plant Pathology; College of Plant Protection; Nanjing Agricultural University; Nanjing P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests; Ministry of Education; Nanjing P. R. China
| | - Yan Du
- Department of Plant Pathology; College of Plant Protection; Nanjing Agricultural University; Nanjing P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests; Ministry of Education; Nanjing P. R. China
| | - Wei Tang
- Department of Plant Pathology; College of Plant Protection; Nanjing Agricultural University; Nanjing P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests; Ministry of Education; Nanjing P. R. China
| | - Xiaobo Zheng
- Department of Plant Pathology; College of Plant Protection; Nanjing Agricultural University; Nanjing P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests; Ministry of Education; Nanjing P. R. China
| | - Ping Wang
- Department of Pediatrics; Louisiana State University Health Sciences Center; New Orleans LA USA
| | - Zhengguang Zhang
- Department of Plant Pathology; College of Plant Protection; Nanjing Agricultural University; Nanjing P. R. China
- Key Laboratory of Integrated Management of Crop Diseases and Pests; Ministry of Education; Nanjing P. R. China
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Sheng X, Gao J, Liu Y, Liu C. Theoretical study on the proton shuttle mechanism of saccharopine dehydrogenase. J Mol Graph Model 2013; 44:17-25. [DOI: 10.1016/j.jmgm.2013.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 04/25/2013] [Accepted: 04/29/2013] [Indexed: 11/16/2022]
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Kumar VP, West AH, Cook PF. Kinetic and chemical mechanisms of homocitrate synthase from Thermus thermophilus. J Biol Chem 2011; 286:29428-29439. [PMID: 21733842 DOI: 10.1074/jbc.m111.246355] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The homocitrate synthase from Thermus thermophilus (TtHCS) is a metal-activated enzyme with either Mg(2+) or Mn(2+) capable of serving as the divalent cation. The enzyme exhibits a sequential kinetic mechanism. The mechanism is steady state ordered with α-ketoglutarate (α-Kg) binding prior to acetyl-CoA (AcCoA) with Mn(2+), whereas it is steady state random with Mg(2+), suggesting a difference in the competence of the E·Mn·α-Kg·AcCoA and E·Mg·α-Kg·AcCoA complexes. The mechanism is supported by product and dead-end inhibition studies. The primary isotope effect obtained with deuterioacetylCoA (AcCoA-d(3)) in the presence of Mg(2+) is unity (value 1.0) at low concentrations of AcCoA, whereas it is 2 at high concentrations of AcCoA. Data suggest the presence of a slow conformational change induced by binding of AcCoA that accompanies deprotonation of the methyl group of AcCoA. The solvent kinetic deuterium isotope effect is also unity at low AcCoA, but is 1.7 at high AcCoA, consistent with the proposed slow conformational change. The maximum rate is pH independent with either Mg(2+) or Mn(2+) as the divalent metal ion, whereas V/K(α-Kg) (with Mn(2+)) decreases at low and high pH giving pK values of about 6.5 and 8.0. Lysine is a competitive inhibitor that binds to the active site of TtHCS, and shares some of the same binding determinants as α-Kg. Lysine binding exhibits negative cooperativity, indicating cross-talk between the two monomers of the TtHCS dimer. Data are discussed in terms of the overall mechanism of TtHCS.
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Affiliation(s)
- Vidya Prasanna Kumar
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Ann H West
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Paul F Cook
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019.
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Bulfer SL, McQuade TJ, Larsen MJ, Trievel RC. Application of a high-throughput fluorescent acetyltransferase assay to identify inhibitors of homocitrate synthase. Anal Biochem 2011; 410:133-40. [PMID: 21073853 PMCID: PMC3115995 DOI: 10.1016/j.ab.2010.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 11/02/2010] [Accepted: 11/03/2010] [Indexed: 01/06/2023]
Abstract
Homocitrate synthase (HCS) catalyzes the first step of l-lysine biosynthesis in fungi by condensing acetyl-coenzyme A and 2-oxoglutarate to form 3R-homocitrate and coenzyme A. Due to its conservation in pathogenic fungi, HCS has been proposed as a candidate for antifungal drug design. Here we report the development and validation of a robust fluorescent assay for HCS that is amenable to high-throughput screening for inhibitors in vitro. Using this assay, Schizosaccharomyces pombe HCS was screened against a diverse library of approximately 41,000 small molecules. Following confirmation, counter screens, and dose-response analysis, we prioritized more than 100 compounds for further in vitro and in vivo analysis. This assay can be readily adapted to screen for small molecule modulators of other acyl-CoA-dependent acyltransferases or enzymes that generate a product with a free sulfhydryl group, including histone acetyltransferases, aminoglycoside N-acetyltransferases, thioesterases, and enzymes involved in lipid metabolism.
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Affiliation(s)
- Stacie L Bulfer
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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Designing a Highly Efficient Chemical Chaperone System Using Chitosan-Coated Alginate. Protein J 2010; 29:343-9. [DOI: 10.1007/s10930-010-9258-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Evaluation of lysine biosynthesis as an antifungal drug target: biochemical characterization of Aspergillus fumigatus homocitrate synthase and virulence studies. EUKARYOTIC CELL 2010; 9:878-93. [PMID: 20363898 DOI: 10.1128/ec.00020-10] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Aspergillus fumigatus is the main cause of severe invasive aspergillosis. To combat this life-threatening infection, only limited numbers of antifungals are available. The fungal alpha-aminoadipate pathway, which is essential for lysine biosynthesis, has been suggested as a potential antifungal drug target. Here we reanalyzed the role of this pathway for establishment of invasive aspergillosis in murine models. We selected the first pathway-specific enzyme, homocitrate synthase (HcsA), for biochemical characterization and for study of its role in virulence. A. fumigatus HcsA was specific for the substrates acetyl-coenzyme A (acetyl-CoA) and alpha-ketoglutarate, and its activity was independent of any metal ions. In contrast to the case for other homocitrate synthases, enzymatic activity was hardly affected by lysine and gene expression increased under conditions of lysine supplementation. An hcsA deletion mutant was lysine auxotrophic and unable to germinate on unhydrolyzed proteins given as a sole nutrient source. However, the addition of partially purified A. fumigatus proteases restored growth, confirming the importance of free lysine to complement auxotrophy. In contrast to lysine-auxotrophic mutants from other fungal species, the mutant grew on blood and serum, indicating the existence of high-affinity lysine uptake systems. In agreement, although the virulence of the mutant was strongly attenuated in murine models of bronchopulmonary aspergillosis, virulence was partially restored by lysine supplementation via the drinking water. Additionally, in contrast to the case for attenuated pulmonary infections, the mutant retained full virulence when injected intravenously. Therefore, we concluded that inhibition of fungal lysine biosynthesis, at least for disseminating invasive aspergillosis, does not appear to provide a suitable target for new antifungals.
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Rezaii N, Khodagholi F. Evaluation of Chaperone-like Activity of Alginate: Microcapsule and Water-soluble Forms. Protein J 2009; 28:124-30. [DOI: 10.1007/s10930-009-9172-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Quezada H, Aranda C, DeLuna A, Hernández H, Calcagno ML, Marín-Hernández Á, González A. Specialization of the paralogue LYS21 determines lysine biosynthesis under respiratory metabolism in Saccharomyces cerevisiae. MICROBIOLOGY-SGM 2008; 154:1656-1667. [PMID: 18524920 DOI: 10.1099/mic.0.2008/017103-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In the yeast Saccharomyces cerevisiae, the first committed step of the lysine biosynthetic pathway is catalysed by two homocitrate synthases encoded by LYS20 and LYS21. We undertook a study of the duplicate homocitrate synthases to analyse whether their retention and presumable specialization have affected the efficiency of lysine biosynthesis in yeast. Our results show that during growth on ethanol, homocitrate is mainly synthesized through Lys21p, while under fermentative metabolism, Lys20p and Lys21p play redundant roles. Furthermore, results presented in this paper indicate that, in contrast to that which had been found for Lys20p, lysine is a strong allosteric inhibitor of Lys21p (K(i) 0.053 mM), which, in addition, induces positive co-operativity for alpha-ketoglutarate (alpha-KG) binding. Differential lysine inhibition and modulation by alpha-KG of the two isozymes, and the regulation of the intracellular amount of the two isoforms, give rise to an exquisite regulatory system, which balances the rate at which alpha-KG is diverted to lysine biosynthesis or to other metabolic pathways. It can thus be concluded that retention and further biochemical specialization of the LYS20- and LYS21-encoded enzymes with partially overlapping roles contributed to the acquisition of facultative metabolism.
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Affiliation(s)
- Héctor Quezada
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México DF 04510, México
| | - Cristina Aranda
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México DF 04510, México
| | - Alexander DeLuna
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México DF 04510, México
| | - Hugo Hernández
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México DF 04510, México
| | - Mario L Calcagno
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México DF 04510, México
| | - Álvaro Marín-Hernández
- Instituto Nacional de Cardiología, Departamento de Bioquímica, Tlalpan, México DF, México
| | - Alicia González
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México DF 04510, México
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Qian J, Khandogin J, West AH, Cook PF. Evidence for a Catalytic Dyad in the Active Site of Homocitrate Synthase from Saccharomyces cerevisiae. Biochemistry 2008; 47:6851-8. [DOI: 10.1021/bi800087k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jinghua Qian
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, Oklahoma 73019
| | - Jana Khandogin
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, Oklahoma 73019
| | - Ann H. West
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, Oklahoma 73019
| | - Paul F. Cook
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, Oklahoma 73019
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Burk DL, Hwang J, Kwok E, Marrone L, Goodfellow V, Dmitrienko GI, Berghuis AM. Structural studies of the final enzyme in the alpha-aminoadipate pathway-saccharopine dehydrogenase from Saccharomyces cerevisiae. J Mol Biol 2007; 373:745-54. [PMID: 17854830 DOI: 10.1016/j.jmb.2007.08.044] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2007] [Revised: 08/03/2007] [Accepted: 08/19/2007] [Indexed: 11/25/2022]
Abstract
The 1.64 A structure of the apoenzyme form of saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae shows the enzyme to be composed of two domains with similar dinucleotide binding folds with a deep cleft at the interface. The structure reveals homology to alanine dehydrogenase, despite low primary sequence similarity. A model of the ternary complex of SDH, NAD, and saccharopine identifies residues Lys77 and Glu122 as potentially important for substrate binding and/or catalysis, consistent with a proton shuttle mechanism. Furthermore, the model suggests that a conformational change is required for catalysis and that residues Lys99 and Asp281 may be instrumental in mediating this change. Analysis of the crystal structure in the context of other homologous enzymes from pathogenic fungi and human sources sheds light into the suitability of SDH as a target for antimicrobial drug development.
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Affiliation(s)
- D L Burk
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada H3A 1A4
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Lin Y, Alguindigue SS, Volkman J, Nicholas KM, West AH, Cook PF. Complete kinetic mechanism of homoisocitrate dehydrogenase from Saccharomyces cerevisiae. Biochemistry 2007; 46:890-8. [PMID: 17223711 PMCID: PMC2527762 DOI: 10.1021/bi062067q] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The kinetic mechanism of homoisocitrate dehydrogenase from Saccharomyces cerevisiae was determined using initial velocity studies in the absence and presence of product and dead end inhibitors in both reaction directions. Data suggest a steady state random kinetic mechanism. The dissociation constant of the Mg-homoisocitrate complex (MgHIc) was estimated to be 11 +/- 2 mM as measured using Mg2+ as a shift reagent. Initial velocity data indicate the MgHIc complex is the reactant in the direction of oxidative decarboxylation, while in the reverse reaction direction, the enzyme likely binds uncomplexed Mg2+ and alpha-ketoadipate. Curvature is observed in the double-reciprocal plots for product inhibition by NADH and the dead-end inhibition by 3-acetylpyridine adenine dinucleotide phosphate when MgHIc is the varied substrate. At low concentrations of MgHIc, the inhibition by both nucleotides is competitive, but as the MgHIc concentration increases, the inhibition changes to uncompetitive, consistent with a steady state random mechanism with preferred binding of MgHIc before NAD. Release of product is preferred and ordered with respect to CO2, alpha-ketoadipate, and NADH. Isocitrate is a slow substrate with a rate (V/E(t)) 216-fold slower than that measured with HIc. In contrast to HIc, the uncomplexed form of isocitrate and Mg2+ bind to the enzyme. The kinetic mechanism in the direction of oxidative decarboxylation of isocitrate, on the basis of initial velocity studies in the absence and presence of dead-end inhibitors, suggests random addition of NAD and isocitrate with Mg2+ binding before isocitrate in rapid equilibrium, and the mechanism approximates rapid equilibrium random. The Keq for the overall reaction measured directly using the change in NADH as a probe is 0.45 M.
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Affiliation(s)
| | | | | | | | | | - Paul F. Cook
- Corresponding author: E-mail: Tel: 405−325−4581 Fax: 405−325−7182
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Abstract
We have studied the catalytic efficiency of acetylcholinesterase (AChE) in various solutions with ion-disturbed water structure to explore the role that the water structure plays in the substrate-enzyme encounter. The extent of water structuring in the different aqueous solutions was determined by near-infrared spectroscopy. The influence of water structure on the degree of solvation and on the intramolecular mobility of AChE was investigated for different aqueous ionic solutions by small-angle x-ray scattering technique and depolarization fluorescence spectroscopy. It was found that the encounter process between AChE and acetylthiocholine was promoted in solutions with less structured water. In these solutions it was also found that AChE is less solvated coinciding with higher intramolecular mobility. The found experimental results suggest that the water structure may influence the substrate-enzyme encounter process by diminishing the AChE solvation shell and may help diffusion of the substrate through the gorge by enhancing the intramolecular mobility of AChE.
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Affiliation(s)
- Angela S F Ramos
- Max-Planck-Institut für biophysikalische Chemie, Abteilung Spektroskopie und Photochemische Kinetik-Strukturdynamik (bio)chemischer Systeme, 37077 Göttingen, Germany
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Andi B, Cook PF. Regulatory mechanism of histidine-tagged homocitrate synthase from Saccharomyces cerevisiae. II. Theory. J Biol Chem 2005; 280:31633-40. [PMID: 15897191 DOI: 10.1074/jbc.m502847200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this study, rate equations that predict the regulatory kinetic behavior of homocitrate synthase were derived, and simulation of the predicted behavior was carried out over a range of values for the kinetic parameters. The data obtained allow application of the resulting expressions to enzyme systems that exhibit activation and inhibition as a result of the interaction of effectors at multiple sites in the free enzyme. Homocitrate synthase was used as an example in terms of its activation by Na+ binding to the active enzyme conformer at an allosteric site, inhibition by binding to the active site, and inhibition by lysine binding to the less active enzyme conformer.
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Affiliation(s)
- Babak Andi
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
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Andi B, West AH, Cook PF. Regulatory mechanism of histidine-tagged homocitrate synthase from Saccharomyces cerevisiae. I. Kinetic studies. J Biol Chem 2005; 280:31624-32. [PMID: 15897192 DOI: 10.1074/jbc.m502846200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Homocitrate synthase (HCS) catalyzes one of the regulated steps of the alpha-aminoadipate pathway for lysine biosynthesis in fungi. The kinetic mechanism of regulation of HCS from Saccharomyces cerevisiae by Na+ and the feedback inhibitor lysine was studied by measuring the initial rate in the absence and presence of the effectors. The data suggest that Na+ is an activator at low concentrations and an inhibitor at high concentrations and that these effects occur as a result of the monovalent ion binding to two different sites in the free enzyme. Inhibition and activation by Na+ can occur simultaneously, with the net rate of the enzyme determined by Na+/K(iNa+) and Na+/K(act), where K(iNa+) and K(act) are the inhibition and activation constants, respectively. The inhibition by Na+ was eliminated at high concentrations of acetyl-CoA, the second substrate bound, but the activation remained. Fluorescence binding studies indicated that lysine bound with high affinity to its binding site as an inhibitor. The inhibition by lysine was competitive versus alpha-ketoglutarate and linear in the physiological range of lysine concentrations up to 5 mm. The effects of Na+ and lysine were independent of one another. A model is developed for regulation of HCS that takes into account all of the effects discussed above.
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Affiliation(s)
- Babak Andi
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
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Paju A, Kanger T, Pehk T, Eek M, Lopp M. A short enantioselective synthesis of homocitric acid-γ-lactone and 4-hydroxy-homocitric acid-γ-lactones. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.07.096] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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