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Omori A, Sasaki S, Kikukawa T, Shimono K, Miyauchi S. Elucidation of a Thermodynamical Feature Attributed to Substrate Binding to the Prokaryotic H +/Oligopeptide Cotransporter YdgR with Calorimetric Analysis: The Substrate Binding Driven by the Change in Entropy Implies the Release of Bound Water Molecules from the Binding Pocket. Biochemistry 2023. [PMID: 37163674 DOI: 10.1021/acs.biochem.2c00673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Here, we have elucidated the substrate recognition mechanism by a prokaryotic H+/oligopeptide cotransporter, YdgR, using isothermal titration calorimetry. Under acidic conditions (pH 6.0), the binding of a dipeptide, Val-Ala, to YdgR elicited endothermic enthalpy, which compensated for the increase in entropy due to dipeptide binding. A series of dipeptides were used in the binding titration. The dipeptides represent Val-X and X-Val, where X is Ala, Ser, Val, Tyr, or Phe. Most dipeptides revealed endothermic enthalpy, which was completely compensated by the increase in entropy due to dipeptide binding. The change in enthalpy due to binding correlated well with the change in entropy, whereas the Gibbs free energy involved in the binding of the dipeptide to YdgR remained unchanged irrespective of dipeptide sequences, implying that the binding reaction was driven by entropy, that is, the release of bound water molecules in the binding pocket. It is also important to clarify that, based on the prediction of water molecules in the ligand-binding pocket of YdgR, the release of three bound water molecules in the putative substrate binding pocket occurred through binding to YdgR. In the comparison of Val-X and X-Val dipeptides, the N-terminal region of the binding pocket might contain more bound water molecules than the C-terminal region. In light of these findings, we suggest that bound water molecules might play an important role in substrate recognition and binding by YdgR.
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Affiliation(s)
- Akiko Omori
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Shotaro Sasaki
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Kazumi Shimono
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda Nishi-ku, Kumamoto 860-0082, Japan
| | - Seiji Miyauchi
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
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Qiao G, Li X, Li J, Zhang M, Shen Y, Zhao Z, Zhang Y, Qi Z, Chen P, Sun Y, Cang P, Liu P, Wangkahart E, Wang Z. An Eco-Friendly Conversion of Aquaculture Suspended Solid Wastes Into High-Quality Fish Food by Improving Poly-β-Hydroxybutyrate Production. Front Physiol 2022; 13:797625. [PMID: 35721543 PMCID: PMC9205610 DOI: 10.3389/fphys.2022.797625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 04/15/2022] [Indexed: 12/03/2022] Open
Abstract
The aquaculture industry is vital in providing a valuable protein food source for humans, but generates a huge amount of solid and dissolved wastes that pose great risks to the environment and aquaculture sustainability. Suspended solids (in short SS), one of the aquaculture wastes, are very difficult to be treated due to their high organic contents. The bioconversion from wastewater, food effluents, and activated sludge into poly-β-hydroxybutyrate (PHB) is a sustainable alternative to generate an additional income and could be highly attractive to the agricultural and environmental management firms. However, little is known about its potential application in aquaculture wastes. In the present study, we first determined that 7.2% of SS was PHB. Then, the production of PHB was increased two-fold by the optimal fermentation conditions of wheat bran and microbial cocktails at a C/N ratio of 12. Also, the PHB-enriched SS showed a higher total ammonia nitrogen removal rate. Importantly, we further demonstrated that the PHB-enriched SS as a feed could promote fish growth and up-regulate the expression of the immune-related genes. Our study developed an eco-friendly and simple approach to transforming problematic SS wastes into PHB-enriched high-quality food for omnivorous fish, which will increase the usage efficiency of SS and provide a cheaper diet for aquatic animals.
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Affiliation(s)
- Guo Qiao
- Yancheng Institute of Technology, Yancheng, China
| | - Xiaoxia Li
- Yancheng Institute of Technology, Yancheng, China.,School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Jun Li
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, Miami, FL, United States
| | | | - Yang Shen
- Yancheng Institute of Technology, Yancheng, China
| | - Zhigang Zhao
- Heilongjiang Provincial Key Laboratory of Cold Water Fish Germplasm Resources and Aquaculture, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Yichan Zhang
- Yancheng Institute of Technology, Yancheng, China
| | - Zhitao Qi
- Yancheng Institute of Technology, Yancheng, China
| | - Peng Chen
- Yancheng Institute of Technology, Yancheng, China
| | - Yuyu Sun
- Yancheng Institute of Technology, Yancheng, China
| | | | - Peng Liu
- Yantai Marine Economic Research Institute, Yantai, China
| | - Eakapol Wangkahart
- Laboratory of Fish Immunology and Nutrigenomics, Applied Animal and Aquatic Sciences Research Unit, Division of Fisheries, Faculty of Technology, Mahasarakham University, Maha Sarakham, Thailand
| | - Zisheng Wang
- Yancheng Institute of Technology, Yancheng, China
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Song C, Li Y, Ma W. ATP is not essential for cadaverine production by Escherichia coli whole-cell bioconversion. J Biotechnol 2022; 353:44-50. [PMID: 35660066 DOI: 10.1016/j.jbiotec.2022.05.014] [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: 06/22/2021] [Revised: 03/08/2022] [Accepted: 05/30/2022] [Indexed: 10/18/2022]
Abstract
ATP plays an essential role in the substrate/product transmembrane transportation during whole-cell bioconversion. This study aimed to address the impact of ATP upon cadaverine synthesis by whole-cell biocatalysts. The results showed no significant change in the ATP content (P = 0.625), and the specific cadaverine yield (P = 0.374) was observed in enzyme-catalyzed cadaverine synthesis with exogenous addition of ATP, indicating that the enzyme-catalyzed process does not require the participation of ATP. Furthermore, a whole-cell biocatalyst co-overexpressed methionine adenosyltransferase (MetK), lysine decarboxylase (CadA), and lysine/cadaverine antiporter (CadB) was constructed and used to investigate the effect of ATP deficiency on the cadaverine production by conversion of L-methionine and L-lysine, simultaneously. The results showed no significant difference (P = 0.585) in the specific cadaverine content between high and low levels of intracellular ATP. In addition, the intra- and extracellular cadaverine concentration and the ratio of ATP/ADP of whole-cell biocatalyst were determined. Results showed that the extracellular cadaverine concentration was much higher than the intracellular concentration, and no significant changes in ATP/ADP ratio during cadaverine synthesis. In contrast, an inhibition effect of the proton motive force (PMF) inhibitor carbonyl cyanide m-chlorophenylhydrazone (CCCP) on cadaverine production was detected. These findings strongly suggest that cadaverine transport in whole-cell biocatalysts was energized by PMF rather than ATP. Finally, a model was proposed to describe cadaverine's PMF-driven transport under different external pHs during whole-cell biocatalysis. This study is the first to experimentally confirm that the cadaverine production by Escherichia coli whole-cell bioconversion is independent of intracellular ATP, which helps guide the subsequent construction of biocatalysts and optimize transformation conditions.
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Affiliation(s)
- Chenbin Song
- Tianshui Engineering Research Center for Agricultural Products Deep Processing, College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui, 741001, China
| | - Yijing Li
- Tianshui Engineering Research Center for Agricultural Products Deep Processing, College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui, 741001, China
| | - Weichao Ma
- Tianshui Engineering Research Center for Agricultural Products Deep Processing, College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui, 741001, China.
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Waldeck-Weiermair M, Yadav S, Spyropoulos F, Krüger C, Pandey AK, Michel T. Dissecting in vivo and in vitro redox responses using chemogenetics. Free Radic Biol Med 2021; 177:360-369. [PMID: 34752919 PMCID: PMC8639655 DOI: 10.1016/j.freeradbiomed.2021.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/08/2021] [Accepted: 11/04/2021] [Indexed: 02/03/2023]
Abstract
Hydrogen peroxide (H2O2) is the most abundant reactive oxygen species (ROS) within mammalian cells. At low concentrations, H2O2 serves as a versatile cell signaling molecule that mediates vital physiological functions. Yet at higher concentrations, H2O2 can be a toxic molecule by promoting pathological oxidative stress in cells and tissues. Within normal cells, H2O2 is differentially distributed in a variety of subcellular locales. Moreover, many redox-active enzymes and their substrates are themselves differentially distributed within cells. Numerous reports have described the biological and biochemical consequences of adding exogenous H2O2 to cultured cells and tissues, but many of these observations are difficult to interpret: the effects of exogenous H2O2 do not necessarily replicate the cellular responses to endogenous H2O2. In recent years, chemogenetic approaches have been developed to dynamically regulate the abundance of H2O2 in specific subcellular locales. Chemogenetic approaches have been applied in multiple experimental systems, ranging from in vitro studies on the intracellular transport and metabolism of H2O2, all the way to in vivo studies that generate oxidative stress in specific organs in living animals. These chemogenetic approaches have exploited a yeast-derived d-amino acid oxidase (DAAO) that synthesizes H2O2 only in the presence of its d-amino acid substrate. DAAO can be targeted to various subcellular locales, and can be dynamically activated by the addition or withdrawal of its d-amino acid substrate. In addition, recent advances in the development of highly sensitive genetically encoded H2O2 biosensors are providing a better understanding of both physiological and pathological oxidative pathways. This review highlights several applications of DAAO as a chemogenetic tool across a wide range of biological systems, from analyses of subcellular H2O2 metabolism in cells to the development of new disease models caused by oxidative stress in vivo.
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Affiliation(s)
- Markus Waldeck-Weiermair
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA; Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010, Graz, Austria
| | - Shambhu Yadav
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Fotios Spyropoulos
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA; Department of Pediatric Newborn Medicine, Harvard Medical School, Brigham and Women's Hospital, 75 Francis Street, Boston, MA, USA
| | - Christina Krüger
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Arvind K Pandey
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Thomas Michel
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA.
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Abstract
We review the mechanisms responsible for amino acid homeostasis in Saccharomyces cerevisiae and other fungi. Amino acid homeostasis is essential for cell growth and survival. Hence, the de novo synthesis reactions, metabolic conversions, and transport of amino acids are tightly regulated. Regulation varies from nitrogen pool sensing to control by individual amino acids and takes place at the gene (transcription), protein (posttranslational modification and allostery), and vesicle (trafficking and endocytosis) levels. The pools of amino acids are controlled via import, export, and compartmentalization. In yeast, the majority of the amino acid transporters belong to the APC (amino acid-polyamine-organocation) superfamily, and the proteins couple the uphill transport of amino acids to the electrochemical proton gradient. Although high-resolution structures of yeast amino acid transporters are not available, homology models have been successfully exploited to determine and engineer the catalytic and regulatory functions of the proteins. This has led to a further understanding of the underlying mechanisms of amino acid sensing and subsequent downregulation of transport. Advances in optical microscopy have revealed a new level of regulation of yeast amino acid transporters, which involves membrane domain partitioning. The significance and the interrelationships of the latest discoveries on amino acid homeostasis are put in context.
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Affiliation(s)
- Liora Werber
- Department of Chemistry and the Institute of Nanotechnology; Bar-Ilan University; Ramat Gan Israel
| | - Yitzhak Mastai
- Department of Chemistry and the Institute of Nanotechnology; Bar-Ilan University; Ramat Gan Israel
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Bianchi F, Klooster JSV', Ruiz SJ, Luck K, Pols T, Urbatsch IL, Poolman B. Asymmetry in inward- and outward-affinity constant of transport explain unidirectional lysine flux in Saccharomyces cerevisiae. Sci Rep 2016; 6:31443. [PMID: 27550794 PMCID: PMC4993999 DOI: 10.1038/srep31443] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/20/2016] [Indexed: 02/01/2023] Open
Abstract
The import of basic amino acids in Saccharomyces cerevisiae has been reported to be unidirectional, which is not typical of how secondary transporters work. Since studies of energy coupling and transport kinetics are complicated in vivo, we purified the major lysine transporter (Lyp1) of yeast and reconstituted the protein into lipid vesicles. We show that the Michaelis constant (KM) of transport from out-to-in is well in the millimolar range and at least 3 to 4-orders of magnitude higher than that of transport in the opposite direction, disfavoring the efflux of solute via Lyp1. We also find that at low values of the proton motive force, the transport by Lyp1 is comparatively slow. We benchmarked the properties of eukaryotic Lyp1 to that of the prokaryotic homologue LysP and find that LysP has a similar KM for transport from in-to-out and out-to-in, consistent with rapid influx and efflux. We thus explain the previously described unidirectional nature of lysine transport in S. cerevisiae by the extraordinary kinetics of Lyp1 and provide a mechanism and rationale for previous observations. The high asymmetry in transport together with secondary storage in the vacuole allow the cell to accumulate basic amino acids to very high levels.
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Affiliation(s)
- Frans Bianchi
- Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Joury S van 't Klooster
- Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Stephanie J Ruiz
- Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Katja Luck
- Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Tjeerd Pols
- Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ina L Urbatsch
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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8
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Nie L, Grell E, Malviya VN, Xie H, Wang J, Michel H. Identification of the High-affinity Substrate-binding Site of the Multidrug and Toxic Compound Extrusion (MATE) Family Transporter from Pseudomonas stutzeri. J Biol Chem 2016; 291:15503-14. [PMID: 27235402 DOI: 10.1074/jbc.m116.728618] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Indexed: 01/05/2023] Open
Abstract
Multidrug and toxic compound extrusion (MATE) transporters exist in all three domains of life. They confer multidrug resistance by utilizing H(+) or Na(+) electrochemical gradients to extrude various drugs across the cell membranes. The substrate binding and the transport mechanism of MATE transporters is a fundamental process but so far not fully understood. Here we report a detailed substrate binding study of NorM_PS, a representative MATE transporter from Pseudomonas stutzeri Our results indicate that NorM_PS is a proton-dependent multidrug efflux transporter. Detailed binding studies between NorM_PS and 4',6-diamidino-2-phenylindole (DAPI) were performed by isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC), and spectrofluorometry. Two exothermic binding events were observed from ITC data, and the high-affinity event was directly correlated with the extrusion of DAPI. The affinities are about 1 μm and 0.1 mm for the high and low affinity binding, respectively. Based on our homology model of NorM_PS, variants with mutations of amino acids that are potentially involved in substrate binding, were constructed. By carrying out the functional characterization of these variants, the critical amino acid residues (Glu-257 and Asp-373) for high-affinity DAPI binding were determined. Taken together, our results suggest a new substrate-binding site for MATE transporters.
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Affiliation(s)
- Laiyin Nie
- From the Tianjin University, School of Chemical Engineering and Technology, State Key Laboratory for Chemical Engineering, Collaborative Innovation Center of Chemical Science and Chemical Engineering, 300072 Tianjin, China and the Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Ernst Grell
- the Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Viveka Nand Malviya
- the Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Hao Xie
- the Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
| | - Jingkang Wang
- From the Tianjin University, School of Chemical Engineering and Technology, State Key Laboratory for Chemical Engineering, Collaborative Innovation Center of Chemical Science and Chemical Engineering, 300072 Tianjin, China and
| | - Hartmut Michel
- the Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany
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Boudker O, Oh S. Isothermal titration calorimetry of ion-coupled membrane transporters. Methods 2015; 76:171-182. [PMID: 25676707 PMCID: PMC4912014 DOI: 10.1016/j.ymeth.2015.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 11/17/2022] Open
Abstract
Binding of ligands, ranging from proteins to ions, to membrane proteins is associated with absorption or release of heat that can be detected by isothermal titration calorimetry (ITC). Such measurements not only provide binding affinities but also afford direct access to thermodynamic parameters of binding--enthalpy, entropy and heat capacity. These parameters can be interpreted in a structural context, allow discrimination between different binding mechanisms and guide drug design. In this review, we introduce advantages and limitations of ITC as a methodology to study molecular interactions of membrane proteins. We further describe case studies where ITC was used to analyze thermodynamic linkage between ions and substrates in ion-coupled transporters. Similar type of linkage analysis will likely be applicable to a wide range of transporters, channels, and receptors.
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Affiliation(s)
- Olga Boudker
- Department of Physiology & Biophysics, Weill Cornell Medical College, New York 10021, USA.
| | - SeCheol Oh
- Department of Physiology & Biophysics, Weill Cornell Medical College, New York 10021, USA.
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Whittaker MM, Penmatsa A, Whittaker JW. The Mtm1p carrier and pyridoxal 5'-phosphate cofactor trafficking in yeast mitochondria. Arch Biochem Biophys 2015; 568:64-70. [PMID: 25637770 DOI: 10.1016/j.abb.2015.01.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 01/21/2015] [Accepted: 01/22/2015] [Indexed: 12/23/2022]
Abstract
Biochemical communication between the cytoplasmic and mitochondrial subsystems of the cell depends on solute carriers in the mitochondrial inner membrane that transport metabolites between the two compartments. We have expressed and purified a yeast mitochondrial carrier protein (Mtm1p, YGR257cp), originally identified as a manganese ion carrier, for biochemical characterization aimed at resolving its function. High affinity, stoichiometric pyridoxal 5'-phosphate (PLP) cofactor binding was characterized by fluorescence titration and calorimetry, and the biochemical effects of mtm1 gene deletion on yeast mitochondria were investigated. The PLP status of the mitochondrial proteome (the mitochondrial 'PLP-ome') was probed by immunoblot analysis of mitochondria isolated from wild type (MTM1(+)) and knockout (MTM1(-)) yeast, revealing depletion of mitochondrial PLP in the latter. A direct activity assay of the enzyme catalyzing the first committed step of heme biosynthesis, the PLP-dependent mitochondrial enzyme 5-aminolevulinate synthase, extends these results, providing a specific example of PLP cofactor limitation. Together, these experiments support a role for Mtm1p in mitochondrial PLP trafficking and highlight the link between PLP cofactor transport and iron metabolism, a remarkable illustration of metabolic integration.
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Affiliation(s)
- Mei M Whittaker
- Institute of Environmental Health, Division of Environmental and Biomolecular Systems, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Aravind Penmatsa
- Vollum Institute, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - James W Whittaker
- Institute of Environmental Health, Division of Environmental and Biomolecular Systems, Oregon Health and Science University, Portland, OR 97239-3098, USA.
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Nji E, Li D, Doyle DA, Caffrey M. Cloning, expression, purification, crystallization and preliminary X-ray diffraction of a lysine-specific permease from Pseudomonas aeruginosa. Acta Crystallogr F Struct Biol Commun 2014; 70:1362-7. [PMID: 25286940 PMCID: PMC4188080 DOI: 10.1107/s2053230x14017865] [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: 05/13/2014] [Accepted: 08/02/2014] [Indexed: 11/10/2022] Open
Abstract
The prokaryotic lysine-specific permease (LysP) belongs to the amino acid-polyamine-organocation (APC) transporter superfamily. In the cell, members of this family are responsible for the uptake and recycling of nutrients, for the maintenance of a constant internal ion concentration and for cell volume regulation. The detailed mechanism of substrate selectivity and transport of L-lysine by LysP is not understood. A high-resolution crystal structure would enormously facilitate such an understanding. To this end, LysP from Pseudomonas aeruginosa was recombinantly expressed in Escherichia coli and purified to near homogeneity by immobilized metal ion-affinity chromatography (IMAC) and size-exclusion chromatography (SEC). Hexagonal- and rod-shaped crystals were obtained in the presence of L-lysine and the L-lysine analogue L-4-thialysine by vapour diffusion and diffracted to 7.5 Å resolution. The diffraction data were indexed in space group P21, with unit-cell parameters a = 169.53, b = 169.53, c = 290.13 Å, γ = 120°.
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Affiliation(s)
- Emmanuel Nji
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Dianfan Li
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Declan A. Doyle
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Martin Caffrey
- Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
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