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Xu G, Ma J, Fang Q, Peng Q, Jiao X, Hu W, Zhao Q, Kong Y, Liu F, Shi X, Tang DJ, Tang JL, Ming Z. Structural insights into Xanthomonas campestris pv. campestris NAD + biosynthesis via the NAM salvage pathway. Commun Biol 2024; 7:255. [PMID: 38429435 PMCID: PMC10907753 DOI: 10.1038/s42003-024-05921-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/15/2024] [Indexed: 03/03/2024] Open
Abstract
Nicotinamide phosphoribosyltransferase (NAMPT) plays an important role in the biosynthesis of nicotinamide adenine dinucleotide (NAD+) via the nicotinamide (NAM) salvage pathway. While the structural biochemistry of eukaryote NAMPT has been well studied, the catalysis mechanism of prokaryote NAMPT at the molecular level remains largely unclear. Here, we demonstrated the NAMPT-mediated salvage pathway is functional in the Gram-negative phytopathogenic bacterium Xanthomonas campestris pv. campestris (Xcc) for the synthesis of NAD+, and the enzyme activity of NAMPT in this bacterium is significantly higher than that of human NAMPT in vitro. Our structural analyses of Xcc NAMPT, both in isolation and in complex with either the substrate NAM or the product nicotinamide mononucleotide (NMN), uncovered significant details of substrate recognition. Specifically, we revealed the presence of a NAM binding tunnel that connects the active site, and this tunnel is essential for both catalysis and inhibitor binding. We further demonstrated that NAM binding in the tunnel has a positive cooperative effect with NAM binding in the catalytic site. Additionally, we discovered that phosphorylation of the His residue at position 229 enhances the substrate binding affinity of Xcc NAMPT and is important for its catalytic activity. This work reveals the importance of NAMPT in bacterial NAD+ synthesis and provides insights into the substrate recognition and the catalytic mechanism of bacterial type II phosphoribosyltransferases.
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Affiliation(s)
- Guolyu Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Jinxue Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Qi Fang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Qiong Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Xi Jiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Wei Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Qiaoqiao Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Yanqiong Kong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Fenmei Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Xueqi Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Dong-Jie Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China.
| | - Zhenhua Ming
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, 530004, P. R. China.
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2
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Zhou Z, Yang X, Huang T, Zheng J, Deng Z, Dai S, Lin S. Bifunctional NadC Homologue PyrZ Catalyzes Nicotinic Acid Formation in Pyridomycin Biosynthesis. ACS Chem Biol 2023; 18:141-150. [PMID: 36517246 DOI: 10.1021/acschembio.2c00773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pyridomycin is a potent antimycobacterial natural product by specifically inhibiting InhA, a clinically validated antituberculosis drug discovery target. Pyridyl moieties of pyridomycin play an essential role in inhibiting InhA by occupying the reduced form of the nicotinamide adenine dinucleotide (NADH) cofactor binding site. Herein, we biochemically characterize PyrZ that is a multifunctional NadC homologue and catalyzes the successive formation, dephosphorylation, and ribose hydrolysis of nicotinic acid mononucleotide (NAMN) to generate nicotinic acid (NA), a biosynthetic precursor for the pyridyl moiety of pyridomycin. Crystal structures of PyrZ in complex with substrate quinolinic acid (QA) and the final product NA revealed a specific salt bridge formed between K184 and the C3-carboxyl group of QA. This interaction positions QA for accepting the phosphoribosyl group to generate NAMN, retains NAMN within the active site, and mediates its translocation to nucleophile D296 for dephosphorylation. Combining kinetic and thermodynamic analysis with site-directed mutagenesis, the catalytic mechanism of PyrZ dephosphorylation was proposed. Our study discovered an alternative and concise NA biosynthetic pathway involving a unique multifunctional enzyme.
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Affiliation(s)
- Zihua Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Tingting Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Shaobo Dai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.,Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai 200240, China
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3
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Midttun Ø, Ulvik A, Meyer K, Zahed H, Giles GG, Manjer J, Sandsveden M, Langhammer A, Sørgjerd EP, Behndig AF, Johansson M, Freedman ND, Huang WY, Chen C, Prentice R, Stevens VL, Wang Y, Le Marchand L, Weinstein SJ, Cai Q, Arslan AA, Chen Y, Shu XO, Zheng W, Yuan JM, Koh WP, Visvanathan K, Sesso HD, Zhang X, Gaziano JM, Fanidi A, Robbins HA, Brennan P, Johansson M, Ueland PM. A cross-sectional study of inflammatory markers as determinants of circulating kynurenines in the Lung Cancer Cohort Consortium. Sci Rep 2023; 13:1011. [PMID: 36653422 PMCID: PMC9849351 DOI: 10.1038/s41598-023-28135-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
Circulating concentrations of metabolites (collectively called kynurenines) in the kynurenine pathway of tryptophan metabolism increase during inflammation, particularly in response to interferon-gamma (IFN-γ). Neopterin and the kynurenine/tryptophan ratio (KTR) are IFN-γ induced inflammatory markers, and together with C-reactive protein (CRP) and kynurenines they are associated with various diseases, but comprehensive data on the strength of associations of inflammatory markers with circulating concentrations of kynurenines are lacking. We measured circulating concentrations of neopterin, CRP, tryptophan and seven kynurenines in 5314 controls from 20 cohorts in the Lung Cancer Cohort Consortium (LC3). The associations of neopterin, KTR and CRP with kynurenines were investigated using regression models. In mixed models, one standard deviation (SD) higher KTR was associated with a 0.46 SD higher quinolinic acid (QA), and 0.31 SD higher 3-hydroxykynurenine (HK). One SD higher neopterin was associated with 0.48, 0.44, 0.36 and 0.28 SD higher KTR, QA, kynurenine and HK, respectively. KTR and neopterin respectively explained 24.1% and 16.7% of the variation in QA, and 11.4% and 7.5% of HK. CRP was only weakly associated with kynurenines in regression models. In summary, QA was the metabolite that was most strongly associated with the inflammatory markers. In general, the inflammatory markers were most strongly related to metabolites located along the tryptophan-NAD axis, which may support suggestions of increased production of NAD from tryptophan during inflammation.
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Affiliation(s)
- Øivind Midttun
- Bevital AS, Laboratory Building, Jonas Lies Veg 87, 5021, Bergen, Norway.
| | - Arve Ulvik
- Bevital AS, Laboratory Building, Jonas Lies Veg 87, 5021, Bergen, Norway
| | - Klaus Meyer
- Bevital AS, Laboratory Building, Jonas Lies Veg 87, 5021, Bergen, Norway
| | - Hana Zahed
- Genomic Epidemiology Branch, International Agency for Research on Cancer, Lyon, France
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Australia
| | - Jonas Manjer
- Department of Surgery, Skane University Hospital, Malmö, Sweden
- Lund University, Malmö, Sweden
| | - Malte Sandsveden
- Department of Clinical Sciences Malmo, Lund University, Malmö, Sweden
| | - Arnulf Langhammer
- Department of Public Health and Nursing, Hunt Research Centre, Norwegian University of Science and Technology, Levanger, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Elin Pettersen Sørgjerd
- Department of Public Health and Nursing, Hunt Research Centre, Norwegian University of Science and Technology, Levanger, Norway
- Department of Endocrinology, St. Olavs Hospital, Trondheim University Hospital, Levanger, Norway
| | - Annelie F Behndig
- Department of Public Health and Clinical Medicine, Umea University, Umeå, Sweden
| | - Mikael Johansson
- Department of Radiation Sciences, Oncology, Umea University, Umeå, Sweden
| | - Neal D Freedman
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wen-Yi Huang
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Chu Chen
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Ross Prentice
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, USA
| | | | - Ying Wang
- American Cancer Society, Atlanta, USA
| | - Loïc Le Marchand
- University of Hawai'i Cancer Center, University of Hawai'i at Mānoa, Honolulu, USA
| | - Stephanie J Weinstein
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Qiuyin Cai
- Vanderbilt University Medical Center, Nashville, USA
| | - Alan A Arslan
- Department of Obstetrics and Gynecology, NYU Langone Health, New York, NY, USA
- Department of Population Health, NYU Langone Health, New York, NY, USA
- Perlmutter Comprehensive Cancer Center, NYU Langone Health, New York, NY, USA
| | - Yu Chen
- Department of Population Health, NYU Langone Health, New York, NY, USA
- Perlmutter Comprehensive Cancer Center, NYU Langone Health, New York, NY, USA
| | - Xiao-Ou Shu
- Department of Population Health, NYU Langone Health, New York, NY, USA
| | - Wei Zheng
- Department of Population Health, NYU Langone Health, New York, NY, USA
| | - Jian-Min Yuan
- University of Pittsburgh and UPMC Hillman Cancer Center, Pittsburgh, USA
| | - Woon-Puay Koh
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kala Visvanathan
- Johns Hopkins Institute for Clinical and Translational Research, Baltimore, USA
| | - Howard D Sesso
- Brigham and Women's Hospital, Harvard Medical School, Boston, USA
- Harvard T.H. Chan School of Public Health, Boston, USA
| | - Xuehong Zhang
- Brigham and Women's Hospital, Harvard Medical School, Boston, USA
- Harvard T.H. Chan School of Public Health, Boston, USA
| | - J Michael Gaziano
- Brigham and Women's Hospital, Boston, USA
- VA Boston Healthcare System, Boston, MA, USA
| | | | - Hilary A Robbins
- Genomic Epidemiology Branch, International Agency for Research on Cancer, Lyon, France
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer, Lyon, France
| | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer, Lyon, France
| | - Per M Ueland
- Bevital AS, Laboratory Building, Jonas Lies Veg 87, 5021, Bergen, Norway
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4
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Xi Y, Wang F. Extreme pathway analysis reveals the organizing rules of metabolic regulation. PLoS One 2019; 14:e0210539. [PMID: 30721240 PMCID: PMC6363282 DOI: 10.1371/journal.pone.0210539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/27/2018] [Indexed: 11/18/2022] Open
Abstract
Cellular systems shift metabolic states by adjusting gene expression and enzyme activities to adapt to physiological and environmental changes. Biochemical and genetic studies are identifying how metabolic regulation affects the selection of metabolic phenotypes. However, how metabolism influences its regulatory architecture still remains unexplored. We present a new method of extreme pathway analysis (the minimal set of conically independent metabolic pathways) to deduce regulatory structures from pure pathway information. Applying our method to metabolic networks of human red blood cells and Escherichia coli, we shed light on how metabolic regulation are organized by showing which reactions within metabolic networks are more prone to transcriptional or allosteric regulation. Applied to a human genome-scale metabolic system, our method detects disease-associated reactions. Thus, our study deepens the understanding of the organizing principle of cellular metabolic regulation and may contribute to metabolic engineering, synthetic biology, and disease treatment.
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Affiliation(s)
- Yanping Xi
- Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China
- School of Computer Science and Technology, Fudan University, Shanghai, China
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Fei Wang
- Shanghai Key Lab of Intelligent Information Processing, Fudan University, Shanghai, China
- School of Computer Science and Technology, Fudan University, Shanghai, China
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5
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Minhas PS, Liu L, Moon PK, Joshi AU, Dove C, Mhatre S, Contrepois K, Wang Q, Lee BA, Coronado M, Bernstein D, Snyder MP, Migaud M, Majeti R, Mochly-Rosen D, Rabinowitz JD, Andreasson KI. Macrophage de novo NAD + synthesis specifies immune function in aging and inflammation. Nat Immunol 2018; 20:50-63. [PMID: 30478397 DOI: 10.1038/s41590-018-0255-3] [Citation(s) in RCA: 294] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/10/2018] [Indexed: 11/09/2022]
Abstract
Recent advances highlight a pivotal role for cellular metabolism in programming immune responses. Here, we demonstrate that cell-autonomous generation of nicotinamide adenine dinucleotide (NAD+) via the kynurenine pathway (KP) regulates macrophage immune function in aging and inflammation. Isotope tracer studies revealed that macrophage NAD+ derives substantially from KP metabolism of tryptophan. Genetic or pharmacological blockade of de novo NAD+ synthesis depleted NAD+, suppressed mitochondrial NAD+-dependent signaling and respiration, and impaired phagocytosis and resolution of inflammation. Innate immune challenge triggered upstream KP activation but paradoxically suppressed cell-autonomous NAD+ synthesis by limiting the conversion of downstream quinolinate to NAD+, a profile recapitulated in aging macrophages. Increasing de novo NAD+ generation in immune-challenged or aged macrophages restored oxidative phosphorylation and homeostatic immune responses. Thus, KP-derived NAD+ operates as a metabolic switch to specify macrophage effector responses. Breakdown of de novo NAD+ synthesis may underlie declining NAD+ levels and rising innate immune dysfunction in aging and age-associated diseases.
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Affiliation(s)
- Paras S Minhas
- Department of Neurology & Neurological Sciences, Stanford School of Medicine, Stanford, CA, USA.,Neurosciences Graduate Program, Stanford University, Stanford, CA, USA
| | - Ling Liu
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.,Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Peter K Moon
- Department of Neurology & Neurological Sciences, Stanford School of Medicine, Stanford, CA, USA
| | - Amit U Joshi
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Christopher Dove
- Department of Hematology, Stanford School of Medicine, Stanford, CA, USA
| | - Siddhita Mhatre
- Department of Neurology & Neurological Sciences, Stanford School of Medicine, Stanford, CA, USA
| | - Kevin Contrepois
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Qian Wang
- Department of Neurology & Neurological Sciences, Stanford School of Medicine, Stanford, CA, USA
| | - Brittany A Lee
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Michael Coronado
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
| | - Daniel Bernstein
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Marie Migaud
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Ravindra Majeti
- Department of Hematology, Stanford School of Medicine, Stanford, CA, USA
| | - Daria Mochly-Rosen
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.,Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Katrin I Andreasson
- Department of Neurology & Neurological Sciences, Stanford School of Medicine, Stanford, CA, USA. .,Stanford Neuroscience Institute, Stanford University, Stanford, CA, USA. .,Stanford Immunology Program, Stanford University, Stanford, CA, USA.
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6
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Quinolinic Acid Amyloid-like Fibrillar Assemblies Seed α-Synuclein Aggregation. J Mol Biol 2018; 430:3847-3862. [PMID: 30098337 DOI: 10.1016/j.jmb.2018.08.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 07/17/2018] [Accepted: 08/01/2018] [Indexed: 01/08/2023]
Abstract
Quinolinic acid (QA), a downstream neurometabolite in the kynurenine pathway, the biosynthetic pathway of tryptophan, is associated with neurodegenerative diseases pathology. Mutations in genes encoding kynurenine pathway enzymes, which control the level of QA production, are linked with elevated risk of developing Parkinson's disease. Recent findings have revealed the accumulation and deposition of QA in post-mortem samples, as well as in cellular models of Alzheimer's disease and related disorders. Furthermore, intrastriatal inoculation of mice with QA results in increased levels of phosphorylated α-synuclein and neurodegenerative pathological and behavioral characteristics. However, the cellular and molecular mechanisms underlying the involvement of QA accumulation in protein aggregation and neurodegeneration remain elusive. We recently established that self-assembled ordered structures are formed by various metabolites and hypothesized that these "metabolite amyloids" may seed amyloidogenic proteins. Here we demonstrate the formation of QA amyloid-like fibrillar assemblies and seeding of α-synuclein aggregation by these nanostructures both in vitro and in cell culture. Notably, α-synuclein aggregation kinetics was accelerated by an order of magnitude. Additional amyloid-like properties of QA assemblies were demonstrated using thioflavin T assay, powder X-ray diffraction and cell apoptosis analysis. Moreover, fluorescently labeled QA assemblies were internalized by neuronal cells and co-localized with α-synuclein aggregates. In addition, we observed cell-to-cell propagation of fluorescently labeled QA assemblies in a co-culture of treated and untreated cells. Our findings suggest that excess QA levels, due to mutations in the kynurenine pathway, for example, may lead to the formation of metabolite assemblies that seed α-synuclein aggregation, resulting in neuronal toxicity and induction of Parkinson's disease.
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7
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Huyet J, Ozeir M, Burgevin MC, Pinson B, Chesney F, Remy JM, Siddiqi AR, Lupoli R, Pinon G, Saint-Marc C, Gibert JF, Morales R, Ceballos-Picot I, Barouki R, Daignan-Fornier B, Olivier-Bandini A, Augé F, Nioche P. Structural Insights into the Forward and Reverse Enzymatic Reactions in Human Adenine Phosphoribosyltransferase. Cell Chem Biol 2018; 25:666-676.e4. [PMID: 29576532 DOI: 10.1016/j.chembiol.2018.02.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 01/05/2018] [Accepted: 02/22/2018] [Indexed: 10/17/2022]
Abstract
Phosphoribosyltransferases catalyze the displacement of a PRPP α-1'-pyrophosphate to a nitrogen-containing nucleobase. How they control the balance of substrates/products binding and activities is poorly understood. Here, we investigated the human adenine phosphoribosyltransferase (hAPRT) that produces AMP in the purine salvage pathway. We show that a single oxygen atom from the Tyr105 side chain is responsible for selecting the active conformation of the 12 amino acid long catalytic loop. Using in vitro, cellular, and in crystallo approaches, we demonstrated that Tyr105 is key for the fine-tuning of the kinetic activity efficiencies of the forward and reverse reactions. Together, our results reveal an evolutionary pressure on the strictly conserved Tyr105 and on the dynamic motion of the flexible loop in phosphoribosyltransferases that is essential for purine biosynthesis in cells. These data also provide the framework for designing novel adenine derivatives that could modulate, through hAPRT, diseases-involved cellular pathways.
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Affiliation(s)
- Jessica Huyet
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France
| | - Mohammad Ozeir
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France
| | | | - Benoît Pinson
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Bordeaux Cedex 33077, France
| | - Françoise Chesney
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin 91385, France
| | - Jean-Marc Remy
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin 91385, France
| | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Roland Lupoli
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France; Université Paris Descartes, Structural and Molecular Analysis Platform, Paris 75006, France
| | - Gregory Pinon
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France; Université Paris Descartes, Structural and Molecular Analysis Platform, Paris 75006, France
| | - Christelle Saint-Marc
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Bordeaux Cedex 33077, France
| | | | - Renaud Morales
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin 91385, France
| | - Irène Ceballos-Picot
- Laboratoire de Biochimie Métabolomique et Protéomique, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Faculté de Médecine Paris Descartes, Paris 75015, France
| | - Robert Barouki
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France; Laboratoire de Biochimie Métabolomique et Protéomique, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Faculté de Médecine Paris Descartes, Paris 75015, France
| | - Bertrand Daignan-Fornier
- Université de Bordeaux, Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, Bordeaux Cedex 33077, France
| | | | - Franck Augé
- Sanofi R&D, Translational Science Unit, Chilly-Mazarin 91385, France.
| | - Pierre Nioche
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR-S 1124, Centre Interdisciplinaire Chimie Biologie-Paris, 45, rue des Saints Pères, Paris 75006, France; INSERM, UMR-S 1124, Paris 75006, France; Université Paris Descartes, Structural and Molecular Analysis Platform, Paris 75006, France.
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8
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Booth WT, Morris TL, Mysona DP, Shah MJ, Taylor LK, Karlin TW, Clary K, Majorek KA, Offermann LR, Chruszcz M. Streptococcus pyogenes quinolinate-salvage pathway-structural and functional studies of quinolinate phosphoribosyl transferase and NH 3 -dependent NAD + synthetase. FEBS J 2017; 284:2425-2441. [PMID: 28618168 PMCID: PMC5551413 DOI: 10.1111/febs.14136] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/08/2017] [Accepted: 06/12/2017] [Indexed: 11/27/2022]
Abstract
Streptococcus pyogenes, also known as Group A Strep (GAS), is an obligate human pathogen that is responsible for millions of infections and numerous deaths per year. Infection manifestations can range from simple, acute pharyngitis to more complex, necrotizing fasciitis. To date, most treatments for GAS infections involve the use of common antibiotics including tetracycline and clindamycin. Unfortunately, new strains have been identified that are resistant to these drugs, therefore, new targets must be identified to treat drug-resistant strains. This work is focused on the structural and functional characterization of three proteins: spNadC, spNadD, and spNadE. These enzymes are involved in the biosynthesis of nicotinamide adenine dinucleotide (NAD+ ). The structures of spNadC and spNadE were determined. SpNadC is suggested to play a role in GAS virulence, while spNadE, functions as an NAD synthetase and is considered to be a new drug target. Determination of the spNadE structure uncovered a putative, NH3 channel, which may provide insight into the mechanistic details of NH3 -dependent NAD+ synthetases in prokaryotes. ENZYMES Quinolinate phosphoribosyltransferase: EC2.4.2.19 and NAD synthetase: EC6.3.1.5. DATABASE Protein structures for spNadC, spNadCΔ69A , and spNadE are deposited into Protein Data Bank under the accession codes 5HUL, 5HUO & 5HUP, and 5HUH & 5HUJ, respectively.
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Affiliation(s)
- William T. Booth
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208
| | - Trevor L. Morris
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208
| | - David P. Mysona
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208
| | - Milan J. Shah
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208
| | - Linda K. Taylor
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208
| | - Taylor W. Karlin
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208
| | - Kathryn Clary
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208
| | - Karolina A. Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908
| | - Lesa R. Offermann
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208
- Department of Chemistry, Davidson College, Davidson, NC 28035
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208
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9
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Wang Z, Gao Y, Zhang C, Hu H, Guo D, Xu Y, Xu Q, Zhang W, Deng S, Lv P, Yang Y, Ding Y, Li Q, Weng C, Chen X, Gong S, Chen H, Niu J, Tang H. Quinolinate Phosphoribosyltransferase is an Antiviral Host Factor Against Hepatitis C Virus Infection. Sci Rep 2017; 7:5876. [PMID: 28724915 PMCID: PMC5517448 DOI: 10.1038/s41598-017-06254-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 06/09/2017] [Indexed: 01/09/2023] Open
Abstract
HCV infection can decrease NAD+/NADH ratio, which could convert lipid metabolism to favor HCV replication. In hepatocytes, quinolinate phosphoribosyl transferase (QPRT) catabolizes quinolinic acid (QA) to nicotinic acid mononucleotide (NAMN) for de novo NAD synthesis. However, whether and how HCV modulates QPRT hence the lipogenesis is unknown. In this work, we found QPRT was reduced significantly in livers of patients or humanized C/OTg mice with persistent HCV infection. Mechanistic studies indicated that HCV NS3/4A promoted proteasomal degradation of QPRT through Smurf2, an E3 ubiquitin-protein ligase, in Huh7.5.1 cells. Furthermore, QPRT enzymatic activity involved in suppression of HCV replication in cells. Activation of QPRT with clofibrate (CLO) or addition of QPRT catabolite NAD both inhibited HCV replication in cells, probably through NAD+-dependent Sirt1 inhibition of cellular lipogenesis. More importantly, administration of CLO, a hypolipidemic drug used in clinics, could significantly reduce the viral load in HCV infected C/OTg mice. Take together, these results suggested that HCV infection triggered proteasomal degradation of QPRT and consequently reduced de novo NAD synthesis and lipogenesis, in favor of HCV replication. Hepatic QPRT thus likely served as a cellular factor that dampened productive HCV replication.
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Affiliation(s)
- Zhilong Wang
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China.,CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Yanhang Gao
- Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Chao Zhang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Haiming Hu
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Dongwei Guo
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Heilong Jiang, 150001, China
| | - Yi Xu
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Guangzhou Women and Children's Medical Center, Guangzhou, 510623, China
| | - Qiuping Xu
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China.,Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Weihong Zhang
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Sisi Deng
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Pingyun Lv
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Yan Yang
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Yanhua Ding
- Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Qingquan Li
- Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Changjiang Weng
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Heilong Jiang, 150001, China
| | - Xinwen Chen
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Sitang Gong
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Guangzhou Women and Children's Medical Center, Guangzhou, 510623, China
| | - Hairong Chen
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Junqi Niu
- Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Hong Tang
- The Joint Laboratory for Translational Precision Medicine of Wuhan Institute of Virology, Chinese Academy of Sciences and Guangzhou Women and Children`s Medical Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China. .,CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.
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10
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Badawy AAB. Kynurenine Pathway of Tryptophan Metabolism: Regulatory and Functional Aspects. Int J Tryptophan Res 2017; 10:1178646917691938. [PMID: 28469468 PMCID: PMC5398323 DOI: 10.1177/1178646917691938] [Citation(s) in RCA: 624] [Impact Index Per Article: 89.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/11/2017] [Indexed: 12/21/2022] Open
Abstract
Regulatory and functional aspects of the kynurenine (K) pathway (KP) of tryptophan (Trp) degradation are reviewed. The KP accounts for ~95% of dietary Trp degradation, of which 90% is attributed to the hepatic KP. During immune activation, the minor extrahepatic KP plays a more active role. The KP is rate-limited by its first enzyme, Trp 2,3-dioxygenase (TDO), in liver and indoleamine 2,3-dioxygenase (IDO) elsewhere. TDO is regulated by glucocorticoid induction, substrate activation and stabilization by Trp, cofactor activation by heme, and end-product inhibition by reduced nicotinamide adenine dinucleotide (phosphate). IDO is regulated by IFN-γ and other cytokines and by nitric oxide. The KP disposes of excess Trp, controls hepatic heme synthesis and Trp availability for cerebral serotonin synthesis, and produces immunoregulatory and neuroactive metabolites, the B3 “vitamin” nicotinic acid, and oxidized nicotinamide adenine dinucleotide. Various KP enzymes are undermined in disease and are targeted for therapy of conditions ranging from immunological, neurological, and neurodegenerative conditions to cancer.
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Affiliation(s)
- Abdulla A-B Badawy
- Cardiff School of Health Sciences, Cardiff Metropolitan University, Cardiff, UK
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11
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González Esquivel D, Ramírez-Ortega D, Pineda B, Castro N, Ríos C, Pérez de la Cruz V. Kynurenine pathway metabolites and enzymes involved in redox reactions. Neuropharmacology 2017; 112:331-345. [DOI: 10.1016/j.neuropharm.2016.03.013] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 02/28/2016] [Accepted: 03/06/2016] [Indexed: 11/27/2022]
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12
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Ueland PM, McCann A, Midttun Ø, Ulvik A. Inflammation, vitamin B6 and related pathways. Mol Aspects Med 2016; 53:10-27. [PMID: 27593095 DOI: 10.1016/j.mam.2016.08.001] [Citation(s) in RCA: 199] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/27/2016] [Indexed: 12/11/2022]
Abstract
The active form of vitamin B6, pyridoxal 5'-phosphate (PLP), serves as a co-factor in more than 150 enzymatic reactions. Plasma PLP has consistently been shown to be low in inflammatory conditions; there is a parallel reduction in liver PLP, but minor changes in erythrocyte and muscle PLP and in functional vitamin B6 biomarkers. Plasma PLP also predicts the risk of chronic diseases like cardiovascular disease and some cancers, and is inversely associated with numerous inflammatory markers in clinical and population-based studies. Vitamin B6 intake and supplementation improve some immune functions in vitamin B6-deficient humans and experimental animals. A possible mechanism involved is mobilization of vitamin B6 to the sites of inflammation where it may serve as a co-factor in pathways producing metabolites with immunomodulating effects. Relevant vitamin B6-dependent inflammatory pathways include vitamin B6 catabolism, the kynurenine pathway, sphingosine 1-phosphate metabolism, the transsulfuration pathway, and serine and glycine metabolism.
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Affiliation(s)
- Per Magne Ueland
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; Laboratory of Clinical Biochemistry, Haukeland University Hospital, 5021 Bergen, Norway.
| | | | | | - Arve Ulvik
- Bevital A/S, Laboratoriebygget, 5021 Bergen, Norway
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13
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Shirota M, Kinoshita K. Discrepancies between human DNA, mRNA and protein reference sequences and their relation to single nucleotide variants in the human population. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw124. [PMID: 27589963 PMCID: PMC5009343 DOI: 10.1093/database/baw124] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 08/04/2016] [Indexed: 01/24/2023]
Abstract
The protein coding sequences of the human reference genome GRCh38, RefSeq mRNA and UniProt protein databases are sometimes inconsistent with each other, due to polymorphisms in the human population, but the overall landscape of the discordant sequences has not been clarified. In this study, we comprehensively listed the discordant bases and regions between the GRCh38, RefSeq and UniProt reference sequences, based on the genomic coordinates of GRCh38. We observed that the RefSeq sequences are more likely to represent the major alleles than GRCh38 and UniProt, by assigning the alternative allele frequencies of the discordant bases. Since some reference sequences have minor alleles, functional and structural annotations may be performed based on rare alleles in the human population, thereby biasing these analyses. Some of the differences between the RefSeq and GRCh38 account for biological differences due to known RNA-editing sites. The definitions of the coding regions are frequently complicated by possible micro-exons within introns and by SNVs with large alternative allele frequencies near exon–intron boundaries. The mRNA or protein regions missing from GRCh38 were mainly due to small deletions, and these sequences need to be identified. Taken together, our results clarify overall consistency and remaining inconsistency between the reference sequences.
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Affiliation(s)
- Matsuyuki Shirota
- Graduate School of Medicine, Tohoku University, Sendai, Miyagi 9808575, Japan Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 9808575, Japan Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi 9808579, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 9808575, Japan Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi 9808579, Japan Institute for Development, Aging and Cancer, Tohoku University, Sendai, Miyagi 9808575, Japan
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14
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Youn HS, Kim TG, Kim MK, Kang GB, Kang JY, Lee JG, An JY, Park KR, Lee Y, Im YJ, Lee JH, Eom SH. Structural Insights into the Quaternary Catalytic Mechanism of Hexameric Human Quinolinate Phosphoribosyltransferase, a Key Enzyme in de novo NAD Biosynthesis. Sci Rep 2016; 6:19681. [PMID: 26805589 PMCID: PMC4726147 DOI: 10.1038/srep19681] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 12/14/2015] [Indexed: 11/09/2022] Open
Abstract
Quinolinate phosphoribosyltransferase (QPRT) catalyses the production of nicotinic
acid mononucleotide, a precursor of de novo biosynthesis of the ubiquitous
coenzyme nicotinamide adenine dinucleotide. QPRT is also essential for maintaining
the homeostasis of quinolinic acid in the brain, a possible neurotoxin causing
various neurodegenerative diseases. Although QPRT has been extensively analysed, the
molecular basis of the reaction catalysed by human QPRT remains unclear. Here, we
present the crystal structures of hexameric human QPRT in the apo form and its
complexes with reactant or product. We found that the interaction between dimeric
subunits was dramatically altered during the reaction process by conformational
changes of two flexible loops in the active site at the dimer-dimer interface. In
addition, the N-terminal short helix α1 was identified as a critical
hexamer stabilizer. The structural features, size distribution, heat aggregation and
ITC studies of the full-length enzyme and the enzyme lacking helix α1
strongly suggest that human QPRT acts as a hexamer for cooperative reactant binding
via three dimeric subunits and maintaining stability. Based on our comparison of
human QPRT structures in the apo and complex forms, we propose a drug design
strategy targeting malignant glioma.
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Affiliation(s)
- Hyung-Seop Youn
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Tae Gyun Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Mun-Kyoung Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Gil Bu Kang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Jung Youn Kang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Jung-Gyu Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Jun Yop An
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Kyoung Ryoung Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Youngjin Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Young Jun Im
- College of Pharmacy, Chonnam National University, Gwangju 500-757, South Korea
| | - Jun Hyuck Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, South Korea.,Department of Polar Sciences, Korea University of Science and Technology, Incheon 406-840, South Korea
| | - Soo Hyun Eom
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
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15
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Abstract
Universal and ubiquitous redox cofactors, nicotinamide adenine dinucleotide (NAD) and its phosphorylated analog (NADP), collectively contribute to approximately 12% of all biochemical reactions included in the metabolic model of Escherichia coli K-12. A homeostasis of the NAD pool faithfully maintained by the cells results from a dynamic balance in a network of NAD biosynthesis, utilization, decomposition, and recycling pathways that is subject to tight regulation at various levels. A brief overview of NAD utilization processes is provided in this review, including some examples of nonredox utilization. The review focuses mostly on those aspects of NAD biogenesis and utilization in E. coli and Salmonella that emerged within the past 12 years. The first pyridine nucleotide cycle (PNC) originally identified in mammalian systems and termed the Preiss-Handler pathway includes a single-step conversion of niacin (Na) to NaMN by nicotinic acid phosphoribosyltransferase (PncB). In E. coli and many other prokaryotes, this enzyme, together with nicotinamide deamidase (PncA), compose the major pathway for utilization of the pyridine ring in the form of amidated (Nm) or deamidated (Na) precursors. The existence of various regulatory mechanisms and checkpoints that control the NAD biosynthetic machinery reflects the importance of maintaining NAD homeostasis in a variety of growth conditions. Among the most important regulatory mechanisms at the level of individual enzymes are a classic feedback inhibition of NadB, the first enzyme of NAD de novo biosynthesis, by NAD and a metabolic regulation of NadK by reduced cofactors.
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16
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Jones SP, Franco NF, Varney B, Sundaram G, Brown DA, de Bie J, Lim CK, Guillemin GJ, Brew BJ. Expression of the Kynurenine Pathway in Human Peripheral Blood Mononuclear Cells: Implications for Inflammatory and Neurodegenerative Disease. PLoS One 2015; 10:e0131389. [PMID: 26114426 PMCID: PMC4482723 DOI: 10.1371/journal.pone.0131389] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/02/2015] [Indexed: 12/14/2022] Open
Abstract
The kynurenine pathway is a fundamental mechanism of immunosuppression and peripheral tolerance. It is increasingly recognized as playing a major role in the pathogenesis of a wide variety of inflammatory, neurodegenerative and malignant disorders. However, the temporal dynamics of kynurenine pathway activation and metabolite production in human immune cells is currently unknown. Here we report the novel use of flow cytometry, combined with ultra high-performance liquid chromatography and gas chromatography-mass spectrometry, to sensitively quantify the intracellular expression of three key kynurenine pathway enzymes and the main kynurenine pathway metabolites in a time-course study. This is the first study to show that up-regulation of indoleamine 2,3-dioxygenase (IDO-1), kynurenine 3-monoxygenase (KMO) and quinolinate phosphoribosyltransferase (QPRT) is lacking in lymphocytes treated with interferon gamma. In contrast, peripheral monocytes showed a significant elevation of kynurenine pathway enzymes and metabolites when treated with interferon gamma. Expression of IDO-1, KMO and QPRT correlated significantly with activation of the kynurenine pathway (kynurenine:tryptophan ratio), quinolinic acid concentration and production of the monocyte derived, pro-inflammatory immune response marker: neopterin. Our results also describe an original and sensitive methodological approach to quantify kynurenine pathway enzyme expression in cells. This has revealed further insights into the potential role of these enzymes in disease processes.
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Affiliation(s)
- Simon P. Jones
- Peter Duncan Neurosciences Research Unit, St Vincent’s Centre for Applied Medical Research, Sydney, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
- * E-mail:
| | - Nunzio F. Franco
- Peter Duncan Neurosciences Research Unit, St Vincent’s Centre for Applied Medical Research, Sydney, Australia
| | - Bianca Varney
- Peter Duncan Neurosciences Research Unit, St Vincent’s Centre for Applied Medical Research, Sydney, Australia
| | - Gayathri Sundaram
- Peter Duncan Neurosciences Research Unit, St Vincent’s Centre for Applied Medical Research, Sydney, Australia
| | - David A. Brown
- Peter Duncan Neurosciences Research Unit, St Vincent’s Centre for Applied Medical Research, Sydney, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
| | - Josien de Bie
- Neuroinflammation group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - Chai K. Lim
- Neuroinflammation group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - Gilles J. Guillemin
- Peter Duncan Neurosciences Research Unit, St Vincent’s Centre for Applied Medical Research, Sydney, Australia
- Neuroinflammation group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - Bruce J. Brew
- Peter Duncan Neurosciences Research Unit, St Vincent’s Centre for Applied Medical Research, Sydney, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
- Department of Neurology, St Vincent’s Hospital, Sydney, Australia
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17
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Marletta AS, Massarotti A, Orsomando G, Magni G, Rizzi M, Garavaglia S. Crystal structure of human nicotinic acid phosphoribosyltransferase. FEBS Open Bio 2015; 5:419-28. [PMID: 26042198 PMCID: PMC4442680 DOI: 10.1016/j.fob.2015.05.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 04/30/2015] [Accepted: 05/01/2015] [Indexed: 01/04/2023] Open
Abstract
Human NaPRTase is a functional dimer. The structural bases for FK866 lack of inhibition of human NaPRTas were identified. Na, Nam and QA phosphoribosyltransferases share a conserved fold. Na, Nam and QA phosphoribosyltransferases show distinctive traits in the active site. Human and Enterococcus faecalis NaPRTase are highly structurally conserved.
Nicotinic acid phosphoribosyltransferase (EC 2.4.2.11) (NaPRTase) is the rate-limiting enzyme in the three-step Preiss–Handler pathway for the biosynthesis of NAD. The enzyme catalyzes the conversion of nicotinic acid (Na) and 5-phosphoribosyl-1-pyrophosphate (PRPP) to nicotinic acid mononucleotide (NaMN) and pyrophosphate (PPi). Several studies have underlined the importance of NaPRTase for NAD homeostasis in mammals, but no crystallographic data are available for this enzyme from higher eukaryotes. Here, we report the crystal structure of human NaPRTase that was solved by molecular replacement at a resolution of 2.9 Å in its ligand-free form. Our structural data allow the assignment of human NaPRTase to the type II phosphoribosyltransferase subfamily and reveal that the enzyme consists of two domains and functions as a dimer with the active site located at the interface of the monomers. The substrate-binding mode was analyzed by molecular docking simulation and provides hints into the catalytic mechanism. Moreover, structural comparison of human NaPRTase with the other two human type II phosphoribosyltransferases involved in NAD biosynthesis, quinolinate phosphoribosyltransferase and nicotinamide phosphoribosyltransferase, reveals that while the three enzymes share a conserved overall structure, a few distinctive structural traits can be identified. In particular, we show that NaPRTase lacks a tunnel that, in nicotinamide phosphoribosiltransferase, represents the binding site of its potent and selective inhibitor FK866, currently used in clinical trials as an antitumoral agent.
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Key Words
- FK866
- NAD biosynthesis
- NAD, nicotinamide adenine dinucleotide
- NMN, nicotinamide mononucleotide
- NMNAT, nicotinamide mononucleotide adenylyltransferase
- Na, nicotinic acid
- NaAD, nicotinic acid dinucleotide
- NaMN, nicotinic acid mononucleotide
- NaPRTase, nicotinic acid phosphoribosyltransferase
- NamR, nicotinamide riboside
- Nicotinic Acid
- PRPP, 5-phosphoribosyl-1-pyrophosphate
- Phosphoribosyltransferase
- Preiss–Handler pathway
- QA, quinolinic acid
- Recycling NAD pathway
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Affiliation(s)
- Ada Serena Marletta
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Alberto Massarotti
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Giuseppe Orsomando
- Department of Clinical Sciences, Section of Biochemistry, Polytechnic University of Marche, Via Ranieri 67, 60131 Ancona, Italy
| | - Giulio Magni
- Department of Clinical Sciences, Section of Biochemistry, Polytechnic University of Marche, Via Ranieri 67, 60131 Ancona, Italy
| | - Menico Rizzi
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Silvia Garavaglia
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
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18
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Ruggieri S, Orsomando G, Sorci L, Raffaelli N. Regulation of NAD biosynthetic enzymes modulates NAD-sensing processes to shape mammalian cell physiology under varying biological cues. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1138-49. [PMID: 25770681 DOI: 10.1016/j.bbapap.2015.02.021] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 02/26/2015] [Accepted: 02/27/2015] [Indexed: 12/25/2022]
Abstract
In addition to its role as a redox coenzyme, NAD is a substrate of various enzymes that split the molecule to either catalyze covalent modifications of target proteins or convert NAD into biologically active metabolites. The coenzyme bioavailability may be significantly affected by these reactions, with ensuing major impact on energy metabolism, cell survival, and aging. Moreover, through the activity of the NAD-dependent deacetylating sirtuins, NAD behaves as a beacon molecule that reports the cell metabolic state, and accordingly modulates transcriptional responses and metabolic adaptations. In this view, NAD biosynthesis emerges as a highly regulated process: it enables cells to preserve NAD homeostasis in response to significant NAD-consuming events and it can be modulated by various stimuli to induce, via NAD level changes, suitable NAD-mediated metabolic responses. Here we review the current knowledge on the regulation of mammalian NAD biosynthesis, with focus on the relevant rate-limiting enzymes. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.
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Affiliation(s)
- Silverio Ruggieri
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Giuseppe Orsomando
- Department of Clinical Sciences, Section of Biochemistry, Polytechnic University of Marche, Ancona, Italy
| | - Leonardo Sorci
- Department of Clinical Sciences, Section of Biochemistry, Polytechnic University of Marche, Ancona, Italy
| | - Nadia Raffaelli
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy.
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Zamporlini F, Ruggieri S, Mazzola F, Amici A, Orsomando G, Raffaelli N. Novel assay for simultaneous measurement of pyridine mononucleotides synthesizing activities allows dissection of the NAD(+) biosynthetic machinery in mammalian cells. FEBS J 2014; 281:5104-19. [PMID: 25223558 DOI: 10.1111/febs.13050] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/10/2014] [Accepted: 09/12/2014] [Indexed: 11/27/2022]
Abstract
The redox coenzyme NAD(+) is also a rate-limiting co-substrate for several enzymes that consume the molecule, thus rendering its continuous re-synthesis indispensable. NAD(+) biosynthesis has emerged as a therapeutic target due to the relevance of NAD(+) -consuming reactions in complex intracellular signaling networks whose alteration leads to many neurologic and metabolic disorders. Distinct metabolic routes, starting from various precursors, are known to support NAD(+) biosynthesis with tissue/cell-specific efficiencies, probably reflecting differential expression of the corresponding rate-limiting enzymes, i.e. nicotinamide phosphoribosyltransferase, quinolinate phosphoribosyltransferase, nicotinate phosphoribosyltransferase and nicotinamide riboside kinase. Understanding the contribution of these enzymes to NAD(+) levels depending on the tissue/cell type and metabolic status is necessary for the rational design of therapeutic strategies aimed at modulating NAD(+) availability. Here we report a simple, fast and sensitive coupled fluorometric assay that enables simultaneous determination of the four activities in whole-cell extracts and biological fluids. Its application to extracts from various mouse tissues, human cell lines and plasma yielded for the first time an overall picture of the tissue/cell-specific distribution of the activities of the various enzymes. The screening enabled us to gather novel findings, including (a) the presence of quinolinate phosphoribosyltransferase and nicotinamide riboside kinase in all examined tissues/cell lines, indicating that quinolinate and nicotinamide riboside are relevant NAD(+) precursors, and (b) the unexpected occurrence of nicotinate phosphoribosyltransferase in human plasma.
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Affiliation(s)
- Federica Zamporlini
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
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Kim H, Shibayama K, Rimbara E, Mori S. Biochemical characterization of quinolinic acid phosphoribosyltransferase from Mycobacterium tuberculosis H37Rv and inhibition of its activity by pyrazinamide. PLoS One 2014; 9:e100062. [PMID: 24949952 PMCID: PMC4065032 DOI: 10.1371/journal.pone.0100062] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 05/22/2014] [Indexed: 11/19/2022] Open
Abstract
Quinolinic acid phosphoribosyltransferase (QAPRTase, EC 2.4.2.19) is a key enzyme in the de novo pathway of nicotinamide adenine dinucleotide (NAD) biosynthesis and a target for the development of new anti-tuberculosis drugs. QAPRTase catalyzes the synthesis of nicotinic acid mononucleotide from quinolinic acid (QA) and 5-phosphoribosyl-1-pyrophosphate (PRPP) through a phosphoribosyl transfer reaction followed by decarboxylation. The crystal structure of QAPRTase from Mycobacterium tuberculosis H37Rv (MtQAPRTase) has been determined; however, a detailed functional analysis of MtQAPRTase has not been published. Here, we analyzed the enzymatic activities of MtQAPRTase and determined the effect on catalysis of the anti-tuberculosis drug pyrazinamide (PZA). The optimum temperature and pH for MtQAPRTase activity were 60°C and pH 9.2. MtQAPRTase required bivalent metal ions and its activity was highest in the presence of Mg2+. Kinetic analyses revealed that the Km values for QA and PRPP were 0.08 and 0.39 mM, respectively, and the kcat values for QA and PRPP were 0.12 and 0.14 [s-1], respectively. When the amino acid residues of MtQAPRTase, which may interact with QA, were substituted with alanine residues, catalytic activity was undetectable. Further, PZA, which is an anti-tuberculosis drug and a structural analog of QA, markedly inhibited the catalytic activity of MtQAPRTase. The structure of PZA may provide the basis for the design of new inhibitors of MtQAPRTase. These findings provide new insights into the catalytic properties of MtQAPRTase.
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Affiliation(s)
- Hyun Kim
- Department of Bacteriology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
| | - Emiko Rimbara
- Department of Bacteriology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
| | - Shigetarou Mori
- Department of Bacteriology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo, Japan
- * E-mail:
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Reyes Ocampo J, Lugo Huitrón R, González-Esquivel D, Ugalde-Muñiz P, Jiménez-Anguiano A, Pineda B, Pedraza-Chaverri J, Ríos C, Pérez de la Cruz V. Kynurenines with neuroactive and redox properties: relevance to aging and brain diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2014; 2014:646909. [PMID: 24693337 PMCID: PMC3945746 DOI: 10.1155/2014/646909] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 12/12/2013] [Accepted: 12/15/2013] [Indexed: 11/18/2022]
Abstract
The kynurenine pathway (KP) is the main route of tryptophan degradation whose final product is NAD(+). The metabolism of tryptophan can be altered in ageing and with neurodegenerative process, leading to decreased biosynthesis of nicotinamide. This fact is very relevant considering that tryptophan is the major source of body stores of the nicotinamide-containing NAD(+) coenzymes, which is involved in almost all the bioenergetic and biosynthetic metabolism. Recently, it has been proposed that endogenous tryptophan and its metabolites can interact and/or produce reactive oxygen species in tissues and cells. This subject is of great importance due to the fact that oxidative stress, alterations in KP metabolites, energetic deficit, cell death, and inflammatory events may converge each other to enter into a feedback cycle where each one depends on the other to exert synergistic actions among them. It is worth mentioning that all these factors have been described in aging and in neurodegenerative processes; however, has so far no one established any direct link between alterations in KP and these factors. In this review, we describe each kynurenine remarking their redox properties, their effects in experimental models, their alterations in the aging process.
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Affiliation(s)
- Jazmin Reyes Ocampo
- Departamento de Neuroquímica, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, S.S.A., Insurgentes Sur 3877, 14269 México, DF, Mexico
- Área de Neurociencias, Departamento de Biología de la Reproducción, Universidad Autónoma Metropolitana-Iztapalapa, 09340 México, DF, Mexico
| | - Rafael Lugo Huitrón
- Departamento de Neuroquímica, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, S.S.A., Insurgentes Sur 3877, 14269 México, DF, Mexico
| | - Dinora González-Esquivel
- Departamento de Neuroquímica, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, S.S.A., Insurgentes Sur 3877, 14269 México, DF, Mexico
| | - Perla Ugalde-Muñiz
- Departamento de Neuroquímica, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, S.S.A., Insurgentes Sur 3877, 14269 México, DF, Mexico
| | - Anabel Jiménez-Anguiano
- Área de Neurociencias, Departamento de Biología de la Reproducción, Universidad Autónoma Metropolitana-Iztapalapa, 09340 México, DF, Mexico
| | - Benjamín Pineda
- Laboratorio de Neuroinmunología, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, S.S.A., 14269 México, DF, Mexico
| | - José Pedraza-Chaverri
- Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, 04510 México, DF, Mexico
| | - Camilo Ríos
- Departamento de Neuroquímica, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, S.S.A., Insurgentes Sur 3877, 14269 México, DF, Mexico
| | - Verónica Pérez de la Cruz
- Departamento de Neuroquímica, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, S.S.A., Insurgentes Sur 3877, 14269 México, DF, Mexico
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Malik SS, Patterson DN, Ncube Z, Toth EA. The crystal structure of human quinolinic acid phosphoribosyltransferase in complex with its inhibitor phthalic acid. Proteins 2013; 82:405-14. [PMID: 24038671 DOI: 10.1002/prot.24406] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/31/2013] [Accepted: 08/21/2013] [Indexed: 11/07/2022]
Abstract
Quinolinic acid (QA), a biologically potent but neurodestructive metabolite is catabolized by quinolinic acid phosphoribosyltransferase (QPRT) in the first step of the de novo NAD(+) biosynthesis pathway. This puts QPRT at the junction of two different pathways, that is, de novo NAD(+) biosynthesis and the kynurenine pathway of tryptophan degradation. Thus, QPRT is an important enzyme in terms of its biological impact and its potential as a therapeutic target. Here, we report the crystal structure of human QPRT bound to its inhibitor phthalic acid (PHT) and kinetic analysis of PHT inhibition of human QPRT. This structure, determined at 2.55 Å resolution, shows an elaborate hydrogen bonding network that helps in recognition of PHT and consequently its substrate QA. In addition to this hydrogen bonding network, we observe extensive van der Waals contacts with the PHT ring that might be important for correctly orientating the substrate QA during catalysis. Moreover, our crystal form allows us to observe an intact hexamer in both the apo- and PHT-bound forms in the same crystal system, which provides a direct comparison of unique subunit interfaces formed in hexameric human QPRT. We call these interfaces "nondimeric interfaces" to distinguish them from the typical dimeric interfaces observed in all QPRTs. We observe significant changes in the nondimeric interfaces in the QPRT hexamer upon binding PHT. Thus, the new structural and functional features of this enzyme we describe here will aid in understanding the function of hexameric QPRTs, which includes all eukaryotic and select prokaryotic QPRTs.
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Affiliation(s)
- Shuja S Malik
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201
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Youn HS, Kim MK, Kang GB, Kim TG, Lee JG, An JY, Park KR, Lee Y, Kang JY, Song HE, Park I, Cho C, Fukuoka SI, Eom SH. Crystal structure of Sus scrofa quinolinate phosphoribosyltransferase in complex with nicotinate mononucleotide. PLoS One 2013; 8:e62027. [PMID: 23626766 PMCID: PMC3633916 DOI: 10.1371/journal.pone.0062027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 03/17/2013] [Indexed: 11/25/2022] Open
Abstract
We have determined the crystal structure of porcine quinolinate phosphoribosyltransferase (QAPRTase) in complex with nicotinate mononucleotide (NAMN), which is the first crystal structure of a mammalian QAPRTase with its reaction product. The structure was determined from protein obtained from the porcine kidney. Because the full protein sequence of porcine QAPRTase was not available in either protein or nucleotide databases, cDNA was synthesized using reverse transcriptase-polymerase chain reaction to determine the porcine QAPRTase amino acid sequence. The crystal structure revealed that porcine QAPRTases have a hexameric structure that is similar to other eukaryotic QAPRTases, such as the human and yeast enzymes. However, the interaction between NAMN and porcine QAPRTase was different from the interaction found in prokaryotic enzymes, such as those of Helicobacter pylori and Mycobacterium tuberculosis. The crystal structure of porcine QAPRTase in complex with NAMN provides a structural framework for understanding the unique properties of the mammalian QAPRTase active site and designing new antibiotics that are selective for the QAPRTases of pathogenic bacteria, such as H. pylori and M. tuberculosis.
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Affiliation(s)
- Hyung-Seop Youn
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
- Stetiz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Mun-Kyoung Kim
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Gil Bu Kang
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Tae Gyun Kim
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
- Stetiz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Jung-Gyu Lee
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
- Stetiz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Jun Yop An
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
- Stetiz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Kyoung Ryoung Park
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
- Stetiz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Youngjin Lee
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
- Stetiz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Jung Youn Kang
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
- Stetiz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Hye-Eun Song
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Inju Park
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Chunghee Cho
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
| | - Shin-Ichi Fukuoka
- School of Culture and Creative Studies, Aoyama Gakuin University, Tokyo, Japan
| | - Soo Hyun Eom
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
- Stetiz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, Republic of Korea
- * E-mail:
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Quinolinate salvage and insights for targeting NAD biosynthesis in group A streptococci. J Bacteriol 2012. [PMID: 23204464 DOI: 10.1128/jb.02002-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The essential coenzyme NAD plays important roles in metabolic reactions and cell regulation in all organisms. As such, NAD synthesis has been investigated as a source for novel antibacterial targets. Cross-species genomics-based reconstructions of NAD metabolism in group A streptococci (GAS), combined with focused experimental testing in Streptococcus pyogenes, led to a better understanding of NAD metabolism in the pathogen. The predicted niacin auxotrophy was experimentally verified, as well as the essential role of the nicotinamidase PncA in the utilization of nicotinamide (Nm). PncA is dispensable in the presence of nicotinate (Na), ruling it out as a viable antibacterial target. The function of the "orphan" NadC enzyme, which is uniquely present in all GAS species despite the absence of other genes of NAD de novo synthesis, was elucidated. Indeed, the quinolinate (Qa) phosphoribosyltransferase activity of NadC from S. pyogenes allows the organism to sustain growth when Qa is present as a sole pyridine precursor. Finally, the redundancy of functional upstream salvage pathways in GAS species narrows the choice of potential drug targets to the two indispensable downstream enzymes of NAD synthesis, nicotinate adenylyltransferase (NadD family) and NAD synthetase (NadE family). Biochemical characterization of NadD confirmed its functional role in S. pyogenes, and its potential as an antibacterial target was supported by inhibition studies with previously identified class I inhibitors of the NadD enzyme family. One of these inhibitors efficiently inhibited S. pyogenes NadD (sp.NadD) in vitro (50% inhibitory concentration [IC(50)], 15 μM), exhibiting a noncompetitive mechanism with a K(i) of 8 μM.
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Youn HS, Kim MK, Kang GB, Kim TG, An JY, Lee JG, Park KR, Lee Y, Fukuoka SI, Eom SH. Crystallization and preliminary X-ray crystallographic analysis of quinolinate phosphoribosyltransferase from porcine kidney in complex with nicotinate mononucleotide. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012. [PMID: 23192029 DOI: 10.1107/s1744309112040638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Quinolinate phosphoribosyltransferase (QAPRTase) is a key enzyme in NAD biosynthesis; it catalyzes the formation of nicotinate mononucleotide (NAMN) from quinolinate and 5-phosphoribosyl-1-pyrophosphate. In order to elucidate the mechanism of NAMN biosynthesis, crystals of Sus scrofa QAPRTase (Ss-QAPRTase) purified from porcine kidney in complex with NAMN were obtained and diffraction data were collected and processed to 2.1 Å resolution. The Ss-QAPRTase-NAMN cocrystals belonged to space group P321, with unit-cell parameters a=119.1, b=119.1, c=93.7 Å, γ=120.0°. The Matthews coefficient and the solvent content were estimated as 3.10 Å3 Da(-1) and 60.3%, respectively, assuming the presence of two molecules in the asymmetric unit.
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Affiliation(s)
- Hyung-Seop Youn
- School of Life Sciences, Cell Dynamics Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
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26
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Gossmann TI, Ziegler M, Puntervoll P, de Figueiredo LF, Schuster S, Heiland I. NAD(+) biosynthesis and salvage--a phylogenetic perspective. FEBS J 2012; 279:3355-63. [PMID: 22404877 DOI: 10.1111/j.1742-4658.2012.08559.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
NAD is best known as an electron carrier and a cosubstrate of various redox reactions. However, over the past 20 years, NAD(+) has been shown to be a key signaling molecule that mediates post-translational protein modifications and serves as precursor of ADP-ribose-containing messenger molecules, which are involved in calcium mobilization. In contrast to its role as a redox carrier, NAD(+)-dependent signaling processes involve the release of nicotinamide (Nam) and require constant replenishment of cellular NAD(+) pools. So far, very little is known about the evolution of NAD(P) synthesis in eukaryotes. In the present study, genes involved in NAD(P) metabolism in 45 species were identified and analyzed with regard to similarities and differences in NAD(P) synthesis. The results show that the Preiss-Handler pathway and NAD(+) kinase are present in all organisms investigated, and thus seem to be ancestral routes. Additionally, two pathways exist that convert Nam to NAD(+); we identified several species that have apparently functional copies of both biosynthetic routes, which have been thought to be mutually exclusive. Furthermore, our findings suggest the parallel phylogenetic appearance of Nam N-methyltransferase, Nam phosphoribosyl transferase, and poly-ADP-ribosyltransferases.
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Affiliation(s)
- Toni I Gossmann
- Department of Molecular Biology, University of Bergen, Norway
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Kang GB, Kim MK, Youn HS, An JY, Lee JG, Park KR, Lee SH, Kim Y, Fukuoka SI, Eom SH. Crystallization and preliminary X-ray crystallographic analysis of human quinolinate phosphoribosyltransferase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 67:38-40. [PMID: 21206019 DOI: 10.1107/s1744309110041011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Accepted: 10/12/2010] [Indexed: 11/10/2022]
Abstract
Quinolinate phosphoribosyltransferase (QPRTase) is a key NAD-biosynthetic enzyme which catalyzes the transfer of quinolinic acid to 5-phosphoribosyl-1-pyrophosphate, yielding nicotinic acid mononucleotide. Homo sapiens QPRTase (Hs-QPRTase) appeared as a hexamer during purification and the protein was crystallized. Diffraction data were collected and processed at 2.8 Å resolution. Native Hs-QPRTase crystals belonged to space group P2(1), with unit-cell parameters a=76.2, b=137.1, c=92.7 Å, β=103.8°. Assuming the presence of six molecules in the asymmetric unit, the calculated Matthews coefficient is 2.46 Å3 Da(-1), which corresponds to a solvent content of 49.9%.
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Affiliation(s)
- Gil Bu Kang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
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Rozenberg A, Lee JK. Theoretical studies of the quinolinic acid to nicotinic acid mononucleotide transformation. J Org Chem 2010; 73:9314-9. [PMID: 18954112 DOI: 10.1021/jo8012379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quinolinate phosphoribosyl transferase (QPRTase) is an essential enzyme that catalyzes the transformation of quinolinic acid (QA) to nicotinic acid mononucleotide (NAMN), a key step on the de novo pathway for nicotinamide adenine dinucleotide (NAD) biosynthesis. We describe herein a theoretical study of the intrinsic energetics associated with the possible mechanistic pathways by which QA forms NAMN. Our main interest is in probing the decarboxylation step, which is intriguing since the product is a vinylic anion, not unlike the reaction catalyzed by orotidine 5'-monophosphate (OMP) decarboxylase, an enzyme whose mechanism is under fierce debate. Our calculations indicate that a path involving a quinolinic acid mononucleotide (QAMN) intermediate is the most energetically attractive, favoring decarboxylation. We also find that the monocarboxylate form of QAMN will decarboxylate much more favorably energetically than will the dicarboxylate form of QAMN. Furthermore, our calculations indicate that decarboxylation is not a likely first step; the substrate in such a mechanism would prefer to decarboxylate at the C3 position, not the desired C2 position. We also discuss our results in the context of existing experimental data.
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Affiliation(s)
- Aleksandr Rozenberg
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
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29
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Lin H, Kwan AL, Dutcher SK. Synthesizing and salvaging NAD: lessons learned from Chlamydomonas reinhardtii. PLoS Genet 2010; 6:e1001105. [PMID: 20838591 PMCID: PMC2936527 DOI: 10.1371/journal.pgen.1001105] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Accepted: 08/02/2010] [Indexed: 01/30/2023] Open
Abstract
The essential coenzyme nicotinamide adenine dinucleotide (NAD+) plays important roles in metabolic reactions and cell regulation in all organisms. Bacteria, fungi, plants, and animals use different pathways to synthesize NAD+. Our molecular and genetic data demonstrate that in the unicellular green alga Chlamydomonas NAD+ is synthesized from aspartate (de novo synthesis), as in plants, or nicotinamide, as in mammals (salvage synthesis). The de novo pathway requires five different enzymes: L-aspartate oxidase (ASO), quinolinate synthetase (QS), quinolate phosphoribosyltransferase (QPT), nicotinate/nicotinamide mononucleotide adenylyltransferase (NMNAT), and NAD+ synthetase (NS). Sequence similarity searches, gene isolation and sequencing of mutant loci indicate that mutations in each enzyme result in a nicotinamide-requiring mutant phenotype in the previously isolated nic mutants. We rescued the mutant phenotype by the introduction of BAC DNA (nic2-1 and nic13-1) or plasmids with cloned genes (nic1-1 and nic15-1) into the mutants. NMNAT, which is also in the de novo pathway, and nicotinamide phosphoribosyltransferase (NAMPT) constitute the nicotinamide-dependent salvage pathway. A mutation in NAMPT (npt1-1) has no obvious growth defect and is not nicotinamide-dependent. However, double mutant strains with the npt1-1 mutation and any of the nic mutations are inviable. When the de novo pathway is inactive, the salvage pathway is essential to Chlamydomonas for the synthesis of NAD+. A homolog of the human SIRT6-like gene, SRT2, is upregulated in the NS mutant, which shows a longer vegetative life span than wild-type cells. Our results suggest that Chlamydomonas is an excellent model system to study NAD+ metabolism and cell longevity. Nicotinamide adenine dinucleotide (NAD+) is an essential coenzyme. NAD+ is necessary for electron transfer in many metabolic reactions. NAD+ functions as a substrate for several enzymes, one of which is sirtuin, an enzyme involved in gene regulation and aging. NAD+ can be synthesized either from amino acids (de novo) or metabolites (salvage). Given the importance of NAD+, enzymes involved in NAD+ synthesis are targets for drug discovery. In the unicellular green alga Chlamydomonas we investigated both the de novo and salvage NAD+ biosynthetic pathways. Mutations in the plant-like de novo synthesis pathway lead to a nicotinamide-requiring phenotype. We identified an insertional mutation in the first enzyme in the mammal-like salvage pathway; it has no growth defect in cells with an active de novo synthesis pathway but causes lethality when the de novo synthesis pathway is inactive. Coupled with NAD+ biosynthesis, sirtuin is involved in NAD+ consumption. Our study links upregulation of a sirtuin gene with extended life span in the nic13-1 mutant strain, which has a defective de novo synthesis pathway and suggests that Chlamydomonas is an excellent genetic model to study NAD+ metabolism and cell longevity.
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Affiliation(s)
- Huawen Lin
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Alan L. Kwan
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Susan K. Dutcher
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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Bello Z, Grubmeyer C. Roles for cationic residues at the quinolinic acid binding site of quinolinate phosphoribosyltransferase. Biochemistry 2010; 49:1388-95. [PMID: 20047306 DOI: 10.1021/bi9018225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quinolinic acid phosphoribosyltransferase (QAPRTase, EC 2.4.2.19) forms nicotinate mononucleotide (NAMN) from quinolinic acid (QA) and 5-phosphoribosyl 1-pyrophosphate (PRPP). Previously determined crystal structures of QAPRTase.QA and QAPRTase.PA.PRPP complexes show positively charged residues (Arg118, Arg152, Arg175, Lys185, and His188) lining the QA binding site. To assess the roles of these residues in the Salmonella typhimurium QAPRTase reaction, they were individually mutated to alanine and the recombinant proteins overexpressed and purified from a recombineered Escherichia coli strain that lacks the QAPRTase gene. Gel filtration indicated that the mutations did not affect the dimeric aggregation state of the enzymes. Arg175 is critical for the QAPRTase reaction, and its mutation to alanine produced an inactive enzyme. The k(cat) values for R152A and K185A were reduced by 33-fold and 625-fold, and binding affinity of PRPP and QA to the enzymes decreased. R152A and K185A mutants displayed 116-fold and 83-fold increases in activity toward the normally inactive QA analogue, nicotinic acid (NA), indicating roles for these residues in defining the substrate specificity of QAPRTase. Moreover, K185A QAPRTase displayed a 300-fold higher k(cat)/K(m) for NA over the natural substrate QA. Pre-steady-state analysis of K185A with QA revealed a burst of nucleotide formation followed by a slower steady-state rate, unlike the linear kinetics of WT. Intriguingly, pre-steady-state analysis of K185A with NA produced a rapid but linear rate for NAMN formation. The result implies a critical role for Lys185 in the chemistry of the QAPRTase intermediate. Arg118 is an essential residue that reaches across the dimer interface. Mutation of Arg118 to alanine resulted in 5000-fold decrease in k(cat) value and a decrease in the binding affinity of QA and PRPP to R152A. Equimolar mixtures of R118A with inactive or virtually inactive mutants produced approximately 50% of the enzymatic activity of WT, establishing an interfacial role for Arg118 during catalysis.
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Affiliation(s)
- Zainab Bello
- Fels Institute for Cancer Research and Molecular Biology and Department of Biochemistry, Temple University School of Medicine, 3307 North Broad Street, Philadelphia, Pennsylvania 19140, USA
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Abstract
This paper describes the cloning, purification, and characterization of thioredoxin (Trx) and thioredoxin reductase (TrxR) and the structure determination of TrxR from the ionizing radiation-tolerant bacterium Deinococcus radiodurans strain R1. The genes from D. radiodurans encoding Trx and TrxR were amplified by PCR, inserted into a pET expression vector, and overexpressed in Escherichia coli. The overexpressed proteins were purified by metal affinity chromatography, and their activity was demonstrated using well-established assays of insulin precipitation (for Trx), 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) reduction, and insulin reduction (for TrxR). In addition, the crystal structure of oxidized TrxR was determined at 1.9-A resolution. The overall structure was found to be very similar to that of E. coli TrxR and homodimeric with both NADPH- and flavin adenine dinucleotide (FAD)-binding domains containing variants of the canonical nucleotide binding fold, the Rossmann fold. The K(m) (5.7 muM) of D. radiodurans TrxR for D. radiodurans Trx was determined and is about twofold higher than that of the E. coli thioredoxin system. However, D. radiodurans TrxR has a much lower affinity for E. coli Trx (K(m), 44.4 muM). Subtle differences in the surface charge and shape of the Trx binding site on TrxR may account for the differences in recognition. Because it has been suggested that TrxR from D. radiodurans may have dual cofactor specificity (can utilize both NADH and NADPH), D. radiodurans TrxR was tested for its ability to utilize NADH as well. Our results show that D. radiodurans TrxR can utilize only NADPH for activity.
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Deng H, Cross SM, McGlinchey RP, Hamilton JT, O'Hagan D. In Vitro Reconstituted Biotransformation of 4-Fluorothreonine from Fluoride Ion: Application of the Fluorinase. ACTA ACUST UNITED AC 2008; 15:1268-76. [DOI: 10.1016/j.chembiol.2008.10.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 10/13/2008] [Accepted: 10/16/2008] [Indexed: 11/16/2022]
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Liu H, Naismith JH. A simple and efficient expression and purification system using two newly constructed vectors. Protein Expr Purif 2008; 63:102-11. [PMID: 18845260 DOI: 10.1016/j.pep.2008.09.008] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2008] [Revised: 09/02/2008] [Accepted: 09/04/2008] [Indexed: 11/25/2022]
Abstract
Structural biology places a high demand on proteins both in terms of quality and quantity. Although many protein expression and purification systems have been developed, an efficient and simple system which can be easily adapted is desirable. Here, we report a new system which combines improved expression, solubility screening and purification efficiency. The system is based on two newly constructed vectors, pEHISTEV and pEHISGFPTEV derived from a pET vector. Both vectors generate a construct with an amino-terminal hexahistidine tag (His-tag). In addition, pEHISGFPTEV expresses a protein with an N-terminal His-tagged green fluorescent protein (GFP) fusion to allow rapid quantitation of soluble protein. Both vectors have a tobacco etch virus (TEV) protease cleavage site that allows for production of protein with only two additional N-terminal residues and have the same multiple cloning site which enables parallel cloning. Protein purification is a simple two-stage nickel affinity chromatography based on the His tag removal. A total of seven genes were tested using this system. Expression was optimised using pEHISGFPTEV constructs by monitoring the GFP fluorescence and the soluble target proteins were quantified using spectrophotometric analysis. All the tested proteins were purified with sufficient quantity and quality to attempt structure determination. This system has been proven to be simple and effective for structural biology. The system is easily adapted to include other vectors, tags or fusions and therefore has the potential to be broadly applicable.
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Affiliation(s)
- Huanting Liu
- Centre for Biomolecular Science, BMS Building, University of St. Andrews, North Haugh, St. Andrews KY16 9ST, Fife, Scotland, UK.
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