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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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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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Ajunwa OM, Odeniyi OA, Garuba EO, Nair M, Marsili E, Onilude AA. Evaluation of extracellular electron transfer in Pseudomonas aeruginosa by co-expression of intermediate genes in NAD synthetase production pathway. World J Microbiol Biotechnol 2022; 38:90. [PMID: 35426517 DOI: 10.1007/s11274-022-03274-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 03/31/2022] [Indexed: 12/11/2022]
Abstract
Pseudomonas aeruginosa (PA) is an electrogenic bacterium, in which extracellular electron transfer (EET) is mediated by microbially-produced phenazines, especially pyocyanin. Increasing EET rate in electrogenic bacteria is key for the development of biosensors and bioelectrofermentation processes. In this work, the production of pyocyanin, Nicotinamide Adenine Dinucleotide (NAD) and NAD synthetase by the electrogenic strain PA-A4 is determined using a Microbial Fuel Cell (MFC). Effects of metabolic inhibition and enhancement of pyocyanin and NAD synthetase on NAD/NADH levels and electrogenicity was demonstrated by short chronoamperometry measurements (0-48 h). Combined overexpression of two intermediate NAD synthetase production genes-nicotinic acid mononucleotide adenyltransferase (nadD) and quinolic acid phosphoribosyltransferase (nadC) genes, which are distant on the PA genomic map, enabled co-transcription and increased NAD synthetase activity. The resulting PA-A4 nadD + nadC shows increases in pyocyanin concentration, NAD synthetase activity, NAD/NADH levels, and MFC potential, all significantly higher than its wild type. Extracellular respiratory mechanisms in PA are linked with NAD metabolism, and targeted increased yield of NAD could directly lead to enhanced EET. A previous attempt at enhancing NAD synthetase for electrogenicity by targeting the terminal NAD synthetase gene (nadE) in standard P. aeruginosa PA01 had earlier been reported. Our work however, poses another route to electrogenicity enhancement in PA using; a combination of nadD and nadC. Further experiments are needed to understand specific intracellular mechanisms governing how over-expression of nadD and nadC induced activity of NadE protein. These findings significantly advance the knowledge of the versatility of NAD biosynthetic genes in PA electrogenicity.
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Affiliation(s)
- Obinna Markraphael Ajunwa
- Department of Chemical and Materials Engineering, Nazarbayev University, Nur-Sultan, Kazakhstan. .,Department of Microbiology, School of Life Sciences, Modibbo Adama University, Yola, Nigeria.
| | - Olubusola Ayoola Odeniyi
- Microbial Physiology and Biochemistry Research Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Nigeria
| | - Emmanuel Oluwaseun Garuba
- Microbial Physiology and Biochemistry Research Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Nigeria
| | - Mrinalini Nair
- Department of Microbiology and Biotechnology Center, Maharaja Sayajirao University of Baroda, Gujarat, India
| | - Enrico Marsili
- Department of Chemical and Materials Engineering, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Abiodun Anthony Onilude
- Microbial Physiology and Biochemistry Research Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Nigeria
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Ma X, Zhao X, Zhang H, Zhang Y, Sun S, Li Y, Long Z, Liu Y, Zhang X, Li R, Tan L, Jiang L, Zhu JK, Li L. MAG2 and MAL Regulate Vesicle Trafficking and Auxin Homeostasis With Functional Redundancy. FRONTIERS IN PLANT SCIENCE 2022; 13:849532. [PMID: 35371137 PMCID: PMC8966843 DOI: 10.3389/fpls.2022.849532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Auxin is a central phytohormone and controls almost all aspects of plant development and stress response. Auxin homeostasis is coordinately regulated by biosynthesis, catabolism, transport, conjugation, and deposition. Endoplasmic reticulum (ER)-localized MAIGO2 (MAG2) complex mediates tethering of arriving vesicles to the ER membrane, and it is crucial for ER export trafficking. Despite important regulatory roles of MAG2 in vesicle trafficking, the mag2 mutant had mild developmental abnormalities. MAG2 has one homolog protein, MAG2-Like (MAL), and the mal-1 mutant also had slight developmental phenotypes. In order to investigate MAG2 and MAL regulatory function in plant development, we generated the mag2-1 mal-1 double mutant. As expected, the double mutant exhibited serious developmental defects and more alteration in stress response compared with single mutants and wild type. Proteomic analysis revealed that signaling, metabolism, and stress response in mag2-1 mal-1 were affected, especially membrane trafficking and auxin biosynthesis, signaling, and transport. Biochemical and cell biological analysis indicated that the mag2-1 mal-1 double mutant had more serious defects in vesicle transport than the mag2-1 and mal-1 single mutants. The auxin distribution and abundance of auxin transporters were altered significantly in the mag2-1 and mal-1 single mutants and mag2-1 mal-1 double mutant. Our findings suggest that MAG2 and MAL regulate plant development and auxin homeostasis by controlling membrane trafficking, with functional redundancy.
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Affiliation(s)
- Xiaohui Ma
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, College of Life Sciences, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Xiaonan Zhao
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, College of Life Sciences, Ministry of Education, Northeast Forestry University, Harbin, China
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Hailong Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, College of Life Sciences, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Yiming Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, College of Life Sciences, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Shanwen Sun
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, College of Life Sciences, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Ying Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, College of Life Sciences, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Zhengbiao Long
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Yuqi Liu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, College of Life Sciences, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Xiaomeng Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, College of Life Sciences, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Rongxia Li
- Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Li Tan
- Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lixi Jiang
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lixin Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, College of Life Sciences, Ministry of Education, Northeast Forestry University, Harbin, China
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5
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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: 46] [Impact Index Per Article: 6.6] [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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Khan S, Pandey SS, Jyotshna, Shanker K, Khan F, Rahman LU. Cloning and functional characterization of quinolinic acid phosphoribosyl transferase (QPT) gene of Nicotiana tabacum. PHYSIOLOGIA PLANTARUM 2017; 160:253-265. [PMID: 28256030 DOI: 10.1111/ppl.12559] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/22/2016] [Accepted: 01/07/2017] [Indexed: 06/06/2023]
Abstract
The quinolinate phosphoribosyl transferase (QPT) is a key enzyme that converts quinolinic acid into nicotinic acid mononucleotide. The QPT gene plays an essential role in the pyridine nucleotide cycle as well as in the biosynthetic pathway of the alkaloid nicotine. However, a clear role for QPT is yet to be characterized to validate the actual function of this gene in planta. In this study, an RNA interference (RNAi) approach was used to reveal the functional role of QPT. Transformation and analysis of the hairy roots (HRs) of the Nicotiana leaf explants was used, followed by plant regeneration and analysis. High-performance liquid chromatography (HPLC) analysis of the HRs and of the regenerated plants both revealed altered alkaloid biosynthetic cycle, with a substantially reduced content of nicotine and anabasine. The transgenic plants exhibited a significantly altered phenotype and growth pattern. Also, silencing of QPT led to a decrease in chlorophyll content, maximum quantum efficiency of PSII, net CO2 assimilation and starch content. Results clearly demonstrated that QPT was not only involved in the biosynthetic pathway of the alkaloids but also affected plant growth and development. Our results provide information to be considered when trying to engineer the secondary metabolite quality and quantity.
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Affiliation(s)
- Sana Khan
- Plant Biotechnology Division, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Shiv Shanker Pandey
- Microbial Technology Department, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Jyotshna
- Analytical Chemistry Department, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Karuna Shanker
- Analytical Chemistry Department, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Feroz Khan
- Metabolic and Structural Biology Department, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
| | - Laiq Ur Rahman
- Plant Biotechnology Division, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow 226015, India
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Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance. Microbiol Mol Biol Rev 2016; 81:81/1/e00040-16. [PMID: 28031352 DOI: 10.1128/mmbr.00040-16] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Phosphoribosyl diphosphate (PRPP) is an important intermediate in cellular metabolism. PRPP is synthesized by PRPP synthase, as follows: ribose 5-phosphate + ATP → PRPP + AMP. PRPP is ubiquitously found in living organisms and is used in substitution reactions with the formation of glycosidic bonds. PRPP is utilized in the biosynthesis of purine and pyrimidine nucleotides, the amino acids histidine and tryptophan, the cofactors NAD and tetrahydromethanopterin, arabinosyl monophosphodecaprenol, and certain aminoglycoside antibiotics. The participation of PRPP in each of these metabolic pathways is reviewed. Central to the metabolism of PRPP is PRPP synthase, which has been studied from all kingdoms of life by classical mechanistic procedures. The results of these analyses are unified with recent progress in molecular enzymology and the elucidation of the three-dimensional structures of PRPP synthases from eubacteria, archaea, and humans. The structures and mechanisms of catalysis of the five diphosphoryltransferases are compared, as are those of selected enzymes of diphosphoryl transfer, phosphoryl transfer, and nucleotidyl transfer reactions. PRPP is used as a substrate by a large number phosphoribosyltransferases. The protein structures and reaction mechanisms of these phosphoribosyltransferases vary and demonstrate the versatility of PRPP as an intermediate in cellular physiology. PRPP synthases appear to have originated from a phosphoribosyltransferase during evolution, as demonstrated by phylogenetic analysis. PRPP, furthermore, is an effector molecule of purine and pyrimidine nucleotide biosynthesis, either by binding to PurR or PyrR regulatory proteins or as an allosteric activator of carbamoylphosphate synthetase. Genetic analyses have disclosed a number of mutants altered in the PRPP synthase-specifying genes in humans as well as bacterial species.
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8
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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: 1.6] [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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9
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Cookson TVM, Evans GL, Castell A, Baker EN, Lott JS, Parker EJ. Structures of Mycobacterium tuberculosis Anthranilate Phosphoribosyltransferase Variants Reveal the Conformational Changes That Facilitate Delivery of the Substrate to the Active Site. Biochemistry 2016; 54:6082-92. [PMID: 26356348 DOI: 10.1021/acs.biochem.5b00612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Anthranilate phosphoribosyltransferase (AnPRT) is essential for the biosynthesis of tryptophan in Mycobacterium tuberculosis (Mtb). This enzyme catalyzes the second committed step in tryptophan biosynthesis, the Mg²⁺-dependent reaction between 5'-phosphoribosyl-1'-pyrophosphate (PRPP) and anthranilate. The roles of residues predicted to be involved in anthranilate binding have been tested by the analysis of six Mtb-AnPRT variant proteins. Kinetic analysis showed that five of six variants were active and identified the conserved residue R193 as being crucial for both anthranilate binding and catalytic function. Crystal structures of these Mtb-AnPRT variants reveal the ability of anthranilate to bind in three sites along an extended anthranilate tunnel and expose the role of the mobile β2-α6 loop in facilitating the enzyme's sequential reaction mechanism. The β2-α6 loop moves sequentially between a "folded" conformation, partially occluding the anthranilate tunnel, via an "open" position to a "closed" conformation, which supports PRPP binding and allows anthranilate access via the tunnel to the active site. The return of the β2-α6 loop to the "folded" conformation completes the catalytic cycle, concordantly allowing the active site to eject the product PRA and rebind anthranilate at the opening of the anthranilate tunnel for subsequent reactions. Multiple anthranilate molecules blocking the anthranilate tunnel prevent the β2-α6 loop from undergoing the conformational changes required for catalysis, thus accounting for the unusual substrate inhibition of this enzyme.
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Affiliation(s)
- Tammie V M Cookson
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, and Department of Chemistry, University of Canterbury , 20 Kirkwood Avenue, Christchurch 8140, New Zealand
| | - Genevieve L Evans
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland , 3 Symonds Street, Auckland 1142, New Zealand
| | - Alina Castell
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland , 3 Symonds Street, Auckland 1142, New Zealand
| | - Edward N Baker
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland , 3 Symonds Street, Auckland 1142, New Zealand
| | - J Shaun Lott
- Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, University of Auckland , 3 Symonds Street, Auckland 1142, New Zealand
| | - Emily J Parker
- Maurice Wilkins Centre for Molecular Biodiscovery, Biomolecular Interaction Centre, and Department of Chemistry, University of Canterbury , 20 Kirkwood Avenue, Christchurch 8140, New Zealand
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10
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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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11
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Hamidou Soumana I, Tchicaya B, Simo G, Geiger A. Comparative gene expression of Wigglesworthia inhabiting non-infected and Trypanosoma brucei gambiense-infected Glossina palpalis gambiensis flies. Front Microbiol 2014; 5:620. [PMID: 25452752 PMCID: PMC4233935 DOI: 10.3389/fmicb.2014.00620] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 10/30/2014] [Indexed: 12/29/2022] Open
Abstract
Tsetse flies (Glossina sp.) that transmit trypanosomes causing human (and animal) African trypanosomiasis (HAT and AAT, respectively) harbor symbiotic microorganisms, including the obligate primary symbiont Wigglesworthia glossinidia. A relationship between Wigglesworthia and tsetse fly infection by trypanosomes has been suggested, as removal of the symbiont results in a higher susceptibility to midgut infection in adult flies. To investigate this relationship and to decipher the role of W. glossinidia in the fly's susceptibility to trypanosome infection, we challenged flies with trypanosomes and subsequently analyzed and compared the transcriptomes of W. glossinidia from susceptible and refractory tsetse flies at three time points (3, 10, and 20 days). More than 200 W. glossinidia genes were found to be differentially expressed between susceptible and refractory flies. The high specificity of these differentially expressed genes makes it possible to distinguish Wigglesworthia inhabiting these two distinct groups of flies. Furthermore, gene expression patterns were observed to evolve during the infection time course, such that very few differentially expressed genes were found in common in Wigglesworthia from the 3-, 10- and 20-day post-feeding fly samples. The overall results clearly demonstrate that the taking up of trypanosomes by flies, regardless of whether flies proceed with the developmental program of Trypanosoma brucei gambiense, strongly alters gene expression in Wigglesworthia. These results therefore provide a novel framework for studies that aim to decrease or even abolish tsetse fly vector competence.
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Affiliation(s)
| | - Bernadette Tchicaya
- UMR 177, Institut de Recherche pour le Développement-CIRAD Montpellier, France
| | - Gustave Simo
- Department of Biochemistry, Faculty of Science, University of Dschang Dschang, Cameroon
| | - Anne Geiger
- UMR 177, Institut de Recherche pour le Développement-CIRAD Montpellier, France
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12
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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: 19] [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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13
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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: 15] [Impact Index Per Article: 1.3] [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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14
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Ochoa-Leyva A, Montero-Morán G, Saab-Rincón G, Brieba LG, Soberón X. Alternative splice variants in TIM barrel proteins from human genome correlate with the structural and evolutionary modularity of this versatile protein fold. PLoS One 2013; 8:e70582. [PMID: 23950966 PMCID: PMC3741200 DOI: 10.1371/journal.pone.0070582] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 06/20/2013] [Indexed: 12/20/2022] Open
Abstract
After the surprisingly low number of genes identified in the human genome, alternative splicing emerged as a major mechanism to generate protein diversity in higher eukaryotes. However, it is still not known if its prevalence along the genome evolution has contributed to the overall functional protein diversity or if it simply reflects splicing noise. The (βα)8 barrel or TIM barrel is one of the most frequent, versatile, and ancient fold encountered among enzymes. Here, we analyze the structural modifications present in TIM barrel proteins from the human genome product of alternative splicing events. We found that 87% of all splicing events involved deletions; most of these events resulted in protein fragments that corresponded to the (βα)2, (βα)4, (βα)5, (βα)6, and (βα)7 subdomains of TIM barrels. Because approximately 7% of all the splicing events involved internal β-strand substitutions, we decided, based on the genomic data, to design β-strand and α-helix substitutions in a well-studied TIM barrel enzyme. The biochemical characterization of one of the chimeric variants suggests that some of the splice variants in the human genome with β-strand substitutions may be evolving novel functions via either the oligomeric state or substrate specificity. We provide results of how the splice variants represent subdomains that correlate with the independently folding and evolving structural units previously reported. This work is the first to observe a link between the structural features of the barrel and a recurrent genetic mechanism. Our results suggest that it is reasonable to expect that a sizeable fraction of splice variants found in the human genome represent structurally viable functional proteins. Our data provide additional support for the hypothesis of the origin of the TIM barrel fold through the assembly of smaller subdomains. We suggest a model of how nature explores new proteins through alternative splicing as a mechanism to diversify the proteins encoded in the human genome.
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Affiliation(s)
- Adrián Ochoa-Leyva
- Instituto Nacional de Medicina Genómica (INMEGEN), México City, México
- * E-mail: (AOL); (XS)
| | - Gabriela Montero-Morán
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Gloria Saab-Rincón
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Xavier Soberón
- Instituto Nacional de Medicina Genómica (INMEGEN), México City, México
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- * E-mail: (AOL); (XS)
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15
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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: 3] [Impact Index Per Article: 0.3] [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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16
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Koch I, Kreuchwig A, May P. Hierarchical representation of supersecondary structures using a graph-theoretical approach. Methods Mol Biol 2013; 932:7-33. [PMID: 22987344 DOI: 10.1007/978-1-62703-065-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The unique representation of proteins becomes more and more important with the growing number of known protein structure data. Graph-theory provides many methods not only for the description but also for comparison and classification of protein structures. Here, we describe a graph-theoretical modeling approach of the protein supersecondary structure. The resulting linear notations are intuitive and can be used to find common substructures very fast and easily. We illustrate the necessary definitions by biological examples and discuss the representation of various supersecondary structure motifs.
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Affiliation(s)
- Ina Koch
- Molecular Bioinformatics Group, Institute of Computer Science, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
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17
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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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18
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Ryan SM, Cane KA, DeBoer KD, Sinclair SJ, Brimblecombe R, Hamill JD. Structure and expression of the quinolinate phosphoribosyltransferase (QPT) gene family in Nicotiana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 188-189:102-10. [PMID: 22525250 DOI: 10.1016/j.plantsci.2012.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 02/08/2012] [Accepted: 02/11/2012] [Indexed: 05/14/2023]
Abstract
Synthesis of wound-inducible pyridine alkaloids is characteristic of species in the genus Nicotiana. The enzyme quinolinate phosphoribosyltransferase (QPT) plays a key role in facilitating the availability of precursors for alkaloid synthesis, in addition to its ubiquitous role in enabling NAD(P)(H) synthesis. In a previous study, we reported that Nicotiana tabacum L. var. NC 95 possesses a QPT RFLP pattern similar to its model paternal progenitor species, Nicotiana tomentosiformis Goodsp. Here we show that although some varieties of N. tabacum (e.g. NC 95 and LAFC 53) possess QPT genomic contributions from only its paternal progenitor species, this is not the case for many other N. tabacum varieties (e.g. Xanthi, Samsun, Petite Havana SR1 and SC 58) where genomic QPT sequences from both diploid progenitor species have been retained. We also report that QPT is encoded by duplicate genes (designated QPT1 and QPT2) not only in N. tabacum, but also its model progenitor species Nicotiana sylvestris Speg. and Comes and N. tomentosiformis as well as in the diploid species Nicotiana glauca Graham. Previous studies have demonstrated that the N. tabacum QPT2 gene encodes a functional enzyme via complementation of a nadC(-)Escherichia coli mutant. Using a similar experimental approach here, we demonstrate that the N. tabacum QPT1 gene also encodes a functional QPT protein. We observe too that QPT2 is the predominate transcript present in both alkaloid and non-alkaloid synthesising tissues in N. tabacum and that promoter regions of both QPT1 and QPT2 are able to produce GUS activity in reproductive tissues. In N. tabacum and in several other Nicotiana species tested, QPT2 transcript levels increase following wounding or methyl jasmonate treatment whilst QPT1 transcript levels remain largely unaltered by these treatments. Together with conclusions from recently published studies involving functional interaction of MYC2-bHLH and specific ERF-type and transcription factors with QPT2-promoter sequences from N. tabacum, our results suggest that whilst both members of the QPT gene family can contribute to the transcript pool in both alkaloid producing and non-producing tissues, it is QPT2 that is regulated in association with inducible defensive pyridine alkaloid synthesis in species across the genus Nicotiana.
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Affiliation(s)
- S M Ryan
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
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19
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Grubmeyer C, Hansen MR, Fedorov AA, Almo SC. Structure of Salmonella typhimurium OMP synthase in a complete substrate complex. Biochemistry 2012; 51:4397-405. [PMID: 22531064 DOI: 10.1021/bi300083p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dimeric Salmonella typhimurium orotate phosphoribosyltransferase (OMP synthase, EC 2.4.2.10), a key enzyme in de novo pyrimidine nucleotide synthesis, has been cocrystallized in a complete substrate E·MgPRPP·orotate complex and the structure determined to 2.2 Å resolution. This structure resembles that of Saccharomyces cerevisiae OMP synthase in showing a dramatic and asymmetric reorganization around the active site-bound ligands but shares the same basic topology previously observed in complexes of OMP synthase from S. typhimurium and Escherichia coli. The catalytic loop (residues 99-109) contributed by subunit A is reorganized to close the active site situated in subunit B and to sequester it from solvent. Furthermore, the overall structure of subunit B is more compact, because of movements of the amino-terminal hood and elements of the core domain. The catalytic loop of subunit B remains open and disordered, and subunit A retains the more relaxed conformation observed in loop-open S. typhimurium OMP synthase structures. A non-proline cis-peptide formed between Ala71 and Tyr72 is seen in both subunits. The loop-closed catalytic site of subunit B reveals that both the loop and the hood interact directly with the bound pyrophosphate group of PRPP. In contrast to dimagnesium hypoxanthine-guanine phosphoribosyltransferases, OMP synthase contains a single catalytic Mg(2+) in the closed active site. The remaining pyrophosphate charges of PRPP are neutralized by interactions with Arg99A, Lys100B, Lys103A, and His105A. The new structure confirms the importance of loop movement in catalysis by OMP synthase and identifies several additional movements that must be accomplished in each catalytic cycle. A catalytic mechanism based on enzymic and substrate-assisted stabilization of the previously documented oxocarbenium transition state structure is proposed.
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Affiliation(s)
- Charles Grubmeyer
- Department of Biochemistry and Fels Research Institute, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, United States.
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20
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Characterization of human nicotinate phosphoribosyltransferase: Kinetic studies, structure prediction and functional analysis by site-directed mutagenesis. Biochimie 2011; 94:300-9. [PMID: 21742010 DOI: 10.1016/j.biochi.2011.06.033] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 06/24/2011] [Indexed: 11/20/2022]
Abstract
Nicotinate phosphoribosyltransferase (NaPRT, EC 2.4.2.11) catalyzes the conversion of nicotinate (Na) to nicotinate mononucleotide, the first reaction of the Preiss-Handler pathway for the biosynthesis of NAD(+). Even though NaPRT activity has been described to be responsible for the ability of Na to increase NAD(+) levels in human cells more effectively than nicotinamide (Nam), so far a limited number of studies on the human NaPRT have appeared. Here, extensive characterization of a recombinant human NaPRT is reported. We determined its major kinetic parameters and assayed the influence of different compounds on its enzymatic activity. In particular, ATP showed an apparent dual stimulation/inhibition effect at low/high substrates saturation, respectively, consistent with a negative cooperativity model, whereas inorganic phosphate was found to act as an activator. Among other metabolites assayed, including nucleotides, nucleosides, and intermediates of carbohydrates metabolism, some showed inhibitory properties, i.e. CoA, several acyl-CoAs, glyceraldehyde 3-phosphate, phosphoenolpyruvate, and fructose 1,6-bisphosphate, whereas dihydroxyacetone phosphate and pyruvate exerted a stimulatory effect. Furthermore, in light of the absence of crystallographic data, we performed homology modeling to predict the protein three-dimensional structure, and molecular docking simulations to identify residues involved in the recognition and stabilization of several ligands. Most of these residues resulted universally conserved among NaPRTs, and, in this study, their importance for enzyme activity was validated through site-directed mutagenesis.
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21
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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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22
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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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Bello Z, Stitt B, Grubmeyer C. Interactions at the 2 and 5 positions of 5-phosphoribosyl pyrophosphate are essential in Salmonella typhimurium quinolinate phosphoribosyltransferase. Biochemistry 2010; 49:1377-87. [PMID: 20047307 DOI: 10.1021/bi9018219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quinolinate phosphoribosyltransferase (QAPRTase, EC 2.4.2.19) catalyzes an unusual phosphoribosyl transfer that is linked to a decarboxylation reaction to form the NAD precursor nicotinate mononucleotide, carbon dioxide, and pyrophosphate from quinolinic acid (QA) and 5-phosphoribosyl 1-pyrophosphate (PRPP). Structural studies and sequence similarities with other PRTases have implicated Glu214, Asp235, Lys153, and Lys284 in contributing to catalysis through direct interaction with PRPP. The four residues were substituted by site-directed mutagenesis. A nadC deletant form of BL21DE3 was created to eliminate trace contamination by chromosomal QAPRTase. The mutant enzymes were readily purified and retained their dimeric aggregation state on gel filtration. Substitution of Lys153 with Ala resulted in an inactive enzyme, indicating its essential nature. Mutation of Glu214 to Ala or Asp caused at least a 4000-fold reduction in k(cat), with 10-fold increases in K(m) and K(D) values for PRPP. However, mutation of Glu214 to Gln had only modest effects on ligand binding and catalysis. pH profiles indicated that the deprotonated form of a residue with pK(a) of 6.9 is essential for catalysis. The WT-like pH profile of the E214Q mutant indicated that Glu214 is not that residue. Mutation of Asp235 to Ala did not affect ligand binding or catalysis. Mutation of Lys284 to Ala decreased k(cat) by 30-fold and increased K(m) and K(D) values for PRPP by 80-fold and at least 20-fold, respectively. The study suggests that Lys153 is necessary for catalysis and important for PRPP binding, Glu214 provides a hydrogen bond necessary for catalysis but does not act as a base or electrostatically to stabilize the transition state, Lys284 is involved in PRPP binding, and Asp235 is not essential.
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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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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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Schlee S, Deuss M, Bruning M, Ivens A, Schwab T, Hellmann N, Mayans O, Sterner R. Activation of anthranilate phosphoribosyltransferase from Sulfolobus solfataricus by removal of magnesium inhibition and acceleration of product release . Biochemistry 2009; 48:5199-209. [PMID: 19385665 DOI: 10.1021/bi802335s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anthranilate phosphoribosyltransferase from the hyperthermophilic archaeon Sulfolobus solfataricus (ssAnPRT) is encoded by the sstrpD gene and catalyzes the reaction of anthranilate (AA) with a complex of Mg(2+) and 5'-phosphoribosyl-alpha1-pyrophosphate (Mg.PRPP) to N-(5'-phosphoribosyl)-anthranilate (PRA) and pyrophosphate (PP(i)) within tryptophan biosynthesis. The ssAnPRT enzyme is highly thermostable (half-life at 85 degrees C = 35 min) but only marginally active at ambient temperatures (turnover number at 37 degrees C = 0.33 s(-1)). To understand the reason for the poor catalytic proficiency of ssAnPRT, we have isolated from an sstrpD library the activated ssAnPRT-D83G + F149S double mutant by metabolic complementation of an auxotrophic Escherichia coli strain. Whereas the activity of purified wild-type ssAnPRT is strongly reduced in the presence of high concentrations of Mg(2+) ions, this inhibition is no longer observed in the double mutant and the ssAnPRT-D83G single mutant. The comparison of the crystal structures of activated and wild-type ssAnPRT shows that the D83G mutation alters the binding mode of the substrate Mg.PRPP. Analysis of PRPP and Mg(2+)-dependent enzymatic activity indicates that this leads to a decreased affinity for a second Mg(2+) ion and thus reduces the concentration of enzymes with the inhibitory Mg(2).PRPP complex bound to the active site. Moreover, the turnover number of the double mutant ssAnPRT-D83G + F149S is elevated 40-fold compared to the wild-type enzyme, which can be attributed to an accelerated release of the product PRA. This effect appears to be mainly caused by an increased conformational flexibility induced by the F149S mutation, a hypothesis which is supported by the reduced thermal stability of the ssAnPRT-F149S single mutant.
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Affiliation(s)
- Sandra Schlee
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Germany
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26
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di Luccio E, Wilson DK. Comprehensive X-ray structural studies of the quinolinate phosphoribosyl transferase (BNA6) from Saccharomyces cerevisiae. Biochemistry 2008; 47:4039-50. [PMID: 18321072 DOI: 10.1021/bi7020475] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quinolinic acid phosphoribosyl transferase (QAPRTase, EC 2.4.2.19) is a 32 kDa enzyme encoded by the BNA6 gene in yeast and catalyzes the formation of nicotinate mononucleotide from quinolinate and 5-phosphoribosyl-1-pyrophosphate (PRPP). QAPRTase plays a key role in the tryptophan degradation pathway via kynurenine, leading to the de novo biosynthesis of NAD (+) and clearing the neurotoxin quinolinate. To improve our understanding of the specificity of the eukaryotic enzyme and the course of events associated with catalysis, we have determined the crystal structures of the apo and singly bound forms with the substrates quinolinate and PRPP. This reveals that the enzyme folds in a manner similar to that of various prokaryotic forms which are approximately 30% identical in sequence. In addition, the structure of the Michaelis complex is approximated by PRPP and the quinolinate analogue phthalate bound to the active site. These results allow insight into the kinetic mechanism of QAPRTase and provide an understanding of structural diversity in the active site of the Saccharomyces cerevisiae enzyme when compared to prokaryotic homologues.
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Affiliation(s)
- Eric di Luccio
- Section of Molecular and Cellular Biology, University of California, Davis, California 95616, USA
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27
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Schwab T, Skegro D, Mayans O, Sterner R. A Rationally Designed Monomeric Variant of Anthranilate Phosphoribosyltransferase from Sulfolobus solfataricus is as Active as the Dimeric Wild-type Enzyme but Less Thermostable. J Mol Biol 2008; 376:506-16. [DOI: 10.1016/j.jmb.2007.11.078] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Revised: 11/14/2007] [Accepted: 11/23/2007] [Indexed: 11/28/2022]
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Kim MK, Kang GB, Song WK, Eom SH. The role of Phe181 in the hexamerization of Helicobacter pylori quinolinate phosphoribosyltransferase. Protein J 2008; 26:517-21. [PMID: 17763926 DOI: 10.1007/s10930-007-9093-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Quinolinic acid phosphoribosyltransferase (QAPRTase; NadC) catalyzes an indispensable step in NAD biosynthesis, one that is essential for cell survival in prokaryotes, which makes it an attractive target for antibacterial drug therapy. We recently reported the crystal structures of Helicobacter pylori QAPRTase with bound quinolinic acid, nicotinamide mononucleotide, and phthalic acid. The enzyme exists as a hexamer organized as a trimer of dimers, which is essential for full enzymatic activity. The loop between helix alpha7 and strand beta8 contributes significantly to the hydrophobic dimer-dimer interactions. Phe181Pro mutation within the alpha7-beta8 loop disrupts the hexamerization of QAPRTase, and the resultant dimer shows dramatically reduced protein stability and no activity. Our findings thus suggest that compounds able to disrupt its proper oligomerization could potentially function as selective inhibitors of Helicobacter pylori QAPRTase and represent a novel set of antibacterial agents.
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Affiliation(s)
- M-K Kim
- Department of Life Science, Gwangju Institute of Science & Technology, Gwangju, 500-712, Republic of Korea
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Liu H, Woznica K, Catton G, Crawford A, Botting N, Naismith JH. Structural and kinetic characterization of quinolinate phosphoribosyltransferase (hQPRTase) from homo sapiens. J Mol Biol 2007; 373:755-63. [PMID: 17868694 PMCID: PMC3326535 DOI: 10.1016/j.jmb.2007.08.043] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Revised: 08/03/2007] [Accepted: 08/20/2007] [Indexed: 11/27/2022]
Abstract
Human quinolinate phosphoribosyltransferase (EC 2.4.2.19) (hQPRTase) is a member of the type II phosphoribosyltransferase family involved in the catabolism of quinolinic acid (QA). It catalyses the formation of nicotinic acid mononucleotide from quinolinic acid, which involves a phosphoribosyl transfer reaction followed by decarboxylation. hQPRTase has been implicated in a number of neurological conditions and in order to study it further, we have carried out structural and kinetic studies on recombinant hQPRTase. The structure of the fully active enzyme overexpressed in Escherichia coli was solved using multiwavelength methods to a resolution of 2.0 A. hQPRTase has a alpha/beta barrel fold sharing a similar overall structure with the bacterial QPRTases. The active site of hQPRTase is located at an alpha/beta open sandwich structure that serves as a cup for the alpha/beta barrel of the adjacent subunit with a QA binding site consisting of three arginine residues (R102, R138 and R161) and two lysine residues (K139 and K171). Mutation of these residues affected substrate binding or abolished the enzymatic activity. The kinetics of the human enzyme are different to the bacterial enzymes studied, hQPRTase is inhibited competitively and non-competitively by one of its substrates, 5-phosphoribosylpyrophosphate (PRPP). The human enzyme adopts a hexameric arrangement, which places the active sites in close proximity to each other.
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Affiliation(s)
- Huanting Liu
- The Centre for Biomolecular Science, The University of St Andrews, North Haugh, St. Andrews KY16 9ST
| | - Kerry Woznica
- The Centre for Biomolecular Science, The University of St Andrews, North Haugh, St. Andrews KY16 9ST
| | - Gemma Catton
- The Centre for Biomolecular Science, The University of St Andrews, North Haugh, St. Andrews KY16 9ST
| | - Amanda Crawford
- The Centre for Biomolecular Science, The University of St Andrews, North Haugh, St. Andrews KY16 9ST
| | - Nigel Botting
- The Centre for Biomolecular Science, The University of St Andrews, North Haugh, St. Andrews KY16 9ST
| | - James H. Naismith
- The Centre for Biomolecular Science, The University of St Andrews, North Haugh, St. Andrews KY16 9ST
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Monzani PS, Trapani S, Thiemann OH, Oliva G. Crystal structure of Leishmania tarentolae hypoxanthine-guanine phosphoribosyltransferase. BMC STRUCTURAL BIOLOGY 2007; 7:59. [PMID: 17894860 PMCID: PMC2228302 DOI: 10.1186/1472-6807-7-59] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Accepted: 09/25/2007] [Indexed: 01/07/2023]
Abstract
BACKGROUND Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) (EC 2.4.2.8) is a central enzyme in the purine recycling pathway. Parasitic protozoa of the order Kinetoplastida cannot synthesize purines de novo and use the salvage pathway to synthesize purine bases, making this an attractive target for antiparasitic drug design. RESULTS The glycosomal HGPRT from Leishmania tarentolae in a catalytically active form purified and co-crystallized with a guanosine monophosphate (GMP) in the active site. The dimeric structure of HGPRT has been solved by molecular replacement and refined against data extending to 2.1 A resolution. The structure reveals the contacts of the active site residues with GMP. CONCLUSION Comparative analysis of the active sites of Leishmania and human HGPRT revealed subtle differences in the position of the ligand and its interaction with the active site residues, which could be responsible for the different reactivities of the enzymes to allopurinol reported in the literature. The solution and analysis of the structure of Leishmania HGPRT may contribute to further investigations leading to a full understanding of this important enzyme family in protozoan parasites.
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Affiliation(s)
- Paulo S Monzani
- Departamento de Física e Informática, Grupo de Cristalografia de Proteínas e Biologia Estrutural, Instituto de Física de São Carlos, USP, Caixa Postal 369, 13560-590, São Carlos – SP, Brazil
| | - Stefano Trapani
- Institut de Biologie Structurale J.P. Ebel, UMR 5075 CNRS, 41 rue Jules Horowitz, 38027 Grenoble cedex 1, France
| | - Otavio H Thiemann
- Departamento de Física e Informática, Grupo de Cristalografia de Proteínas e Biologia Estrutural, Instituto de Física de São Carlos, USP, Caixa Postal 369, 13560-590, São Carlos – SP, Brazil
| | - Glaucius Oliva
- Departamento de Física e Informática, Grupo de Cristalografia de Proteínas e Biologia Estrutural, Instituto de Física de São Carlos, USP, Caixa Postal 369, 13560-590, São Carlos – SP, Brazil
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Khan JA, Forouhar F, Tao X, Tong L. Nicotinamide adenine dinucleotide metabolism as an attractive target for drug discovery. Expert Opin Ther Targets 2007; 11:695-705. [PMID: 17465726 DOI: 10.1517/14728222.11.5.695] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD(+)) has crucial roles in many cellular processes, both as a coenzyme for redox reactions and as a substrate to donate ADP-ribose units. Enzymes involved in NAD(+) metabolism are attractive targets for drug discovery against a variety of human diseases, including cancer, multiple sclerosis, neurodegeneration and Huntington's disease. A small-molecule inhibitor of nicotinamide phosphoribosyltransferase, an enzyme in the salvage pathway of NAD(+) biosynthesis, is presently in clinical trials against cancer. An analog of a kynurenine pathway intermediate is efficacious against multiple sclerosis in an animal model. Indoleamine 2,3-dioxygenase plays an important role in immune evasion by cancer cells and other disease processes. Inhibitors against kynurenine 3-hydroxylase can reduce the production of neurotoxic metabolites while increasing the production of neuroprotective compounds. This review summarizes the existing knowledge on NAD(+) metabolic enzymes, with emphasis on their relevance for drug discovery.
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Affiliation(s)
- Javed A Khan
- Columbia University, Department of Biological Sciences, New York, NY 10027, USA
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32
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Kim MK, Lee JH, Kim H, Park SJ, Kim SH, Kang GB, Lee YS, Kim JB, Kim KK, Suh SW, Eom SH. Crystal structure of visfatin/pre-B cell colony-enhancing factor 1/nicotinamide phosphoribosyltransferase, free and in complex with the anti-cancer agent FK-866. J Mol Biol 2006; 362:66-77. [PMID: 16901503 DOI: 10.1016/j.jmb.2006.06.082] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2006] [Revised: 06/28/2006] [Accepted: 06/29/2006] [Indexed: 01/24/2023]
Abstract
Visfatin/pre-B cell colony-enhancing factor 1 (PBEF)/nicotinamide phosphoribosyltransferase (NAmPRTase) is a multifunctional protein having phosphoribosyltransferase, cytokine and adipokine activities. Originally isolated as a cytokine promoting the differentiation of B cell precursors, it was recently suggested to act as an insulin analog via the insulin receptor. Here, we describe the first crystal structure of visfatin in three different forms: apo and in complex with either nicotinamide mononucleotide (NMN) or the NAmPRTase inhibitor FK-866 which was developed as an anti-cancer agent, interferes with NAD biosynthesis, showing a particularly high specificity for NAmPRTase. The crystal structures of the complexes with either NMN or FK-866 show that the enzymatic active site of visfatin is optimized for nicotinamide binding and that the nicotinamide-binding site is important for inhibition by FK-866. Interestingly, visfatin mimics insulin signaling by binding to the insulin receptor with an affinity similar to that of insulin and does not share the binding site with insulin on the insulin receptor. To predict binding sites, the potential interaction patches of visfatin and the L1-CR-L2 domain of insulin receptor were generated and analyzed. Although the relationship between the insulin-mimetic property and the enzymatic function of visfatin has not been clearly established, our structures raise the intriguing possibility that the glucose metabolism and the NAD biosynthesis are linked by visfatin.
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Affiliation(s)
- Mun-Kyoung Kim
- Department of Life Science, Gwangju Institute of Science & Technology, Gwangju 500-712, Korea
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Wang T, Zhang X, Bheda P, Revollo JR, Imai SI, Wolberger C. Structure of Nampt/PBEF/visfatin, a mammalian NAD+ biosynthetic enzyme. Nat Struct Mol Biol 2006; 13:661-2. [PMID: 16783373 DOI: 10.1038/nsmb1114] [Citation(s) in RCA: 218] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Accepted: 05/23/2006] [Indexed: 02/07/2023]
Abstract
Nicotinamide phosphoribosyltransferase (Nampt) synthesizes nicotinamide mononucleotide (NMN) from nicotinamide in a mammalian NAD+ biosynthetic pathway and is required for SirT1 activity in vivo. Nampt has also been presumed to be a cytokine (PBEF) or a hormone (visfatin). The crystal structure of Nampt in the presence and absence of NMN shows that Nampt is a dimeric type II phosphoribosyltransferase and provides insights into the enzymatic mechanism.
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Affiliation(s)
- Tao Wang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe St., Baltimore, Maryland 21205, USA
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Khan JA, Tao X, Tong L. Molecular basis for the inhibition of human NMPRTase, a novel target for anticancer agents. Nat Struct Mol Biol 2006; 13:582-8. [PMID: 16783377 DOI: 10.1038/nsmb1105] [Citation(s) in RCA: 212] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Accepted: 05/09/2006] [Indexed: 01/07/2023]
Abstract
Nicotinamide phosphoribosyltransferase (NMPRTase) has a crucial role in the salvage pathway of NAD+ biosynthesis, and a potent inhibitor of NMPRTase, FK866, can reduce cellular NAD+ levels and induce apoptosis in tumors. We have determined the crystal structures at up to 2.1-A resolution of human and murine NMPRTase, alone and in complex with the reaction product nicotinamide mononucleotide or the inhibitor FK866. The structures suggest that Asp219 is a determinant of substrate specificity of NMPRTase, which is confirmed by our mutagenesis studies. FK866 is bound in a tunnel at the interface of the NMPRTase dimer, and mutations in this binding site can abolish the inhibition by FK866. Contrary to current knowledge, the structures show that FK866 should compete directly with the nicotinamide substrate. Our structural and biochemical studies provide a starting point for the development of new anticancer agents.
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Affiliation(s)
- Javed A Khan
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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35
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Kim MK, Im YJ, Lee JH, Eom SH. Crystal structure of quinolinic acid phosphoribosyltransferase from Helicobacter pylori. Proteins 2006; 63:252-5. [PMID: 16419067 DOI: 10.1002/prot.20834] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mun-kyoung Kim
- Department of Life Science, Gwangju Institute of Science & Technology, Gwangju, South Korea
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36
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Marino M, Deuss M, Svergun DI, Konarev PV, Sterner R, Mayans O. Structural and mutational analysis of substrate complexation by anthranilate phosphoribosyltransferase from Sulfolobus solfataricus. J Biol Chem 2006; 281:21410-21421. [PMID: 16714288 DOI: 10.1074/jbc.m601403200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The metabolic synthesis and degradation of essential nucleotide compounds are primarily carried out by phosphoribosyltransferases (PRT) and nucleoside phosphorylases (NP), respectively. Despite the resemblance of their reactions, five classes of PRTs and NPs exist, where anthranilate PRT (AnPRT) constitutes the only evolutionary link between synthesis and degradation processes. We have characterized the active site of dimeric AnPRT from Sulfolobus solfataricus by elucidating crystal structures of the wild-type enzyme complexed to its two natural substrates anthranilate and 5-phosphoribosyl-1-pyrophosphate/Mg(2+). These bind into two different domains within each protomer and are brought together during catalysis by rotational domain motions as shown by small angle x-ray scattering data. Steady-state kinetics of mutated AnPRT variants address the role of active site residues in binding and catalysis. Results allow the comparative analysis of PRT and pyrimidine NP families and expose related structural motifs involved in nucleotide/nucleoside recognition by these enzyme families.
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Affiliation(s)
- Marco Marino
- Division of Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Miriam Deuss
- Institut für Biophysik und physikalische Biochemie, Universität Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany; Institut für Biochemie, Universität zu Köln, Otto-Fischer-Strasse 12-14, D-50674 Köln, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany; Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333 Moscow, Russia
| | - Petr V Konarev
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany; Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333 Moscow, Russia
| | - Reinhard Sterner
- Institut für Biophysik und physikalische Biochemie, Universität Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany; Institut für Biochemie, Universität zu Köln, Otto-Fischer-Strasse 12-14, D-50674 Köln, Germany
| | - Olga Mayans
- Division of Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.
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37
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Chappie JS, Cànaves JM, Han GW, Rife CL, Xu Q, Stevens RC. The structure of a eukaryotic nicotinic acid phosphoribosyltransferase reveals structural heterogeneity among type II PRTases. Structure 2005; 13:1385-96. [PMID: 16154095 DOI: 10.1016/j.str.2005.05.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2005] [Revised: 05/18/2005] [Accepted: 05/18/2005] [Indexed: 11/16/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD) is an essential cofactor for cellular redox reactions and can act as an important substrate in numerous biological processes. As a result, nature has evolved multiple biosynthetic pathways to meet this high chemical demand. In Saccharomyces cerevisiae, the NAD salvage pathway relies on the activity of nicotinic acid phosphoribosyltransferase (NAPRTase), a member of the phosphoribosyltransferase (PRTase) superfamily. Here, we report the structure of a eukaryotic (yeast) NAPRTase at 1.75 A resolution (locus name: YOR209C, gene name: NPT1). The structure reveals a two-domain fold that resembles the architecture of quinolinic acid phosphoribosyltransferases (QAPRTases), but with completely different dispositions that provide evidence for structural heterogeneity among the Type II PRTases. The identification of a third domain in NAPRTases provides a structural basis and possible mechanism for the functional modulation of this family of enzymes by ATP.
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Affiliation(s)
- Joshua S Chappie
- The Joint Center for Structural Genomics, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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38
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Sterner R, Höcker B. Catalytic Versatility, Stability, and Evolution of the (βα)8-Barrel Enzyme Fold. Chem Rev 2005; 105:4038-55. [PMID: 16277370 DOI: 10.1021/cr030191z] [Citation(s) in RCA: 166] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Reinhard Sterner
- Institut für Biophysik und physikalische Biochemie, Universität Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany.
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Champagne KS, Sissler M, Larrabee Y, Doublié S, Francklyn CS. Activation of the hetero-octameric ATP phosphoribosyl transferase through subunit interface rearrangement by a tRNA synthetase paralog. J Biol Chem 2005; 280:34096-104. [PMID: 16051603 DOI: 10.1074/jbc.m505041200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ATP phosphoribosyl transferase (ATP-PRT) joins ATP and 5-phosphoribosyl-1-pyrophosphate (PRPP) in a highly regulated reaction that initiates histidine biosynthesis. The unusual hetero-octameric version of ATP-PRT includes four HisG(S) catalytic subunits based on the periplasmic binding protein fold and four HisZ regulatory subunits that resemble histidyl-tRNA synthetases. Here, we present the first structure of a PRPP-bound ATP-PRT at 2.9 A and provide a structural model for allosteric activation based on comparisons with other inhibited and activated ATP-PRTs from both the hetero-octameric and hexameric families. The activated state of the octameric enzyme is characterized by an interstitial phosphate ion in the HisZ-HisG interface and new contacts between the HisZ motif 2 loop and the HisG(S) dimer interface. These contacts restructure the interface to recruit conserved residues to the active site, where they activate pyrophosphate to promote catalysis. Additionally, mutational analysis identifies the histidine binding sites within a region highly conserved between HisZ and the functional HisRS. Through the oligomerization and functional re-assignment of protein domains associated with aminoacylation and phosphate binding, the HisZ-HisG octameric ATP-PRT acquired the ability to initiate the synthesis of a key metabolic intermediate in an allosterically regulated fashion.
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Affiliation(s)
- Karen S Champagne
- Department of Microbiology and Molecular Genetics and Biochemistry, University of Vermont, Burlington, Vermont 05405, USA
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Vega MC, Zou P, Fernandez FJ, Murphy GE, Sterner R, Popov A, Wilmanns M. Regulation of the hetero-octameric ATP phosphoribosyl transferase complex from Thermotoga maritima by a tRNA synthetase-like subunit. Mol Microbiol 2005; 55:675-86. [PMID: 15660995 DOI: 10.1111/j.1365-2958.2004.04422.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The molecular structure of the ATP phosphoribosyl transferase from the hyperthermophile Thermotoga maritima is composed of a 220 kDa hetero-octameric complex comprising four catalytic subunits (HisGS) and four regulatory subunits (HisZ). Steady-state kinetics indicate that only the complete octameric complex is active and non-competitively inhibited by the pathway product histidine. The rationale for these findings is provided by the crystal structure revealing a total of eight histidine binding sites that are located within each of the four HisGS-HisZ subunit interfaces formed by the ATP phosphoribosyl transferase complex. While the structure of the catalytic HisGS subunit is related to the catalytic domain of another family of (HisGL)2 ATP phosphoribosyl transferases that is functional in the absence of additional regulatory subunits, the structure of the regulatory HisZ subunit is distantly related to class II aminoacyl-tRNA synthetases. However, neither the mode of the oligomeric subunit arrangement nor the type of histidine binding pockets is found in these structural relatives. Common ancestry of the regulatory HisZ subunit and class II aminoacyl-tRNA synthetase may reflect the balanced need of regulated amounts of a cognate amino acid (histidine) in the translation apparatus, ultimately linking amino acid biosynthesis and protein biosynthesis in terms of function, structure and evolution.
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Affiliation(s)
- M Cristina Vega
- EMBL Hamburg Outstation, Notkestrasse 85, Building 25A, D-22603 Hamburg, Germany
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41
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Shin DH, Oganesyan N, Jancarik J, Yokota H, Kim R, Kim SH. Crystal Structure of a Nicotinate Phosphoribosyltransferase from Thermoplasma acidophilum. J Biol Chem 2005; 280:18326-35. [PMID: 15753098 DOI: 10.1074/jbc.m501622200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have determined the crystal structure of nicotinate phosphoribosyltransferase from Themoplasma acidophilum (TaNAPRTase). The TaNAPRTase has three domains, an N-terminal domain, a central functional domain, and a unique C-terminal domain. The crystal structure revealed that the functional domain has a type II phosphoribosyltransferase fold that may be a common architecture for both nicotinic acid and quinolinic acid (QA) phosphoribosyltransferases (PRTase) despite low sequence similarity between them. Unlike QAPRTase, TaNAPRTase has a unique extra C-terminal domain containing a zinc knuckle-like motif containing 4 cysteines. The TaNAPRTase forms a trimer of dimers in the crystal. The active site pocket is formed at dimer interfaces. The complex structures with phosphoribosylpyrophosphate (PRPP) and nicotinate mononucleotide (NAMN) showed, surprisingly, that functional residues lining on the active site of TaNAPRTase are quite different from those of QAPRTase, although their substrates are quite similar to each other. The phosphate moiety of PRPP and NAMN is anchored to the phosphate-binding loops formed by backbone amides, as found in many alpha/beta barrel enzymes. The pyrophosphate moiety of PRPP is located at the entrance of the active site pocket, whereas the nicotinate moiety of NAMN is located deep inside. Interestingly, the nicotinate moiety of NAMN is intercalated between highly conserved aromatic residues Tyr(21) and Phe(138). Careful structural analyses combined with other NAPRTase sequence subfamilies reveal that TaNAPRTase represents a unique sequence subfamily of NAPRTase. The structures of TaNAPRTase also provide valuable insight for other sequence subfamilies such as pre-B cell colony-enhancing factor, known to have nicotinamide phosphoribosyltransferase activity.
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Affiliation(s)
- Dong Hae Shin
- Berkeley Structural Genomics Center, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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42
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Kukimoto-Niino M, Shibata R, Murayama K, Hamana H, Nishimoto M, Bessho Y, Terada T, Shirouzu M, Kuramitsu S, Yokoyama S. Crystal structure of a predicted phosphoribosyltransferase (TT1426) from Thermus thermophilus HB8 at 2.01 A resolution. Protein Sci 2005; 14:823-7. [PMID: 15689504 PMCID: PMC2279281 DOI: 10.1110/ps.041229405] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
TT1426, from Thermus thermophilus HB8, is a conserved hypothetical protein with a predicted phosphoribosyltransferase (PRTase) domain, as revealed by a Pfam database search. The 2.01 A crystal structure of TT1426 has been determined by the multiwavelength anomalous dispersion (MAD) method. TT1426 comprises a core domain consisting of a central five-stranded beta sheet surrounded by four alpha-helices, and a subdomain in the C terminus. The core domain structure resembles those of the type I PRTase family proteins, although a significant structural difference exists in an inserted 43-residue region. The C-terminal subdomain corresponds to the "hood," which contains a substrate-binding site in the type I PRTases. The hood structure of TT1426 differs from those of the other type I PRTases, suggesting the possibility that TT1426 binds an unknown substrate. The structure-based sequence alignment provides clues about the amino acid residues involved in catalysis and substrate binding.
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Schwarzenbacher R, Jaroszewski L, von Delft F, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Cambell J, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA. Crystal structure of a type II quinolic acid phosphoribosyltransferase (TM1645) from Thermotoga maritima at 2.50 A resolution. Proteins 2004; 55:768-71. [PMID: 15103640 DOI: 10.1002/prot.20029] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Robert Schwarzenbacher
- The Joint Center for Structural Genomics, The San Diego Supercomputer Center, La Jolla, California 92093, USA
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Krungkrai SR, Aoki S, Palacpac NMQ, Sato D, Mitamura T, Krungkrai J, Horii T. Human malaria parasite orotate phosphoribosyltransferase: functional expression, characterization of kinetic reaction mechanism and inhibition profile. Mol Biochem Parasitol 2004; 134:245-55. [PMID: 15003844 DOI: 10.1016/j.molbiopara.2003.12.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2003] [Revised: 11/04/2003] [Accepted: 12/19/2003] [Indexed: 11/22/2022]
Abstract
Plasmodium falciparum, the causative agent of the most lethal form of human malaria, relies on de novo pyrimidine biosynthesis. A gene encoding orotate phosphoribosyltransferase (OPRT), the fifth enzyme of the de novo pathway catalyzing formation of orotidine 5'-monophosphate (OMP) and pyrophosphate (PP(i)) from 5-phosphoribosyl-1-pyrophosphate (PRPP) and orotate, was identified from P. falciparum (pfOPRT). The deduced amino acid sequence for pfOPRT was compared with OPRTs from other organisms and found to be most similar to that of Escherichia coli. The catalytic residues and consensus sequences for substrate binding in the enzyme were conserved among other organisms. The pfOPRT was exceptional in that it contained a unique insertion of 20 amino acids and an amino-terminal extension of 66 amino acids, making the longest amino acid sequence (281 amino acids with a predicted molecular mass of 33kDa). The cDNA of the pfOPRT gene was cloned, sequenced and functionally expressed in soluble form. The recombinant pfOPRT was purified from the E. coli lysate by two steps, nickel metal-affinity and gel-filtration chromatography. From 1l E. coli culture, 1.2-1.5mg of pure pfOPRT was obtained. SDS-PAGE revealed that the pfOPRT had a molecular mass of 33kDa and analytical gel-filtration chromatography showed that the enzyme activity eluted at approximately 67kDa. Using dimethyl suberimidate to cross-link neighboring subunits of the pfOPRT, it was confirmed that the native enzyme exists in a dimeric form. The steady state kinetics of initial velocity and product inhibition studies indicate that the enzyme pfOPRT follows a random sequential kinetic mechanism. Compounds aimed at the pfOPRT nexus may act against the parasite through at least two mechanisms: by directly inhibiting the enzyme activity, or be processed to an inhibitor of thymidylate synthase. This study provides a working system with which to investigate new antimalarial agents targeted against P. falciparum OPRT.
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Affiliation(s)
- Sudaratana R Krungkrai
- Department of Molecular Protozoology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan.
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45
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Lohkamp B, McDermott G, Campbell SA, Coggins JR, Lapthorn AJ. The structure of Escherichia coli ATP-phosphoribosyltransferase: identification of substrate binding sites and mode of AMP inhibition. J Mol Biol 2004; 336:131-44. [PMID: 14741209 DOI: 10.1016/j.jmb.2003.12.020] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ATP-phosphoribosyltransferase (ATP-PRT), the first enzyme of the histidine pathway, is a complex allosterically regulated enzyme, which controls the flow of intermediates through this biosynthetic pathway. The crystal structures of Escherichia coli ATP-PRT have been solved in complex with the inhibitor AMP at 2.7A and with product PR-ATP at 2.9A (the ribosyl-triphosphate could not be resolved). On the basis of binding of AMP and PR-ATP and comparison with type I PRTs, the PRPP and parts of the ATP-binding site are identified. These structures clearly identify the AMP as binding in the 5-phosphoribosyl-alpha-1-pyrophosphate (PRPP)-binding site, with the adenosine ring occupying the ATP-binding site. Comparison with the recently solved Mycobacterium tuberculosis ATP-PRT structures indicates that histidine is solely responsible for the large conformational changes observed between the hexameric forms of the enzyme. The role of oligomerisation in inhibition and the structural basis for the synergistic inhibition by histidine and AMP are discussed.
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Affiliation(s)
- Bernhard Lohkamp
- Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
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46
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Schramm VL, Grubmeyer C. Phosphoribosyltransferase Mechanisms and Roles in Nucleic Acid Metabolism. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2004; 78:261-304. [PMID: 15210333 DOI: 10.1016/s0079-6603(04)78007-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA
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47
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Smith CV, Sacchettini JC. Mycobacterium tuberculosis: a model system for structural genomics. Curr Opin Struct Biol 2003; 13:658-64. [PMID: 14675542 DOI: 10.1016/j.sbi.2003.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Over the past five years, genomics has had a major impact on Mycobacterium tuberculosis research. With the publication of the sequences of two virulent strains (H37Rv and CDC1551) and three closely related sequences, M. tuberculosis is becoming a model system for proteomics and structural genomics initiatives. Together with the promise of structures of proteins with novel folds, high-resolution structures of drug targets are providing the basis for rational inhibitor design, with the goal of the development of novel anti-tuberculars. In addition, this work is aiding scientists in the quest for an effective vaccine against this persistent pathogen.
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Affiliation(s)
- Clare V Smith
- Department of Biochemistry and Biophysics, Texas A and M University, College Station, TX 77843-2128, USA
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48
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Cho Y, Sharma V, Sacchettini JC. Crystal structure of ATP phosphoribosyltransferase from Mycobacterium tuberculosis. J Biol Chem 2003; 278:8333-9. [PMID: 12511575 DOI: 10.1074/jbc.m212124200] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The N-1-(5'-phosphoribosyl)-ATP transferase catalyzes the first step of the histidine biosynthetic pathway and is regulated by a feedback mechanism by the product histidine. The crystal structures of the N-1-(5'-phosphoribosyl)-ATP transferase from Mycobacterium tuberculosis in complex with inhibitor histidine and AMP has been determined to 1.8 A resolution and without ligands to 2.7 A resolution. The active enzyme exists primarily as a dimer, and the histidine-inhibited form is a hexamer. The structure represents a new fold for a phosphoribosyltransferase, consisting of three continuous domains. The inhibitor AMP binds in the active site cavity formed between the two catalytic domains. A model for the mechanism of allosteric inhibition has been derived from conformational differences between the AMP:His-bound and apo structures.
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Affiliation(s)
- Yoonsang Cho
- Department of Biochemistry and Biophysics, Texas A & M University, College Station 77843-2128, USA
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49
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Grabner GK, Switzer RL. Kinetic studies of the uracil phosphoribosyltransferase reaction catalyzed by the Bacillus subtilis pyrimidine attenuation regulatory protein PyrR. J Biol Chem 2003; 278:6921-7. [PMID: 12482852 DOI: 10.1074/jbc.m211111200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The PyrR protein from Bacillus subtilis and many other bacteria is a bifunctional protein. Its primary function is the regulation of expression of pyrimidine biosynthetic (pyr) genes by binding to specific sites on pyr mRNA in a uridine nucleotide-dependent manner and altering the folding of downstream RNA to promote termination of transcription. PyrR also catalyzes the uracil phosphoribosyltransferase (UPRTase) reaction even though it bears little amino acid sequence similarity to other bacterial UPRTases. The PyrR-catalyzed UPRTase reaction obeyed a Ping Pong steady state kinetic pattern under all conditions examined, but no catalysis of [(14)C]uracil-UMP and [(32)P]PP(i)-phosphoribosylpyrophosphate exchange reactions could be detected. Steady state equations for Ordered Bi Bi mechanisms for PyrR that include a kinetically irreversible conformational change after binding of PRPP but before uracil binding were shown to account for the Ping Pong pattern of the enzyme. This mechanism was supported by the following experimental observations. The reverse reaction was extremely slow with a catalytic rate constant 3300 times smaller than for the forward reaction. Patterns of product inhibition of the forward reaction were consistent with a version of the irreversible conformational change model in which PyrR returns to the unliganded conformation before dissociation of UMP and were inconsistent with several other kinetic mechanisms. UMP and phosphoribosylpyrophosphate were shown by equilibrium dialysis to bind to free PyrR (dissociation constants of 27 +/- 3 and 18 +/- 2 microm, respectively), but uracil and PP(i) did not bind at equilibrium concentrations up to 750 microm. We propose that the conformational change kinetic model developed for PyrR can also account for numerous other reports of Ping Pong kinetics for various phosphoribosyltransferases that do not form the phosphoribosyl-enzyme intermediate predicted by classic Ping Pong kinetics.
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Affiliation(s)
- Gail K Grabner
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA
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50
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Kim C, Xuong NH, Edwards S, Yee MC, Spraggon G, Mills SE. The crystal structure of anthranilate phosphoribosyltransferase from the enterobacterium Pectobacterium carotovorum. FEBS Lett 2002; 523:239-46. [PMID: 12123839 DOI: 10.1016/s0014-5793(02)02905-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The structure of anthranilate phosphoribosyltransferase from the enterobacterium Pectobacterium carotovorum has been solved at 2.4 A in complex with Mn(2+)-pyrophosphate, and at 1.9 A without ligands. The enzyme structure has a novel phosphoribosyltransferase (PRT) fold and displays close homology to the structures of pyrimidine nucleoside phosphorylases. The enzyme is a homodimer with a monomer of 345 residues. Each monomer consists of two subdomains, alpha and alpha/beta, which form a cleft containing the active site. The nature of the active site is inferred from the trapped MnPPi complex and detailed knowledge of the active sites of nucleoside phosphorylases. With the anthranilate (An)PRT structure solved, the structures of all the enzymes required for tryptophan biosynthesis are now known.
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Affiliation(s)
- Choel Kim
- Department of Chemistry/Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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