1
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Nemoto N, Baba S, Kawai G, Sampei GI. Crystal structure of guanosine 5'-monophosphate synthetase from the thermophilic bacterium Thermus thermophilus HB8. Acta Crystallogr F Struct Biol Commun 2024; 80:278-285. [PMID: 39291305 DOI: 10.1107/s2053230x2400877x] [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: 05/02/2024] [Accepted: 09/09/2024] [Indexed: 09/19/2024] Open
Abstract
Guanosine 5'-monophosphate (GMP) synthetase (GuaA) catalyzes the last step of GMP synthesis in the purine nucleotide biosynthetic pathway. This enzyme catalyzes a reaction in which xanthine 5'-monophosphate (XMP) is converted to GMP in the presence of Gln and ATP through an adenyl-XMP intermediate. A structure of an XMP-bound form of GuaA from the domain Bacteria has not yet been determined. In this study, the crystal structure of an XMP-bound form of GuaA from the thermophilic bacterium Thermus thermophilus HB8 (TtGuaA) was determined at a resolution of 2.20 Å and that of an apo form of TtGuaA was determined at 2.10 Å resolution. TtGuaA forms a homodimer, and the monomer is composed of three domains, which is a typical structure for GuaA. Disordered regions in the crystal structure were obtained from the AlphaFold2-predicted model structure, and a model with substrates (Gln, XMP and ATP) was constructed for molecular-dynamics (MD) simulations. The structural fluctuations of the TtGuaA dimer as well as the interactions between the active-site residues were analyzed by MD simulations.
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Affiliation(s)
- Naoki Nemoto
- Faculty of Advanced Engineering, Chiba Institute of Technology, Narashino, Chiba 275-0016, Japan
| | - Seiki Baba
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Gota Kawai
- Faculty of Advanced Engineering, Chiba Institute of Technology, Narashino, Chiba 275-0016, Japan
| | - Gen Ichi Sampei
- Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
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2
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Ballut L, Violot S, Kumar S, Aghajari N, Balaram H. GMP Synthetase: Allostery, Structure, and Function. Biomolecules 2023; 13:1379. [PMID: 37759779 PMCID: PMC10526850 DOI: 10.3390/biom13091379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Glutamine amidotransferases (GATs) catalyze the hydrolysis of glutamine and transfer the generated ammonia to diverse metabolites. The two catalytic activities, glutaminolysis and the subsequent amination of the acceptor substrate, happen in two distinct catalytic pockets connected by a channel that facilitates the movement of ammonia. The de novo pathway for the synthesis of guanosine monophosphate (GMP) from xanthosine monophosphate (XMP) is enabled by the GAT GMP synthetase (GMPS). In most available crystal structures of GATs, the ammonia channel is evident in their native state or upon ligand binding, providing molecular details of the conduit. In addition, conformational changes that enable the coordination of the two catalytic chemistries are also informed by the available structures. In contrast, despite the first structure of a GMPS being published in 1996, the understanding of catalysis in the acceptor domain and inter-domain crosstalk became possible only after the structure of a glutamine-bound mutant of Plasmodium falciparum GMPS was determined. In this review, we present the current status of our understanding of the molecular basis of catalysis in GMPS, becoming the first comprehensive assessment of the biochemical function of this intriguing enzyme.
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Affiliation(s)
- Lionel Ballut
- Molecular Microbiology and Structural Biochemistry, CNRS, University of Lyon1, UMR5086, 7 Passage du Vercors, CEDEX 07, F-69367 Lyon, France; (L.B.); (S.V.)
| | - Sébastien Violot
- Molecular Microbiology and Structural Biochemistry, CNRS, University of Lyon1, UMR5086, 7 Passage du Vercors, CEDEX 07, F-69367 Lyon, France; (L.B.); (S.V.)
| | - Sanjeev Kumar
- Trivedi School of Biosciences, Ashoka University, Rajiv Gandhi Education City, Sonipat 131029, Haryana, India;
| | - Nushin Aghajari
- Molecular Microbiology and Structural Biochemistry, CNRS, University of Lyon1, UMR5086, 7 Passage du Vercors, CEDEX 07, F-69367 Lyon, France; (L.B.); (S.V.)
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur 560064, Bangalore, India
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Shivakumaraswamy S, Kumar S, Bellur A, Polisetty SD, Balaram H. Mechanistic Insights into the Functioning of a Two-Subunit GMP Synthetase, an Allosterically Regulated, Ammonia Channeling Enzyme. Biochemistry 2022; 61:1988-2006. [PMID: 36040251 DOI: 10.1021/acs.biochem.2c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Guanosine 5'-monophosphate (GMP) synthetases, enzymes that catalyze the conversion of xanthosine 5'-monophosphate (XMP) to GMP, are composed of two different catalytic units, which are either two domains of a polypeptide chain or two subunits that associate to form a complex. The glutamine amidotransferase (GATase) unit hydrolyzes glutamine generating ammonia, and the ATP pyrophosphatase (ATPPase) unit catalyzes the formation of an AMP-XMP intermediate. The substrate-bound ATPPase allosterically activates GATase, and the ammonia thus generated is tunneled to the ATPPase active site where it reacts with AMP-XMP generating GMP. In ammonia channeling enzymes reported thus far, a tight complex of the two subunits is observed, while the interaction of the two subunits of Methanocaldococcus jannaschii GMP synthetase (MjGMPS) is transient with the underlying mechanism of allostery and substrate channeling largely unclear. Here, we present a mechanistic model encompassing the various steps in the catalytic cycle of MjGMPS based on biochemical experiments, crystal structure, and cross-linking mass spectrometry guided integrative modeling. pH dependence of enzyme kinetics establishes that ammonia is tunneled across the subunits with the lifetime of the complex being ≤0.5 s. The crystal structure of the XMP-bound ATPPase subunit reported herein highlights the role of conformationally dynamic loops in enabling catalysis. The structure of MjGMPS derived using restraints obtained from cross-linking mass spectrometry has enabled the visualization of subunit interactions that enable allostery under catalytic conditions. We integrate the results and propose a functional mechanism for MjGMPS detailing the various steps involved in catalysis.
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Affiliation(s)
- Santosh Shivakumaraswamy
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Sanjeev Kumar
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Asutosh Bellur
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Satya Dev Polisetty
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bengaluru 560064, India
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4
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Huang F, Abbas F, Fiaz S, Imran M, Yanguo K, Hassan W, Ashraf U, He Y, Cai X, Wang Z, Yu L, Ye X, Chen X. Comprehensive characterization of Guanosine monophosphate synthetase in Nicotiana tabacum. Mol Biol Rep 2022; 49:5265-5272. [PMID: 34689282 DOI: 10.1007/s11033-021-06718-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 09/27/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Guanosine monophosphate (GMP) synthetase is an enzyme that converts xanthosine monophosphate to GMP. GMP plays an essential role in plant development and responses to internal and external stimuli. It also plays a crucial role in several plant physiochemical processes, such as stomata closure, cation flux regulation, pathogen responses and chloroplast development. METHODS AND RESULTS The mRNA sequences of NtGMP synthase in tobacco (Nicotiana tabacum) were rapidly amplified from cDNA. The GMP synthase open reading frame contains a 1617 bp sequence encoding 538 amino acids. A sequence analysis showed that this sequence shares high homology with that of Nicotiana sylvestris, Nicotiana attenuata, N. tomentosiformis, Solanum tuberosum, Lycopersicon pennellii, L. esculentum, Capsicum annuum, C. chinense and C. baccatum GMP synthase. A BLAST analysis with a tobacco high-throughput genomic sequence database revealed that the tobacco GMP synthase gene has five introns and six exons. A phylogenetic analysis showed a close genetic evolutionary relationship with N. sylvestris GMP synthase. The tissue-specific expression profile was evaluated using quantitative real-time PCR. The data showed that NtGMP synthase was highly expressed in leaves and moderately expressed in roots, flowers, and stems. The subcellular localization was predicted using the WOLF PSORT webserver, which strongly suggested that it might be localized to the cytoplasm. CONCLUSIONS In the current study, we cloned and comprehensively characterized GMP synthase in tobacco (Nicotiana tabacum). Our results establish a basis for further research to explore the precise role of this enzyme in tobacco.
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Affiliation(s)
- Feiyan Huang
- College of Agriculture and Life Sciences, Yunnan Urban Agricultural Engineering & Technological Research Center, Kunming University, Kunming, China
| | - Farhat Abbas
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, University of Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Imran
- Department of Crop Science and Technology, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Ke Yanguo
- College of Agriculture and Life Sciences, Yunnan Urban Agricultural Engineering & Technological Research Center, Kunming University, Kunming, China.
- College of Economics and Management, Kunming University, Kunming, China.
| | - Waseem Hassan
- Institute of Environment and Sustainable Development in Agricultural, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Umair Ashraf
- Department of Botany, Division of Science and Technology, University of Education Lahore, Punjab, Pakistan
| | - Yuansheng He
- Lincang Tobacco Corporation of Yunnan Province, Kunming, China
| | - Xuanjie Cai
- Material Procurement Center, Shanghai Tobacco Group Co., Ltd, Shanghai, 200082, China
| | - Zhijiang Wang
- Kunming Tobacco Corporation of Yunnan Province, Kunming, 650021, China
| | - Lei Yu
- College of Agriculture and Life Sciences, Yunnan Urban Agricultural Engineering & Technological Research Center, Kunming University, Kunming, China
| | - Xianwen Ye
- Kunming Tobacco Corporation of Yunnan Province, Kunming, 650021, China.
| | - Xiaolong Chen
- Tobacco Leaf Technology Centre, China Tobacco Henan Industrial Co., Ltd, Zhengzhou, 450000, China.
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Pareek V, Sha Z, He J, Wingreen NS, Benkovic SJ. Metabolic channeling: predictions, deductions, and evidence. Mol Cell 2021; 81:3775-3785. [PMID: 34547238 PMCID: PMC8485759 DOI: 10.1016/j.molcel.2021.08.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/18/2021] [Accepted: 08/21/2021] [Indexed: 12/19/2022]
Abstract
With the elucidation of myriad anabolic and catabolic enzyme-catalyzed cellular pathways crisscrossing each other, an obvious question arose: how could these networks operate with maximal catalytic efficiency and minimal interference? A logical answer was the postulate of metabolic channeling, which in its simplest embodiment assumes that the product generated by one enzyme passes directly to a second without diffusion into the surrounding medium. This tight coupling of activities might increase a pathway's metabolic flux and/or serve to sequester unstable/toxic/reactive intermediates as well as prevent their access to other networks. Here, we present evidence for this concept, commencing with enzymes that feature a physical molecular tunnel, to multi-enzyme complexes that retain pathway substrates through electrostatics or enclosures, and finally to metabolons that feature collections of enzymes assembled into clusters with variable stoichiometric composition. Lastly, we discuss the advantages of reversibly assembled metabolons in the context of the purinosome, the purine biosynthesis metabolon.
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Affiliation(s)
- Vidhi Pareek
- Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Zhou Sha
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Jingxuan He
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Ned S Wingreen
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Stephen J Benkovic
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.
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6
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Nan J, Zhang S, Zhan P, Jiang L. Discovery of Novel GMPS Inhibitors of Candidatus Liberibacter Asiaticus by Structure Based Design and Enzyme Kinetic. BIOLOGY 2021; 10:biology10070594. [PMID: 34203217 PMCID: PMC8301025 DOI: 10.3390/biology10070594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/12/2022]
Abstract
Simple Summary The spread of citrus Huanglongbing caused significant damage to the world’s citrus industry. Thermotherapy and chemical agents were used to control this disease; however, the effectiveness of these treatments is frequently inconsistent. In addition, CLas cannot be cultured in vitro. Therefore, structure-based virtual screening is a novel method to find compounds that work against CLas. This study used CLas GMPS as a target for high-throughput screening and selected some compounds which have a higher binding affinity to test their inhibition of CLas GMPS. Finally, two molecules were identified as the lead compound to control citrus HLB. Abstract Citrus production is facing an unprecedented problem because of huanglongbing (HLB) disease. Presently, no effective HLB-easing method is available when citrus becomes infected. Guanosine 5′-monophosphate synthetase (GMPS) is a key protein in the de novo synthesis of guanine nucleotides. GMPS is used as an attractive target for developing agents that are effective against the patogen infection. In this research, homology modeling, structure-based virtual screening, and molecular docking were used to discover the new inhibitors against CLas GMPS. Enzyme assay showed that folic acid and AZD1152 showed high inhibition at micromole concentrations, with AZD1152 being the most potent molecule. The inhibition constant (Ki) value of folic acid and AZD1152 was 51.98 µM and 4.05 µM, respectively. These results suggested that folic acid and AZD1152 could be considered as promising candidates for the development of CLas agents.
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Affiliation(s)
- Jing Nan
- Ministry of Education Key Laboratory of Plant Biology, Huazhong Agricultural University, Wuhan 430070, China; (J.N.); (P.Z.)
| | - Shaoran Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Ping Zhan
- Ministry of Education Key Laboratory of Plant Biology, Huazhong Agricultural University, Wuhan 430070, China; (J.N.); (P.Z.)
| | - Ling Jiang
- Ministry of Education Key Laboratory of Plant Biology, Huazhong Agricultural University, Wuhan 430070, China; (J.N.); (P.Z.)
- Correspondence:
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7
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Shivakumaraswamy S, Pandey N, Ballut L, Violot S, Aghajari N, Balaram H. Helices on Interdomain Interface Couple Catalysis in the ATPPase Domain with Allostery in Plasmodium falciparum GMP Synthetase. Chembiochem 2020; 21:2805-2817. [PMID: 32358899 DOI: 10.1002/cbic.202000158] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/30/2020] [Indexed: 11/07/2022]
Abstract
GMP synthetase catalyses the conversion of XMP to GMP through a series of reactions that include hydrolysis of Gln to generate ammonia in the glutamine amidotransferase (GATase) domain, activation of XMP to adenyl-XMP intermediate in the ATP pyrophosphatase (ATPPase) domain and reaction of ammonia with the intermediate to generate GMP. The functioning of GMP synthetases entails bidirectional domain crosstalk, which leads to allosteric activation of the GATase domain, synchronization of catalytic events and tunnelling of ammonia. Herein, we have taken recourse to the analysis of structures of GMP synthetases, site-directed mutagenesis and steady-state and transient kinetics on the Plasmodium falciparum enzyme to decipher the molecular basis of catalysis in the ATPPase domain and domain crosstalk. Our results suggest an arrangement at the interdomain interface, of helices with residues that play roles in ATPPase catalysis as well as domain crosstalk enabling the coupling of ATPPase catalysis with GATase activation. Overall, the study enhances our understanding of GMP synthetases, which are drug targets in many infectious pathogens.
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Affiliation(s)
- Santosh Shivakumaraswamy
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka, 560064, India
| | - Nivedita Pandey
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka, 560064, India
| | - Lionel Ballut
- Biocrystallography and Structural Biology of Therapeutic Targets Molecular Microbiology and Structural Biochemistry UMR 5086 CNRS -, University of Lyon 1, 7 passage du Vercors, 69367, Lyon Cedex 07, France
| | - Sébastien Violot
- Biocrystallography and Structural Biology of Therapeutic Targets Molecular Microbiology and Structural Biochemistry UMR 5086 CNRS -, University of Lyon 1, 7 passage du Vercors, 69367, Lyon Cedex 07, France
| | - Nushin Aghajari
- Biocrystallography and Structural Biology of Therapeutic Targets Molecular Microbiology and Structural Biochemistry UMR 5086 CNRS -, University of Lyon 1, 7 passage du Vercors, 69367, Lyon Cedex 07, France
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka, 560064, India
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Fellner M, Hausinger RP, Hu J. A structural perspective on the PP-loop ATP pyrophosphatase family. Crit Rev Biochem Mol Biol 2018; 53:607-622. [DOI: 10.1080/10409238.2018.1516728] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Matthias Fellner
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Robert P. Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
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9
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Chitty JL, Tatzenko TL, Williams SJ, Koh YQAE, Corfield EC, Butler MS, Robertson AAB, Cooper MA, Kappler U, Kobe B, Fraser JA. GMP Synthase Is Required for Virulence Factor Production and Infection by Cryptococcus neoformans. J Biol Chem 2017; 292:3049-3059. [PMID: 28062578 DOI: 10.1074/jbc.m116.767533] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/04/2017] [Indexed: 11/06/2022] Open
Abstract
Over the last four decades the HIV pandemic and advances in medical treatments that also cause immunosuppression have produced an ever-growing cohort of individuals susceptible to opportunistic pathogens. Of these, AIDS patients are particularly vulnerable to infection by the encapsulated yeast Cryptococcus neoformans Most commonly found in the environment in purine-rich bird guano, C. neoformans experiences a drastic change in nutrient availability during host infection, ultimately disseminating to colonize the purine-poor central nervous system. Investigating the consequences of this challenge, we have characterized C. neoformans GMP synthase, the second enzyme in the guanylate branch of de novo purine biosynthesis. We show that in the absence of GMP synthase, C. neoformans becomes a guanine auxotroph, the production of key virulence factors is compromised, and the ability to infect nematodes and mice is abolished. Activity assays performed using recombinant protein unveiled differences in substrate binding between the C. neoformans and human enzymes, with structural insights into these kinetic differences acquired via homology modeling. Collectively, these data highlight the potential of GMP synthase to be exploited in the development of new therapeutic agents for the treatment of disseminated, life-threatening fungal infections.
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Affiliation(s)
- Jessica L Chitty
- From the Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences.,the Institute for Molecular Bioscience, and
| | - Tayla L Tatzenko
- From the Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences
| | - Simon J Williams
- From the Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences.,the ANU Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - Y Q Andre E Koh
- From the Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences
| | - Elizabeth C Corfield
- From the Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences
| | | | | | - Matthew A Cooper
- From the Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences.,the Institute for Molecular Bioscience, and
| | - Ulrike Kappler
- From the Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences.,the Centre for Metals in Biology, University of Queensland, St. Lucia, Queensland 4072, Australia and
| | - Bostjan Kobe
- From the Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences.,the Institute for Molecular Bioscience, and
| | - James A Fraser
- From the Australian Infectious Diseases Research Centre, School of Chemistry & Molecular Biosciences,
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10
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Active site coupling in Plasmodium falciparum GMP synthetase is triggered by domain rotation. Nat Commun 2015; 6:8930. [PMID: 26592566 PMCID: PMC4673825 DOI: 10.1038/ncomms9930] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/19/2015] [Indexed: 11/24/2022] Open
Abstract
GMP synthetase (GMPS), a key enzyme in the purine biosynthetic pathway performs catalysis through a coordinated process across two catalytic pockets for which the mechanism remains unclear. Crystal structures of Plasmodium falciparum GMPS in conjunction with mutational and enzyme kinetic studies reported here provide evidence that an 85° rotation of the GATase domain is required for ammonia channelling and thus for the catalytic activity of this two-domain enzyme. We suggest that conformational changes in helix 371–375 holding catalytic residues and in loop 376–401 along the rotation trajectory trigger the different steps of catalysis, and establish the central role of Glu374 in allostery and inter-domain crosstalk. These studies reveal the mechanism of domain rotation and inter-domain communication, providing a molecular framework for the function of all single polypeptide GMPSs and form a solid basis for rational drug design targeting this therapeutically important enzyme. GMP synthetase, a key enzyme in purine biosynthesis, is of interest for understanding purine metabolism processes and for developing therapeutic applications. Here, the authors propose a molecular mechanism and the structural basis for the catalytic activity of this enzyme.
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11
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Oliver JC, Gudihal R, Burgner JW, Pedley AM, Zwierko AT, Davisson VJ, Linger RS. Conformational changes involving ammonia tunnel formation and allosteric control in GMP synthetase. Arch Biochem Biophys 2014; 545:22-32. [PMID: 24434004 DOI: 10.1016/j.abb.2014.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 12/27/2013] [Accepted: 01/06/2014] [Indexed: 11/17/2022]
Abstract
GMP synthetase is the glutamine amidotransferase that catalyzes the final step in the guanylate branch of de novo purine biosynthesis. Conformational changes are required to efficiently couple distal active sites in the protein; however, the nature of these changes has remained elusive. Structural information derived from both limited proteolysis and sedimentation velocity experiments support the hypothesis of nucleotide-induced loop- and domain-closure in the protein. These results were combined with information from sequence conservation and precedents from other glutamine amidotransferases to develop the first structural model of GMPS in a closed, active state. In analyzing this Catalytic model, an interdomain salt bridge was identified residing in the same location as seen in other triad glutamine amidotransferases. Using mutagenesis and kinetic analysis, the salt bridge between H186 and E383 was shown to function as a connection between the two active sites. Mutations at these residues uncoupled the two half-reactions of the enzyme. The chemical events of nucleotide binding initiate a series of conformational changes that culminate in the establishment of a tunnel for ammonia as well as an activated glutaminase catalytic site. The results of this study provide a clearer understanding of the allostery of GMPS, where, for the first time, key substrate binding and interdomain contacts are modeled and analyzed.
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Affiliation(s)
- Justin C Oliver
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - Ravidra Gudihal
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - John W Burgner
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, United States
| | - Anthony M Pedley
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - Alexander T Zwierko
- Department of Pharmaceutical and Administrative Sciences, University of Charleston, Charleston, WV 25304, United States
| | - V Jo Davisson
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - Rebecca S Linger
- Department of Pharmaceutical and Administrative Sciences, University of Charleston, Charleston, WV 25304, United States.
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12
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Oliver JC, Linger RS, Chittur SV, Davisson VJ. Substrate activation and conformational dynamics of guanosine 5'-monophosphate synthetase. Biochemistry 2013; 52:5225-35. [PMID: 23841499 DOI: 10.1021/bi3017075] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glutamine amidotransferases catalyze the amination of a wide range of molecules using the amide nitrogen of glutamine. The family provides numerous examples for study of multi-active-site regulation and interdomain communication in proteins. Guanosine 5'-monophosphate synthetase (GMPS) is one of three glutamine amidotransferases in de novo purine biosynthesis and is responsible for the last step in the guanosine branch of the pathway, the amination of xanthosine 5'-monophosphate (XMP). In several amidotransferases, the intramolecular path of ammonia from glutamine to substrate is understood; however, the crystal structure of GMPS only hinted at the details of such transfer. Rapid kinetics studies provide insight into the mechanism of the substrate-induced changes in this complex enzyme. Rapid mixing of GMPS with substrates also manifests absorbance changes that report on the kinetics of formation of a reactive intermediate as well as steps in the process of rapid transfer of ammonia to this intermediate. Isolation and use of the adenylylated nucleotide intermediate allowed the study of the amido transfer reaction distinct from the ATP-dependent reaction. Changes in intrinsic tryptophan fluorescence upon mixing of enzyme with XMP suggest a conformational change upon substrate binding, likely the ordering of a highly conserved loop in addition to global domain motions. In the GMPS reaction, all forward rates before product release appear to be faster than steady-state turnover, implying that release is likely rate-limiting. These studies establish the functional role of a substrate-induced conformational change in the GMPS catalytic cycle and provide a kinetic context for the formation of an ammonia channel linking the distinct active sites.
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Affiliation(s)
- Justin C Oliver
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University , West Lafayette, Indiana 47907, United States
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Welin M, Lehtiö L, Johansson A, Flodin S, Nyman T, Trésaugues L, Hammarström M, Gräslund S, Nordlund P. Substrate specificity and oligomerization of human GMP synthetase. J Mol Biol 2013; 425:4323-33. [PMID: 23816837 DOI: 10.1016/j.jmb.2013.06.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 06/20/2013] [Accepted: 06/21/2013] [Indexed: 10/26/2022]
Abstract
Guanine monophosphate (GMP) synthetase is a bifunctional two-domain enzyme. The N-terminal glutaminase domain generates ammonia from glutamine and the C-terminal synthetase domain aminates xanthine monophosphate (XMP) to form GMP. Mammalian GMP synthetases (GMPSs) contain a 130-residue-long insert in the synthetase domain in comparison to bacterial proteins. We report here the structure of a eukaryotic GMPS. Substrate XMP was bound in the crystal structure of the human GMPS enzyme. XMP is bound to the synthetase domain and covered by a LID motif. The enzyme forms a dimer in the crystal structure with subunit orientations entirely different from the bacterial counterparts. The inserted sub-domain is shown to be involved in substrate binding and dimerization. Furthermore, the structural basis for XMP recognition is revealed as well as a potential allosteric site. Enzymes in the nucleotide metabolism typically display an increased activity in proliferating cells due to the increased need for nucleotides. Many drugs used as immunosuppressants and for treatment of cancer and viral diseases are indeed nucleobase- and nucleoside-based compounds, which are acting on or are activated by enzymes in this pathway. The information obtained from the crystal structure of human GMPS might therefore aid in understanding interactions of nucleoside-based drugs with GMPS and in structure-based design of GMPS-specific inhibitors.
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Affiliation(s)
- Martin Welin
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden
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14
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Ali R, Kumar S, Balaram H, Sarma SP. Solution nuclear magnetic resonance structure of the GATase subunit and structural basis of the interaction between GATase and ATPPase subunits in a two-subunit-type GMPS from Methanocaldococcus jannaschii. Biochemistry 2013; 52:4308-23. [PMID: 23724776 DOI: 10.1021/bi400472e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solution structure of the monomeric glutamine amidotransferase (GATase) subunit of the Methanocaldococcus janaschii (Mj) guanosine monophosphate synthetase (GMPS) has been determined using high-resolution nuclear magnetic resonance methods. Gel filtration chromatography and ¹⁵N backbone relaxation studies have shown that the Mj GATase subunit is present in solution as a 21 kDa (188-residue) monomer. The ensemble of 20 lowest-energy structures showed root-mean-square deviations of 0.35 ± 0.06 Å for backbone atoms and 0.8 ± 0.06 Å for all heavy atoms. Furthermore, 99.4% of the backbone dihedral angles are present in the allowed region of the Ramachandran map, indicating the stereochemical quality of the structure. The core of the tertiary structure of the GATase is composed of a seven-stranded mixed β-sheet that is fenced by five α-helices. The Mj GATase is similar in structure to the Pyrococcus horikoshi (Ph) GATase subunit. Nuclear magnetic resonance (NMR) chemical shift perturbations and changes in line width were monitored to identify residues on GATase that were responsible for interaction with magnesium and the ATPPase subunit, respectively. These interaction studies showed that a common surface exists for the metal ion binding as well as for the protein-protein interaction. The dissociation constant for the GATase-Mg(2+) interaction has been found to be ∼1 mM, which implies that interaction is very weak and falls in the fast chemical exchange regime. The GATase-ATPPase interaction, on the other hand, falls in the intermediate chemical exchange regime on the NMR time scale. The implication of this interaction in terms of the regulation of the GATase activity of holo GMPS is discussed.
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Affiliation(s)
- Rustam Ali
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India
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15
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Franco TMA, Rostirolla DC, Ducati RG, Lorenzini DM, Basso LA, Santos DS. Biochemical characterization of recombinant guaA-encoded guanosine monophosphate synthetase (EC 6.3.5.2) from Mycobacterium tuberculosis H37Rv strain. Arch Biochem Biophys 2011; 517:1-11. [PMID: 22119138 DOI: 10.1016/j.abb.2011.11.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 11/08/2011] [Accepted: 11/09/2011] [Indexed: 12/29/2022]
Abstract
Administration of the current tuberculosis (TB) vaccine to newborns is not a reliable route for preventing TB in adults. The conversion of XMP to GMP is catalyzed by guaA-encoded GMP synthetase (GMPS), and deletions in the Shiguella flexneri guaBA operon led to an attenuated auxotrophic strain. Here we present the cloning, expression, and purification of recombinant guaA-encoded GMPS from Mycobacterium tuberculosis (MtGMPS). Mass spectrometry data, oligomeric state determination, steady-state kinetics, isothermal titration calorimetry (ITC), and multiple sequence alignment are also presented. The homodimeric MtGMPS catalyzes the conversion of XMP, MgATP, and glutamine into GMP, ADP, PP(i), and glutamate. XMP, NH(4)(+), and Mg(2+) displayed positive homotropic cooperativity, whereas ATP and glutamine displayed hyperbolic saturation curves. The activity of ATP pyrophosphatase domain is independent of glutamine amidotransferase domain, whereas the latter cannot catalyze hydrolysis of glutamine to NH(3) and glutamate in the absence of substrates. ITC data suggest random order of binding of substrates, and PP(i) is the last product released. Sequence comparison analysis showed conservation of both Cys-His-Glu catalytic triad of N-terminal Class I amidotransferase and of amino acid residues of the P-loop of the N-type ATP pyrophosphatase family.
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Affiliation(s)
- Tathyana Mar A Franco
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
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16
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Bhat JY, Venkatachala R, Balaram H. Substrate-induced conformational changes in Plasmodium falciparum guanosine monophosphate synthetase. FEBS J 2011; 278:3756-68. [PMID: 21827625 DOI: 10.1111/j.1742-4658.2011.08296.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
GMP synthetase is a glutamine amidotransferase that incorporates ammonia derived from glutamine into the nucleotide xanthosine 5'-monophosphate (XMP) to form guanosine 5'-monophosphate (GMP). Functional coordination of domains in glutamine amidotransferases leads to upregulation of glutamine hydrolysis in the presence of acceptor substrates and is a common feature in this class of enzymes. We have shown earlier that binding of substrates to the acceptor domain of Plasmodium falciparum GMP synthetase (PfGMPS) leads to enhancement in both glutaminase activity and rate of glutaminase inactivation, by the irreversible inhibitors acivicin and diazo-oxonorleucine [Bhat JY et al. (2008) Biochem J409, 263-273], a process that must be driven by conformational alterations. In this paper, through the combined use of biochemical assays, optical spectroscopy and mass spectrometry, we demonstrate that PfGMPS undergoes conformational transitions upon binding of substrates to the acceptor domain. Limited proteolysis and hydrogen-deuterium exchange in conjunction with mass spectrometry unveil region-specific conformational changes in the ATP + XMP bound state of PfGMPS. Decreased accessibility of R294 and K428 residues to trypsin in the ATP pyrophosphatase domain and reduced deuterium incorporation in the 143-155 region, pertaining to the glutaminase domain, suggest that in PfGMPS ligand-induced conformational changes are not only local but also transmitted over a long range across the domains. Overall, these results provide a detailed understanding of the substrate-induced changes in PfGMPS that could be essential for the overall catalytic process.
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Affiliation(s)
- Javaid Y Bhat
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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17
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Bhat JY, Venkatachala R, Singh K, Gupta K, Sarma SP, Balaram H. Ammonia Channeling in Plasmodium falciparum GMP Synthetase: Investigation by NMR Spectroscopy and Biochemical Assays. Biochemistry 2011; 50:3346-56. [DOI: 10.1021/bi1017057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Javaid Yousuf Bhat
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Roopa Venkatachala
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Kavita Singh
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Kallol Gupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Siddhartha P. Sarma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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