1
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Xia Y, Zhu G, Zhang X, Li S, Du L, Zhu W. Biosynthesis of 4-Acyl-5-aminoimidazole Alkaloids Featuring a New Friedel-Crafts Acyltransferase. J Am Chem Soc 2023; 145:26308-26317. [PMID: 37983668 DOI: 10.1021/jacs.3c09522] [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: 11/22/2023]
Abstract
Friedel-Crafts acylation (FCA) is a highly beneficial approach in organic chemistry for creating the important C-C bonds that are necessary for building intricate frameworks between aromatic substrates and an acyl group. However, there are few reports about enzyme catalyzed FCA reactions. In this study, 4-acyl-5-aminoimidazole alkaloids (AAIAs), streptimidazoles A-C (1-3), and the enantiopure (+)-nocarimidazole C (4) as well as their ribosides, streptimidazolesides A-D (5-8), were identified from the fermentation broth of Streptomyces sp. OUCMDZ-944 or heterologous S. coelicolor M1154 mutant. The biosynthetic gene cluster (smz) was identified, and the biosynthetic pathway of AAIAs was elucidated for the first time. In vivo and in vitro studies proved the catalytic activity of the four essential genes smzB, -C, -E, and -F for AAIAs biosynthesis and clarified the biosynthetic process of the alkaloids. The ligase SmzE activates fatty acyl groups and connects them to the acyl carrier protein (ACP) holo-SmzF. Then, the acyl group is transferred onto the key residue Cys49 of SmzB, a new Friedel-Crafts acyltransferase (FCase). Subsequently, the FCA reaction between the acyl groups and 5-aminoimidazole ribonucleotide (AIR) occurs to generate the key intermediate AAIA-nucleotides catalyzed by SmzB. Finally, the hydrolase SmzC catalyzes the N-glycosidic bond cleavage of the intermediates to form AAIAs. Structural simulation, molecular modeling, and mutational analysis of SmzB showed that Tyr26, Cys49, and Tyr93 are the key catalytic residues in the C-C bond formation of the acyl chain of AAIAs, providing mechanistic insights into the enzymatic FCA reaction.
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Affiliation(s)
- Yuwei Xia
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Guoliang Zhu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Xingwang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Lei Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Weiming Zhu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Laoshan Laboratory, Qingdao 266237, China
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2
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Graf F, Zehentner B, Fellner L, Scherer S, Neuhaus K. Three Novel Antisense Overlapping Genes in E. coli O157:H7 EDL933. Microbiol Spectr 2023; 11:e0235122. [PMID: 36533921 PMCID: PMC9927249 DOI: 10.1128/spectrum.02351-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 12/03/2022] [Indexed: 12/23/2022] Open
Abstract
The abundance of long overlapping genes in prokaryotic genomes is likely to be significantly underestimated. To date, only a few examples of such genes are fully established. Using RNA sequencing and ribosome profiling, we found expression of novel overlapping open reading frames in Escherichia coli O157:H7 EDL933 (EHEC). Indeed, the overlapping candidate genes are equipped with typical structural elements required for transcription and translation, i.e., promoters, transcription start sites, as well as terminators, all of which were experimentally verified. Translationally arrested mutants, unable to produce the overlapping encoded protein, were found to have a growth disadvantage when grown competitively against the wild type. Thus, the phenotypes found imply biological functionality of the genes at the level of proteins produced. The addition of 3 more examples of prokaryotic overlapping genes to the currently limited, yet constantly growing pool of such genes emphasizes the underestimated coding capacity of bacterial genomes. IMPORTANCE The abundance of long overlapping genes in prokaryotic genomes is likely to be significantly underestimated, since such genes are not allowed in genome annotations. However, ribosome profiling catches mRNA in the moment of being template for protein production. Using this technique and subsequent experiments, we verified 3 novel overlapping genes encoded in antisense of known genes. This adds more examples of prokaryotic overlapping genes to the currently limited, yet constantly growing pool of such genes.
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Affiliation(s)
- Franziska Graf
- Core Facility Microbiome, ZIEL – Institute for Food & Health, Technische Universität München, Freising, Germany
- Chair for Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Freising, Germany
| | - Barbara Zehentner
- Chair for Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Freising, Germany
| | - Lea Fellner
- Chair for Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Freising, Germany
| | - Siegfried Scherer
- Core Facility Microbiome, ZIEL – Institute for Food & Health, Technische Universität München, Freising, Germany
- Chair for Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Freising, Germany
| | - Klaus Neuhaus
- Core Facility Microbiome, ZIEL – Institute for Food & Health, Technische Universität München, Freising, Germany
- Chair for Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Freising, Germany
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3
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Magnetic Multi-Enzymatic System for Cladribine Manufacturing. Int J Mol Sci 2022; 23:ijms232113634. [DOI: 10.3390/ijms232113634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/09/2022] Open
Abstract
Enzyme-mediated processes have proven to be a valuable and sustainable alternative to traditional chemical methods. In this regard, the use of multi-enzymatic systems enables the realization of complex synthetic schemes, while also introducing a number of additional advantages, including the conversion of reversible reactions into irreversible processes, the partial or complete elimination of product inhibition problems, and the minimization of undesirable by-products. In addition, the immobilization of biocatalysts on magnetic supports allows for easy reusability and streamlines the downstream process. Herein we have developed a cascade system for cladribine synthesis based on the sequential action of two magnetic biocatalysts. For that purpose, purine 2′-deoxyribosyltransferase from Leishmania mexicana (LmPDT) and Escherichia coli hypoxanthine phosphoribosyltransferase (EcHPRT) were immobilized onto Ni2+-prechelated magnetic microspheres (MagReSyn®NTA). Among the resulting derivatives, MLmPDT3 (activity: 11,935 IU/gsupport, 63% retained activity, operational conditions: 40 °C and pH 5–7) and MEcHPRT3 (12,840 IU/gsupport, 45% retained activity, operational conditions: pH 5–8 and 40–60 °C) emerge as optimal catalysts for further synthetic application. Moreover, the MLmPDT3/MEcHPRT3 system was biochemically characterized and successfully applied to the one-pot synthesis of cladribine under various conditions. This methodology not only displayed a 1.67-fold improvement in cladribine synthesis (compared to MLmPDT3), but it also implied a practically complete transformation of the undesired by-product into a high-added-value product (90% conversion of Hyp into IMP). Finally, MLmPDT3/MEcHPRT3 was reused for 16 cycles, which displayed a 75% retained activity.
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4
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Keough DT, Wun SJ, Baszczyňski O, Eng WS, Špaček P, Panjikar S, Naesens L, Pohl R, Rejman D, Hocková D, Ferrero RL, Guddat LW. Helicobacter pylori Xanthine-Guanine-Hypoxanthine Phosphoribosyltransferase-A Putative Target for Drug Discovery against Gastrointestinal Tract Infections. J Med Chem 2021; 64:5710-5729. [PMID: 33891818 DOI: 10.1021/acs.jmedchem.0c02184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Helicobacter pylori (Hp) is a human pathogen that lives in the gastric mucosa of approximately 50% of the world's population causing gastritis, peptic ulcers, and gastric cancer. An increase in resistance to current drugs has sparked the search for new Hp drug targets and therapeutics. One target is the disruption of nucleic acid production, which can be achieved by impeding the synthesis of 6-oxopurine nucleoside monophosphates, the precursors of DNA and RNA. These metabolites are synthesized by Hp xanthine-guanine-hypoxanthine phosphoribosyltransferase (XGHPRT). Here, nucleoside phosphonates have been evaluated, which inhibit the activity of this enzyme with Ki values as low as 200 nM. The prodrugs of these compounds arrest the growth of Hp at a concentration of 50 μM in cell-based assays. The kinetic properties of HpXGHPRT have been determined together with its X-ray crystal structure in the absence and presence of 9-[(N-3-phosphonopropyl)-aminomethyl-9-deazahypoxanthine, providing a basis for new antibiotic development.
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Affiliation(s)
- Dianne T Keough
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Shun Jie Wun
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Ondřej Baszczyňski
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Wai Soon Eng
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Petr Špaček
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Santosh Panjikar
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton 3168, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Australia
| | - Lieve Naesens
- Katholieke Universiteit, Leuven, Rega Institute for Medical Research, Leuven 3000, Belgium
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Dana Hocková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6 CZ-166 10, Czech Republic
| | - Richard L Ferrero
- Hudson Institute of Medical Research, Clayton 3800, Victoria, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton 3800, Australia.,Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton 3800, Australia
| | - Luke W Guddat
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
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5
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Acyclic nucleoside phosphonates as possible chemotherapeutics against Trypanosoma brucei. Drug Discov Today 2020; 25:1043-1053. [PMID: 32135205 DOI: 10.1016/j.drudis.2020.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/24/2020] [Accepted: 02/20/2020] [Indexed: 11/20/2022]
Abstract
Human African trypanosomiasis is a life-threatening illness caused by Trypanosoma brucei. Owing to the toxic side effects of the available therapeutics, new medications for this disease are needed. One potential drug target is the 6-oxopurine phosphoribosyltransferases (PRTs), the activity of which is crucial to produce purine nucleotide monophosphates required for DNA and RNA synthesis. Inhibitors of the 6-oxopurine PRTs that show promising results as drug leads are the acyclic nucleoside phosphonates (ANPs). ANPs are very flexible in their structure, enabling important conformational changes to facilitate the binding of this class of compounds in the active site of the 6-oxopurine PRTs.
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6
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Anderson BW, Liu K, Wolak C, Dubiel K, She F, Satyshur KA, Keck JL, Wang JD. Evolution of (p)ppGpp-HPRT regulation through diversification of an allosteric oligomeric interaction. eLife 2019; 8:e47534. [PMID: 31552824 PMCID: PMC6783271 DOI: 10.7554/elife.47534] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 09/24/2019] [Indexed: 12/31/2022] Open
Abstract
The alarmone (p)ppGpp regulates diverse targets, yet its target specificity and evolution remain poorly understood. Here, we elucidate the mechanism by which basal (p)ppGpp inhibits the purine salvage enzyme HPRT by sharing a conserved motif with its substrate PRPP. Intriguingly, HPRT regulation by (p)ppGpp varies across organisms and correlates with HPRT oligomeric forms. (p)ppGpp-sensitive HPRT exists as a PRPP-bound dimer or an apo- and (p)ppGpp-bound tetramer, where a dimer-dimer interface triggers allosteric structural rearrangements to enhance (p)ppGpp inhibition. Loss of this oligomeric interface results in weakened (p)ppGpp regulation. Our results reveal an evolutionary principle whereby protein oligomerization allows evolutionary change to accumulate away from a conserved binding pocket to allosterically alter specificity of ligand interaction. This principle also explains how another (p)ppGpp target GMK is variably regulated across species. Since most ligands bind near protein interfaces, we propose that this principle extends to many other protein-ligand interactions.
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Affiliation(s)
- Brent W Anderson
- Department of BacteriologyUniversity of WisconsinMadisonUnited States
| | - Kuanqing Liu
- Department of BacteriologyUniversity of WisconsinMadisonUnited States
| | - Christine Wolak
- Department of Biomolecular ChemistryUniversity of WisconsinMadisonUnited States
| | - Katarzyna Dubiel
- Department of Biomolecular ChemistryUniversity of WisconsinMadisonUnited States
| | - Fukang She
- Department of BacteriologyUniversity of WisconsinMadisonUnited States
| | - Kenneth A Satyshur
- Department of Biomolecular ChemistryUniversity of WisconsinMadisonUnited States
| | - James L Keck
- Department of Biomolecular ChemistryUniversity of WisconsinMadisonUnited States
| | - Jue D Wang
- Department of BacteriologyUniversity of WisconsinMadisonUnited States
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7
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Terán D, Doleželová E, Keough DT, Hocková D, Zíková A, Guddat LW. Crystal structures of Trypanosoma brucei hypoxanthine - guanine - xanthine phosphoribosyltransferase in complex with IMP, GMP and XMP. FEBS J 2019; 286:4721-4736. [PMID: 31287615 DOI: 10.1111/febs.14987] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 04/16/2019] [Accepted: 07/06/2019] [Indexed: 11/27/2022]
Abstract
The 6-oxopurine phosphoribosyltransferases (PRTs) are drug targets for the treatment of parasitic diseases. This is due to the fact that parasites are auxotrophic for the 6-oxopurine bases relying on salvage enzymes for the synthesis of their 6-oxopurine nucleoside monophosphates. In Trypanosoma brucei, the parasite that is the aetiological agent for sleeping sickness, there are three 6-oxopurine PRT isoforms. Two are specific for hypoxanthine and guanine, whilst the third, characterized here, uses all three naturally occurring bases with similar efficiency. Here, we have determined crystal structures for TbrHGXPRT in complex with GMP, XMP and IMP to investigate the structural basis for substrate specificity. The results show that Y201 and E208, not commonly observed within the purine binding pocket of 6-oxopurine PRTs, contribute to the versatility of this enzyme. The structures further show that a nearby water can act as an adaptor to facilitate the binding of XMP and GMP. When GMP binds, a water can accept a proton from the 2-amino group but when XMP binds, the equivalent water can donate its proton to the 2-oxo group. However, when IMP is bound, no water molecule is observed at that location. DATABASE: Coordinates and structure factors were submitted to the Protein Data Bank and have accession codes of 6MXB, 6MXC, 6MXD and 6MXG for the TbrHGXPRT.XMP complex, TbrHGXPRT.GMP complex, TbrHGXPRT.IMP complex, and TbrHGPRT.XMP complex, respectively.
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Affiliation(s)
- David Terán
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Eva Doleželová
- Biology Centre CAS, Institute of Parasitology, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Dianne T Keough
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Dana Hocková
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic
| | - Alena Zíková
- Biology Centre CAS, Institute of Parasitology, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Luke W Guddat
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
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8
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In vitro and in vivo characterization of the multiple isoforms of Schistosoma mansoni hypoxanthine-guanine phosphoribosyltransferases. Mol Biochem Parasitol 2019; 229:24-34. [PMID: 30772423 DOI: 10.1016/j.molbiopara.2019.02.005] [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: 12/03/2018] [Revised: 01/30/2019] [Accepted: 02/12/2019] [Indexed: 10/27/2022]
Abstract
Schistosoma mansoni, the parasite responsible for schistosomiasis, lacks the "de novo" purine biosynthetic pathway and depends entirely on the purine salvage pathway for the supply of purines. Numerous reports of praziquantel resistance have been described, as well as stimulated efforts to develop new drugs against schistosomiasis. Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) is a key enzyme of the purine salvage pathway. Here, we describe a crystallographic structure of the S. mansoni HPGRT-1 (SmHGPRT), complexed with IMP at a resolution of 2.8 Ǻ. Four substitutions were identified in the region of the active site between SmHGPRT-1 and human HGPRT. We also present data from RNA-Seq and WISH, suggesting that some isoforms of HGPRT might be involved in the process related to sexual maturation and reproduction in worms; furthermore, its enzymatic assays show that the isoform SmHGPRT-3 does not present the same catalytic efficiency as other isoforms. Finally, although other studies have previously suggested this enzyme as a potential antischistosomal chemotherapy target, the kinetics parameters reveal the impossibility to use SmHGPRT as an efficient chemotherapeutic target.
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9
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Eng WS, Rejman D, Pohl R, West NP, Woods K, Naesens LMJ, Keough DT, Guddat LW. Pyrrolidine nucleoside bisphosphonates as antituberculosis agents targeting hypoxanthine-guanine phosphoribosyltransferase. Eur J Med Chem 2018; 159:10-22. [PMID: 30265958 DOI: 10.1016/j.ejmech.2018.09.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 08/10/2018] [Accepted: 09/14/2018] [Indexed: 11/28/2022]
Abstract
Therapeutic treatment of tuberculosis (TB) is becoming increasingly problematic due to the emergence of drug resistant Mycobacterium tuberculosis (Mt). Thus, new targets for anti-TB drug discovery need to be identified to combat and eradicate this disease. One such target is hypoxanthine-guanine phosphoribosyltransferase (HGPRT) which synthesises the 6-oxopurine nucleoside monophosphates essential for DNA/RNA production. [3R,4R]-4-Hypoxanthin-9-yl-3-((S)-2-hydroxy-2-phosphonoethyl)oxy-1-N-(phosphonopropionyl)pyrrolidine and [3R,4R]-4-guanin-9-yl-3-((S)-2-hydroxy-2-phosphonoethyl)oxy-1-N-(phosphonopropionyl)pyrrolidine (compound 6) are the most potent inhibitors of MtHGPRT yet discovered having Ki values of 60 nM. The crystal structure of the MtHGPRT.6 complex was obtained and compared with that of human HGPRT in complex with the same inhibitor. These structures provide explanations for the 60-fold difference in the inhibition constants between these two enzymes and a foundation for the design of next generation inhibitors. In addition, crystal structures of MtHGPRT in complex with two pyrrolidine nucleoside phosphosphonate inhibitors plus pyrophosphate provide insights into the final stage of the catalytic reaction. As the first step in ascertaining if such compounds have the potential to be developed as anti-TB therapeutics, the tetra-(ethyl L-phenylalanine) tetraamide prodrug of 6 was tested in cell based assays. This compound arrested the growth of virulent Mt not only in its replicating phase (IC50 of 14 μΜ) but also in its latent phase (IC50 of 29 μΜ). Furthermore, it arrested the growth of Mt in infected macrophages (MIC50 of 85 μΜ) and has a low cytotoxicity in mammalian cells (CC50 of 132 ± 20 μM). These inhibitors are therefore viewed as forerunners of new anti-TB chemotherapeutics.
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Affiliation(s)
- Wai Soon Eng
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. Flemingovo nam. 2, CZ-166 10 Prague 6, Czech Republic.
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. Flemingovo nam. 2, CZ-166 10 Prague 6, Czech Republic
| | - Nicholas P West
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Kyra Woods
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Lieve M J Naesens
- Rega Institute for Medical Research, KU Leuven - University of Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - Dianne T Keough
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, QLD, Australia.
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10
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Doleželová E, Terán D, Gahura O, Kotrbová Z, Procházková M, Keough D, Špaček P, Hocková D, Guddat L, Zíková A. Evaluation of the Trypanosoma brucei 6-oxopurine salvage pathway as a potential target for drug discovery. PLoS Negl Trop Dis 2018; 12:e0006301. [PMID: 29481567 PMCID: PMC5843355 DOI: 10.1371/journal.pntd.0006301] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 03/08/2018] [Accepted: 02/05/2018] [Indexed: 01/19/2023] Open
Abstract
Due to toxicity and compliance issues and the emergence of resistance to current medications new drugs for the treatment of Human African Trypanosomiasis are needed. A potential approach to developing novel anti-trypanosomal drugs is by inhibition of the 6-oxopurine salvage pathways which synthesise the nucleoside monophosphates required for DNA/RNA production. This is in view of the fact that trypanosomes lack the machinery for de novo synthesis of the purine ring. To provide validation for this approach as a drug target, we have RNAi silenced the three 6-oxopurine phosphoribosyltransferase (PRTase) isoforms in the infectious stage of Trypanosoma brucei demonstrating that the combined activity of these enzymes is critical for the parasites’ viability. Furthermore, we have determined crystal structures of two of these isoforms in complex with several acyclic nucleoside phosphonates (ANPs), a class of compound previously shown to inhibit 6-oxopurine PRTases from several species including Plasmodium falciparum. The most potent of these compounds have Ki values as low as 60 nM, and IC50 values in cell based assays as low as 4 μM. This data provides a solid platform for further investigations into the use of this pathway as a target for anti-trypanosomal drug discovery. Human African Trypanosomiasis (HAT) is a life-threatening infectious disease caused by the protozoan parasite, Trypanosoma brucei. Current treatments suffer from low efficacy, toxicity issues and complex medication regimens. Moreover, an alarming number of these parasites are demonstrating resistance to current drugs. For these reasons, there is a renewed effort to develop new classes of modern therapeutics based upon the unique T. brucei cellular processes. One potential new drug target is 6-oxopurine phosphoribosyltransferase (PRTase), an enzyme central to the purine salvage pathway and whose activity is critical for the production of the nucleotides (GMP and IMP) required for DNA/RNA synthesis within this protozoan parasite. We demonstrated that T. brucei encodes two isoforms of hypoxanthine-guanine PRTases (HGPRT) and one hypoxanthine-guanine-xanthine PRTase (HGXPRT). The concurrent activity of these enzymes is required for the normal cell growth in vitro. Moreover, acyclic nucleoside phosphonates represent a promising class of potent and selective compounds as they inhibit the enzymes with Ki values in nanomolar range and exert cytotoxic effects on T. brucei cells grown in vitro with EC50 values in the single digit micromolar range. Our results provide a new foundation for further investigations of these compounds in vivo and suggest that 6-oxopurine salvage pathway represents a possible target for future drug discovery efforts directed at eliminating HAT.
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Affiliation(s)
- Eva Doleželová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská, České Budějovice, Czech Republic
| | - David Terán
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská, České Budějovice, Czech Republic
| | - Zuzana Kotrbová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská, České Budějovice, Czech Republic
| | - Michaela Procházková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská, České Budějovice, Czech Republic
| | - Dianne Keough
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Petr Špaček
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. Prague, Czech Republic
| | - Dana Hocková
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. Prague, Czech Republic
| | - Luke Guddat
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- * E-mail: (AZ); (LWG)
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská, České Budějovice, Czech Republic
- * E-mail: (AZ); (LWG)
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11
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Niu H, Yang W, Zhuang K, Chen X, Chen Y, Liu D, Wu J, Zhu C, Ying H. Screening of promoters from Arthrobacter sp. CGMCC 3584 using a green fluorescent protein reporter system. World J Microbiol Biotechnol 2017; 33:208. [DOI: 10.1007/s11274-017-2375-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 10/29/2017] [Indexed: 11/29/2022]
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12
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Del Arco J, Cejudo-Sanches J, Esteban I, Clemente-Suárez VJ, Hormigo D, Perona A, Fernández-Lucas J. Enzymatic production of dietary nucleotides from low-soluble purine bases by an efficient, thermostable and alkali-tolerant biocatalyst. Food Chem 2017; 237:605-611. [PMID: 28764042 DOI: 10.1016/j.foodchem.2017.05.136] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 05/16/2017] [Accepted: 05/28/2017] [Indexed: 11/17/2022]
Abstract
Traditionally, enzymatic synthesis of nucleoside-5'-monophosphates (5'-NMPs) using low water-soluble purine bases has been described as less efficient due to their low solubility in aqueous media. The use of enzymes from extremophiles, such as thermophiles or alkaliphiles, offers the potential to increase solubilisation of these bases by employing high temperatures or alkaline pH. This study describes the cloning, expression and purification of hypoxanthine-guanine-xanthine phosphoribosyltransferase from Thermus thermophilus (TtHGXPRT). Biochemical characterization indicates TtHGXPRT as a homotetramer with excellent activity and stability across a broad range of temperatures (50-90°C) and ionic strengths (0-500mMNaCl), but it also reveals an unusually high activity and stability under alkaline conditions (pH range 8-11). In order to explore the potential of TtHGXPRT as an industrial biocatalyst, enzymatic production of several dietary 5'-NMPs, such as 5'-GMP and 5'-IMP, was carried out at high concentrations of guanine and hypoxanthine.
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Affiliation(s)
- J Del Arco
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670 Villaviciosa de Odón, Madrid, Spain
| | - J Cejudo-Sanches
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670 Villaviciosa de Odón, Madrid, Spain
| | - I Esteban
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670 Villaviciosa de Odón, Madrid, Spain
| | - V J Clemente-Suárez
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670 Villaviciosa de Odón, Madrid, Spain
| | - D Hormigo
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670 Villaviciosa de Odón, Madrid, Spain
| | - A Perona
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670 Villaviciosa de Odón, Madrid, Spain
| | - J Fernández-Lucas
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670 Villaviciosa de Odón, Madrid, Spain; Grupo de Investigación en Desarrollo Agroindustrial Sostenible, Universidad de la Costa, CUC, Calle 58 # 55-66, Barranquilla, Colombia.
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13
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Eng WS, Keough DT, Hockova D, Winzor DJ, Guddat LW. Oligomeric state of hypoxanthine-guanine phosphoribosyltransferase from Mycobacterium tuberculosis. Biochimie 2017; 135:6-14. [PMID: 28082125 DOI: 10.1016/j.biochi.2016.12.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/29/2016] [Accepted: 12/30/2016] [Indexed: 10/20/2022]
Abstract
Sedimentation equilibrium and size-exclusion chromatography experiments on Mycobacterium tuberculosis hypoxanthine-guanine phosphoribosyltransferase (MtHGPRT) have established the existence of this enzyme as a reversibly associating mixture of dimeric and tetrameric species in 0.1 M Tris-HCl-0.012 M MgCl2, pH 7.4. Displacement of the equilibrium position towards the larger oligomer by phosphate signifies the probable existence of MtHGPRT as a tetramer in the biological environment. These data thus add credibility to the relevance of considering enzyme function in the light of a published tetrameric structure deduced from X-ray crystallography. Failure of 5-phospho-α-d-ribosyl-1-pyrophosphate (PRib-PP) to perturb the dimer-tetramer equilibrium position indicates the equivalence and independence of binding for this substrate (the first to bind in an ordered sequential mechanism) to the two oligomers. By virtue of the displacement of the equilibrium position towards dimer that is affected by removing MgCl2 from the Tris-HCl buffer, it can be concluded that divalent metal ions, as well as phosphate, can affect the oligomerization. These characteristics of MtHGPRT in solution are correlated with published crystal structures of four enzyme-ligand complexes.
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Affiliation(s)
- Wai Soon Eng
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Dianne T Keough
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Dana Hockova
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. Flemingovo nam. 2, CZ-166 10 Prague 6, Czechia
| | - Donald J Winzor
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia.
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14
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Eng WS, Hocková D, Špaček P, Baszczyňski O, Janeba Z, Naesens L, Keough DT, Guddat LW. Crystal Structures of Acyclic Nucleoside Phosphonates in Complex withEscherichia coliHypoxanthine Phosphoribosyltransferase. ChemistrySelect 2016. [DOI: 10.1002/slct.201601679] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Wai Soon Eng
- The School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane, Queensland 4068 Australia
| | - Dana Hocková
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i. Flemingovo nam. 2, CZ- 166 10 Prague 6 Czech Republic
| | - Petr Špaček
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i. Flemingovo nam. 2, CZ- 166 10 Prague 6 Czech Republic
| | - Ondřej Baszczyňski
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i. Flemingovo nam. 2, CZ- 166 10 Prague 6 Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i. Flemingovo nam. 2, CZ- 166 10 Prague 6 Czech Republic
| | - Lieve Naesens
- Rega Institute for Medical Research, KU Leuven; University of Leuven; Minderbroedersstraat 10, B- 3000 Leuven Belgium
| | - Dianne T. Keough
- The School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane, Queensland 4068 Australia
| | - Luke W. Guddat
- The School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane, Queensland 4068 Australia
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15
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Crystal structures and inhibition of Trypanosoma brucei hypoxanthine-guanine phosphoribosyltransferase. Sci Rep 2016; 6:35894. [PMID: 27786284 PMCID: PMC5081515 DOI: 10.1038/srep35894] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/06/2016] [Indexed: 01/29/2023] Open
Abstract
Human African Trypanosomiasis (HAT) is a life-threatening infectious disease caused by the protozoan parasite, Trypanosoma brucei (Tbr). Due to the debilitating side effects of the current therapeutics and the emergence of resistance to these drugs, new medications for this disease need to be developed. One potential new drug target is 6-oxopurine phosphoribosyltransferase (PRT), an enzyme central to the purine salvage pathway and whose activity is critical for the production of the nucleotides (GMP and IMP) required for DNA/RNA synthesis within this protozoan parasite. Here, the first crystal structures of this enzyme have been determined, these in complex with GMP and IMP and with three acyclic nucleoside phosphonate (ANP) inhibitors. The Ki values for GMP and IMP are 30.5 μM and 77 μM, respectively. Two of the ANPs have Ki values considerably lower than for the nucleotides, 2.3 μM (with guanine as base) and 15.8 μM (with hypoxanthine as base). The crystal structures show that when two of the ANPs bind, they induce an unusual conformation change to the loop where the reaction product, pyrophosphate, is expected to bind. This and other structural differences between the Tbr and human enzymes suggest selective inhibitors for the Tbr enzyme can be designed.
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16
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Serpi M, Ferrari V, Pertusati F. Nucleoside Derived Antibiotics to Fight Microbial Drug Resistance: New Utilities for an Established Class of Drugs? J Med Chem 2016; 59:10343-10382. [PMID: 27607900 DOI: 10.1021/acs.jmedchem.6b00325] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Novel antibiotics are urgently needed to combat the rise of infections due to drug-resistant microorganisms. Numerous natural nucleosides and their synthetically modified analogues have been reported to have moderate to good antibiotic activity against different bacterial and fungal strains. Nucleoside-based compounds target several crucial processes of bacterial and fungal cells such as nucleoside metabolism and cell wall, nucleic acid, and protein biosynthesis. Nucleoside analogues have also been shown to target many other bacterial and fungal cellular processes although these are not well characterized and may therefore represent opportunities to discover new drugs with unique mechanisms of action. In this Perspective, we demonstrate that nucleoside analogues, cornerstones of anticancer and antiviral treatments, also have great potential to be repurposed as antibiotics so that an old drug can learn new tricks.
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Affiliation(s)
- Michaela Serpi
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
| | - Valentina Ferrari
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
| | - Fabrizio Pertusati
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
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17
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Transcriptome Analysis of Escherichia coli during dGTP Starvation. J Bacteriol 2016; 198:1631-44. [PMID: 27002130 DOI: 10.1128/jb.00218-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 03/16/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Our laboratory recently discovered that Escherichia coli cells starved for the DNA precursor dGTP are killed efficiently (dGTP starvation) in a manner similar to that described for thymineless death (TLD). Conditions for specific dGTP starvation can be achieved by depriving an E. coli optA1 gpt strain of the purine nucleotide precursor hypoxanthine (Hx). To gain insight into the mechanisms underlying dGTP starvation, we conducted genome-wide gene expression analyses of actively growing optA1 gpt cells subjected to hypoxanthine deprivation for increasing periods. The data show that upon Hx withdrawal, the optA1 gpt strain displays a diminished ability to derepress the de novo purine biosynthesis genes, likely due to internal guanine accumulation. The impairment in fully inducing the purR regulon may be a contributing factor to the lethality of dGTP starvation. At later time points, and coinciding with cell lethality, strong induction of the SOS response was observed, supporting the concept of replication stress as a final cause of death. No evidence was observed in the starved cells for the participation of other stress responses, including the rpoS-mediated global stress response, reinforcing the lack of feedback of replication stress to the global metabolism of the cell. The genome-wide expression data also provide direct evidence for increased genome complexity during dGTP starvation, as a markedly increased gradient was observed for expression of genes located near the replication origin relative to those located toward the replication terminus. IMPORTANCE Control of the supply of the building blocks (deoxynucleoside triphosphates [dNTPs]) for DNA replication is important for ensuring genome integrity and cell viability. When cells are starved specifically for one of the four dNTPs, dGTP, the process of DNA replication is disturbed in a manner that can lead to eventual death. In the present study, we investigated the transcriptional changes in the bacterium E. coli during dGTP starvation. The results show increasing DNA replication stress with an increased time of starvation, as evidenced by induction of the bacterial SOS system, as well as a notable lack of induction of other stress responses that could have saved the cells from cell death by slowing down cell growth.
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18
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Karmakar T, Roy S, Balaram H, Balasubramanian S. Structural and dynamical correlations in PfHGXPRT oligomers: A molecular dynamics simulation study. J Biomol Struct Dyn 2016; 34:1590-605. [PMID: 26441001 DOI: 10.1080/07391102.2015.1085441] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PfHGXPRT is a key enzyme involved in purine nucleotide salvage pathway of the malarial parasite, Plasmodium falciparum. Atomistic molecular dynamics simulations have been performed on two types of PfHGXPRT dimers (D1 and D3) and its tetramer in their apo and ligand-bound states. A significant event in the catalytic cycle is the dynamics of a gate that provides access for the ligand molecules to the reaction center. The gate is formed by loops II and IV, the former being the most flexible. Large amplitude conformational changes have been observed in active site loop II. Upon complete occupancy of the active site, loop II gets stabilized due to specific interactions between its residues and the ligand molecules. Remote loop, X, is seen to be less fluxional in the D3 dimer than in D1 which is rationalized as due to the greater number of inter-subunit contacts in the former. The presence of ligand molecules in subunits of the tetramer further reduces the flexibility of loop X epitomizing a communication between this region and the active sites in the tetramer. These observations are in accordance with the outcomes of several experimental investigations. Participation of loop X in the oligomerization process has also been discerned. Between the two types of dimers in solution, D1 tetramerizes readily and thus would not be present as free dimers. We conjecture an equilibrium to exist between D3 and the tetramer in solution; upon binding of the ligand molecules to the D3 dimer, this equilibrium shifts toward the tetramer.
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Affiliation(s)
- Tarak Karmakar
- a Chemistry and Physics of Materials Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore , 560 064 India
| | - Sourav Roy
- b Molecular Biology and Genetics Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore , 560 064 India
| | - Hemalatha Balaram
- b Molecular Biology and Genetics Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore , 560 064 India
| | - Sundaram Balasubramanian
- a Chemistry and Physics of Materials Unit , Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore , 560 064 India
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19
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Zhang N, Gong X, Lu M, Chen X, Qin X, Ge H. Crystal structures of Apo and GMP bound hypoxanthine-guanine phosphoribosyltransferase from Legionella pneumophila and the implications in gouty arthritis. J Struct Biol 2016; 194:311-6. [PMID: 26968365 DOI: 10.1016/j.jsb.2016.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/07/2016] [Accepted: 03/08/2016] [Indexed: 01/10/2023]
Abstract
Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) (EC 2.4.2.8) reversibly catalyzes the transfer of the 5-phophoribosyl group from 5-phosphoribosyl-alpha-1-pyrophosphate (PRPP) to hypoxanthine or guanine to form inosine monophosphate (IMP) or guanosine monophosphate (GMP) in the purine salvage pathway. To investigate the catalytic mechanism of this enzyme in the intracellular pathogen Legionella pneumophila, we determined the crystal structures of the L. pneumophila HGPRT (LpHGPRT) both in its apo-form and in complex with GMP. The structures reveal that LpHGPRT comprises a core domain and a hood domain which are packed together to create a cavity for GMP-binding and the enzymatic catalysis. The binding of GMP induces conformational changes of the stable loop II. This new binding site is closely related to the Gout arthritis-linked human HGPRT mutation site (Ser103Arg). Finally, these structures of LpHGPRT provide insights into the catalytic mechanism of HGPRT.
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Affiliation(s)
- Nannan Zhang
- Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui 230601, China
| | - Xiaojian Gong
- Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui 230601, China
| | - Min Lu
- Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui 230601, China
| | - Xiaofang Chen
- Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui 230601, China
| | - Ximing Qin
- Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui 230601, China
| | - Honghua Ge
- Institute of Health Sciences and School of Life Science, Anhui University, Hefei, Anhui 230601, China; Modern Experiment Technology Center, Anhui University, Hefei, Anhui 230601, China.
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20
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Roy S, Nagappa LK, Prahladarao VS, Balaram H. Kinetic mechanism of Plasmodium falciparum hypoxanthine-guanine-xanthine phosphoribosyltransferase. Mol Biochem Parasitol 2015; 204:111-120. [DOI: 10.1016/j.molbiopara.2016.02.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 02/08/2016] [Accepted: 02/16/2016] [Indexed: 11/28/2022]
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21
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Abstract
We review literature on the metabolism of ribo- and deoxyribonucleotides, nucleosides, and nucleobases in Escherichia coli and Salmonella,including biosynthesis, degradation, interconversion, and transport. Emphasis is placed on enzymology and regulation of the pathways, at both the level of gene expression and the control of enzyme activity. The paper begins with an overview of the reactions that form and break the N-glycosyl bond, which binds the nucleobase to the ribosyl moiety in nucleotides and nucleosides, and the enzymes involved in the interconversion of the different phosphorylated states of the nucleotides. Next, the de novo pathways for purine and pyrimidine nucleotide biosynthesis are discussed in detail.Finally, the conversion of nucleosides and nucleobases to nucleotides, i.e.,the salvage reactions, are described. The formation of deoxyribonucleotides is discussed, with emphasis on ribonucleotidereductase and pathways involved in fomation of dUMP. At the end, we discuss transport systems for nucleosides and nucleobases and also pathways for breakdown of the nucleobases.
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22
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Eng WS, Hocková D, Špaček P, Janeba Z, West NP, Woods K, Naesens LMJ, Keough DT, Guddat LW. First Crystal Structures of Mycobacterium tuberculosis 6-Oxopurine Phosphoribosyltransferase: Complexes with GMP and Pyrophosphate and with Acyclic Nucleoside Phosphonates Whose Prodrugs Have Antituberculosis Activity. J Med Chem 2015; 58:4822-38. [PMID: 25915781 DOI: 10.1021/acs.jmedchem.5b00611] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human tuberculosis is a chronic infectious disease affecting millions of lives. Because of emerging resistance to current medications, new therapeutic drugs are needed. One potential new target is hypoxanthine-guanine phosphoribosyltransferase (MtHGPRT), a key enzyme of the purine salvage pathway. Here, newly synthesized acyclic nucleoside phosphonates (ANPs) have been shown to be competitive inhibitors of MtHGPRT with Ki values as low as 0.69 μM. Prodrugs of these compounds arrest the growth of a virulent strain of M. tuberculosis with MIC50 values as low as 4.5 μM and possess low cytotoxicity in mammalian cells (CC50 values as high as >300 μM). In addition, the first crystal structures of MtHGPRT (2.03-2.76 Å resolution) have been determined, three of these in complex with novel ANPs and one with GMP and pyrophosphate. These data provide a solid foundation for the further development of ANPs as selective inhibitors of MtHGPRT and as antituberculosis agents.
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Affiliation(s)
- Wai Soon Eng
- †The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072 QLD Australia
| | - Dana Hocková
- ‡Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. Flemingovo nam. 2, CZ-166 10 Prague 6, Czech Republic
| | - Petr Špaček
- ‡Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. Flemingovo nam. 2, CZ-166 10 Prague 6, Czech Republic
| | - Zlatko Janeba
- ‡Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. Flemingovo nam. 2, CZ-166 10 Prague 6, Czech Republic
| | - Nicholas P West
- †The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072 QLD Australia
| | - Kyra Woods
- †The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072 QLD Australia
| | - Lieve M J Naesens
- §Rega Institute for Medical Research, KU Leuven - University of Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Dianne T Keough
- †The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072 QLD Australia
| | - Luke W Guddat
- †The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072 QLD Australia
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23
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Roy S, Karmakar T, S. Prahlada Rao V, K. Nagappa L, Balasubramanian S, Balaram H. Slow ligand-induced conformational switch increases the catalytic rate in Plasmodium falciparum hypoxanthine guanine xanthine phosphoribosyltransferase. MOLECULAR BIOSYSTEMS 2015; 11:1410-24. [DOI: 10.1039/c5mb00136f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coupled events of ligand-induced isomerization and oligomerization in catalysis by PfHGXPRT.
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Affiliation(s)
- Sourav Roy
- Molecular Biology and Genetics Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
| | - Tarak Karmakar
- Chemistry and Physics of Materials Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
| | - Vasudeva S. Prahlada Rao
- Molecular Biology and Genetics Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
| | - Lakshmeesha K. Nagappa
- Molecular Biology and Genetics Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
| | - Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
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24
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Keough DT, Hocková D, Rejman D, Spaček P, Vrbková S, Krečmerová M, Eng WS, Jans H, West NP, Naesens LMJ, de Jersey J, Guddat LW. Inhibition of the Escherichia coli 6-oxopurine phosphoribosyltransferases by nucleoside phosphonates: potential for new antibacterial agents. J Med Chem 2013; 56:6967-84. [PMID: 23927482 DOI: 10.1021/jm400779n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Escherichia coli (Ec) cells possess two purine salvage enzymes: xanthine-guanine phosphoribosyltransferase (XGPRT) and hypoxanthine phosphoribosyltransferase (HPRT). EcXGPRT shares a common structural feature with other members of this family, a flexible loop that closes over the active site during catalysis. The replacement of six of these amino acids by alanine has no effect on the Km for the two substrates. However, the Ki for the nucleoside monophosphate increases by 27-fold, and the kcat is reduced by ∼200-fold. Nucleoside phosphonates (NP) are good inhibitors of EcXGPRT and EcHPRT, with Ki values as low as 10 nM. In the absence of the flexible loop, these values increase by 5- to 30-fold, indicating the importance of the loop for high-affinity inhibition. Crystal structures of two NPs in complex with EcXGPRT explain the tight binding. Prodrugs of NPs with low Ki values for EcXGPRT or EcHPRT exhibit IC50 values between 5 and 23 μM against Mycobacterium tuberculosis in cell-based assays, suggesting that these compounds are therapeutic leads against pathogenic bacteria.
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Affiliation(s)
- Dianne T Keough
- The School of Chemistry and Molecular Biosciences, The University of Queensland , Brisbane, 4072 QLD, Australia
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25
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Keough DT, Špaček P, Hocková D, Tichý T, Vrbková S, Slavětínská L, Janeba Z, Naesens L, Edstein MD, Chavchich M, Wang TH, de Jersey J, Guddat LW. Acyclic Nucleoside Phosphonates Containing a Second Phosphonate Group Are Potent Inhibitors of 6-Oxopurine Phosphoribosyltransferases and Have Antimalarial Activity. J Med Chem 2013; 56:2513-26. [DOI: 10.1021/jm301893b] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dianne T. Keough
- The School of Chemistry and
Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Petr Špaček
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
| | - Dana Hocková
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
| | - Tomáš Tichý
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
| | - Silvie Vrbková
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
| | - Lenka Slavětínská
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
| | - Lieve Naesens
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat
10, B-3000 Leuven, Belgium
| | - Michael D. Edstein
- Australian Army Malaria Institute, Enoggera, Brisbane, Queensland 4051,
Australia
| | - Marina Chavchich
- Australian Army Malaria Institute, Enoggera, Brisbane, Queensland 4051,
Australia
| | - Tzu-Hsuan Wang
- The School of Chemistry and
Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - John de Jersey
- The School of Chemistry and
Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
| | - Luke W. Guddat
- The School of Chemistry and
Molecular Biosciences, The University of Queensland, Brisbane 4072, Queensland, Australia
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26
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Kanjee U, Ogata K, Houry WA. Direct binding targets of the stringent response alarmone (p)ppGpp. Mol Microbiol 2012; 85:1029-43. [PMID: 22812515 DOI: 10.1111/j.1365-2958.2012.08177.x] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Escherichia coli stringent response, mediated by the alarmone ppGpp, is responsible for the reorganization of cellular transcription upon nutritional starvation and other stresses. These transcriptional changes occur mainly as a result of the direct effects of ppGpp and its partner transcription factor DksA on RNA polymerase. An often overlooked feature of the stringent response is the direct targeting of other proteins by ppGpp. Here we review the literature on proteins that are known to bind ppGpp and, based on sequence homology, X-ray crystal structures and in silico docking, we propose new potential protein binding targets for ppGpp. These proteins were found to fall into five main categories: (i) cellular GTPases, (ii) proteins involved in nucleotide metabolism, (iii) proteins involved in lipid metabolism, (iv) general metabolic proteins and (v) PLP-dependent basic aliphatic amino acid decarboxylases. Bioinformatic rationale is provided for expanding the role of ppGpp in regulating the activities of the cellular GTPases. Proteins involved in nucleotide and lipid metabolism and general metabolic proteins provide an interesting set of structurally varied stringent response targets. While the inhibition of some PLP-dependent decarboxylases by ppGpp suggests the existence of cross-talk between the acid stress and stringent response systems.
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Affiliation(s)
- Usheer Kanjee
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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Expression, purification and analysis of the activity of enzymes from the pentose phosphate pathway. Protein Expr Purif 2010; 76:229-37. [PMID: 21111048 DOI: 10.1016/j.pep.2010.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 11/12/2010] [Accepted: 11/14/2010] [Indexed: 11/20/2022]
Abstract
RNAs, more than ever before, are increasingly viewed as biomolecules of the future, in the versatility of their functions and intricate three-dimensional folding. To effectively study them by nuclear magnetic resonance (NMR) spectroscopy, structural biologists need to tackle two critical challenges of spectral overcrowding and fast signal decay for large RNAs. Stable-isotope nucleotide labeling is one attractive solution to the overlap problem. Hence, developing effective methods for nucleotide labeling is highly desirable. In this work, we have developed a facile and streamlined source of recombinant enzymes from the pentose phosphate pathway for making such labeled nucleotides. The Escherichia coli (E. coli) genes encoding ribokinase (RK), adenine phosphoribosyltransferase (APRT), xanthine/guanine phosphoribosyltransferase (XGPRT), and uracil phosphoribosyltransferase (UPRT) were sub-cloned into pET15b vectors. All four constructs together with cytidine triphosphate synthetase (CTPS) and human phosphoribosyl pyrophosphate synthetase isoform 1 (PRPPS) were transformed into the E. coli BL21(AI) strain for protein over-expression. The enzyme preparations were purified to >90% homogeneity by a one-step Ni-NTA affinity chromatography, without the need of a further size-exclusion chromatography step. We obtained yields of 1530, 22, 482, 3120, 2120 and 2280 units of activity per liter of culture for RK, PRPPS, APRT, XGPRT, UPRT and CTPS, respectively; the specific activities were found to be 70, 22, 21, 128, 144 and 113 U/mg, respectively. These specific activities of these enzyme constructs are comparable to or higher than those previously reported. In addition, both the growth conditions and purification protocols have been streamlined so that all the recombinant proteins can be expressed, purified and characterized in at most 2 days. The availability and reliability of these constructs should make production of fully and site-specific labeled nucleotides for making labeled RNA accessible and straightforward, to facilitate high-resolution NMR spectroscopic and other biophysical studies.
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Kanagawa M, Baba S, Ebihara A, Shinkai A, Hirotsu K, Mega R, Kim K, Kuramitsu S, Sampei GI, Kawai G. Structures of hypoxanthine-guanine phosphoribosyltransferase (TTHA0220) from Thermus thermophilus HB8. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:893-8. [PMID: 20693661 DOI: 10.1107/s1744309110023079] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Accepted: 06/15/2010] [Indexed: 11/10/2022]
Abstract
Hypoxanthine-guanine phosphoribosyltransferase (HGPRTase), which is a key enzyme in the purine-salvage pathway, catalyzes the synthesis of IMP or GMP from alpha-D-phosphoribosyl-1-pyrophosphate and hypoxanthine or guanine, respectively. Structures of HGPRTase from Thermus thermophilus HB8 in the unliganded form, in complex with IMP and in complex with GMP have been determined at 2.1, 1.9 and 2.2 A resolution, respectively. The overall fold of the IMP complex was similar to that of the unliganded form, but the main-chain and side-chain atoms of the active site moved to accommodate IMP. The overall folds of the IMP and GMP complexes were almost identical to each other. Structural comparison of the T. thermophilus HB8 enzyme with 6-oxopurine PRTases for which structures have been determined showed that these enzymes can be tentatively divided into groups I and II and that the T. thermophilus HB8 enzyme belongs to group I. The group II enzymes are characterized by an N-terminal extension with additional secondary elements and a long loop connecting the second alpha-helix and beta-strand compared with the group I enzymes.
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Affiliation(s)
- Mayumi Kanagawa
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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Keough DT, Hocková D, Krecmerová M, Cesnek M, Holý A, Naesens L, Brereton IM, Winzor DJ, de Jersey J, Guddat LW. Plasmodium vivax hypoxanthine-guanine phosphoribosyltransferase: a target for anti-malarial chemotherapy. Mol Biochem Parasitol 2010; 173:165-9. [PMID: 20595032 DOI: 10.1016/j.molbiopara.2010.05.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 05/25/2010] [Accepted: 05/25/2010] [Indexed: 11/30/2022]
Abstract
The malarial parasite, Plasmodium vivax (Pv), causes a serious infectious disease found primarily in Asia and the Americas. For protozoan parasites, 6-oxopurine phosphoribosyltransferases (PRTases) provide the only metabolic pathway to synthesize the purine nucleoside monophosphates essential for DNA/RNA production. We have purified the recombinant Pv 6-oxopurine (PRTase) and compared its properties with the human and Pf enzymes. The Pv enzyme uses hypoxanthine and guanine with similar catalytic efficiency to the Pf enzyme but xanthine is not a substrate, hence we identify this enzyme as PvHGPRT. Mass spectrometry suggests that PvHGPRT contains bound magnesium ions that are removed by EDTA resulting in loss of activity. However, the addition of Mg(2+) restores activity. Acyclic nucleoside phosphonates (ANPs) are good inhibitors of PvHGPRT having K(i) values as low as 3 microM. These compounds can form the basis for the design of new drugs aimed at combating malaria caused by Pv.
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Affiliation(s)
- Dianne T Keough
- The School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, QLD, Australia
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Deng H, Callender R, Schramm VL, Grubmeyer C. Pyrophosphate activation in hypoxanthine--guanine phosphoribosyltransferase with transition state analogue. Biochemistry 2010; 49:2705-14. [PMID: 20170081 DOI: 10.1021/bi100012u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isotope-edited difference Raman and FTIR studies complemented by ab initio calculations have been applied to the transition state analogue complex of HGPRT.ImmHP.MgPP(i) to determine the ionic states of the 5'-phosphate moiety of ImmHP and of PP(i). These measurements characterize electrostatic interactions within the enzyme active site as deduced from frequency shifts of the phosphate groups. The bound 5'-phosphate moiety of ImmHP is dianionic, and this phosphate group exists in two different conformations within the protein complex. In one conformation, a hydrogen bond between the 5'-phosphate of ImmHP and the OH group of Tyr104 in the catalytic loop appears to be stronger. With the stronger H-bond, the OH of Tyr104 approaches one of the P..O bonds from the bridging oxygen side to cause distortion of the PO(3) moiety, as indicated by a lowered symmetric P..O stretch frequency. The asymmetric stretch frequencies are similar in both phosphate conformations. Bound PP(i) in this complex is fully ionized to P(2)O(7)(4-). Bond frequency changes for bound PP(i) indicate coordination to Mg(2+) ions but show no indication of significant P..O bond polarization. Extrapolation of these results to reaction coordinate motion for HGPRT suggests that bond formation between C1' of the nucleotide ribose and the oxygen of PP(i) is accomplished by migration of the ribocation toward immobilized pyrophosphate.
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Affiliation(s)
- Hua Deng
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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de Souza Dantas D, Ramos Dos Santos C, Guimarães Pereira GA, Medrano FJ. Biochemical and structural characterization of the hypoxanthine-guanine-xanthine phosphoribosyltransferase from Pyrococcus horikoshii. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:953-60. [PMID: 18405676 DOI: 10.1016/j.bbapap.2008.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Revised: 03/06/2008] [Accepted: 03/07/2008] [Indexed: 11/15/2022]
Abstract
The 6-oxopurine phosphoribosyltransferase (HPRT, EC 2.4.2.8) from the hyperthermophile Pyrococcus horikoshii was expressed in Escherichia coli and purified. Steady-state kinetic studies indicated that the enzyme is able to use hypoxanthine, guanine and xanthine. The first two substrates showed similar catalytic efficiencies, and xanthine presented a much lower value (around 20 times lower), but the catalytic constant was comparable to that of hypoxanthine. The enzyme was not able to bind to GMP-agarose, but was able to bind the other reverse reaction substrate, inorganic pyrophosphate, with low affinity (K(d) of 4.7+/-0.1 mM). Dynamic light scattering and analytical gel filtration suggested that the enzyme exists as a homohexamer in solution.
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Affiliation(s)
- Deyse de Souza Dantas
- Laboratorio de Genômica e Expressão, Departamento de Genética e Evolução, IB-UNICAMP, Caixa Postal 6109, CEP 13083-970, Campinas, Brazil
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Nauli S, Farr S, Lee YJ, Kim HY, Faham S, Bowie JU. Polymer-driven crystallization. Protein Sci 2007; 16:2542-51. [PMID: 17962407 PMCID: PMC2211692 DOI: 10.1110/ps.073074207] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 07/31/2007] [Accepted: 08/01/2007] [Indexed: 10/22/2022]
Abstract
Obtaining well-diffracting crystals of macromolecules remains a significant barrier to structure determination. Here we propose and test a new approach to crystallization, in which the crystallization target is fused to a polymerizing protein module, so that polymer formation drives crystallization of the target. We test the approach using a polymerization module called 2TEL, which consists of two tandem sterile alpha motif (SAM) domains from the protein translocation Ets leukemia (TEL). The 2TEL module is engineered to polymerize as the pH is lowered, which allows the subtle modulation of polymerization needed for crystal formation. We show that the 2TEL module can drive the crystallization of 11 soluble proteins, including three that resisted prior crystallization attempts. In addition, the 2TEL module crystallizes in the presence of various detergents, suggesting that it might facilitate membrane protein crystallization. The crystal structures of two fusion proteins show that the TELSAM polymer is responsible for the majority of contacts in the crystal lattice. The results suggest that biological polymers could be designed as crystallization modules.
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Affiliation(s)
- Sehat Nauli
- UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles 90095-1570, USA
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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: 1.2] [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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Duckworth M, Ménard A, Megraud F, Mendz GL. Bioinformatic analysis of Helicobacter pylori XGPRTase: a potential therapeutic target. Helicobacter 2006; 11:287-95. [PMID: 16882332 DOI: 10.1111/j.1523-5378.2006.00409.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Xanthine-guanine phosphoribosyltransferase (XGPRTase) is an enzyme of purine nucleotide salvage synthesis. The gpt gene of Helicobacter pylori has been annotated as encoding an XGPRTase and proposed as essential for survival of the bacterium in vitro. The aims of this work were to investigate the structure of H. pylori XGPRTase and to compare the key features of the enzyme to other phosphoribosyltransferases employing computational, modelling, and bioinformatic tools. MATERIALS AND METHODS XGPRTase activity was measured in the cytosolic fraction of H. pylori by (31)P-nuclear magnetic resonance spectroscopy, and also in recombinant XGPRTase produced by a cell-free expression system. Bioinformatics was employed to analyze the phylogeny of XGPRTase, and a structural model of the XGPRTase was built using threading techniques. The observed interactions of purine phosphoribosyltransferases with immucillin-GP were used to study the theoretical interactions of H. pylori XGPRTase with this transition-state analog. RESULTS It was demonstrated that the gpt gene of H. pylori encodes a functional XGPRTase enzyme. Analyses of the XGPRTase sequence showed that the enzyme is significantly divergent from equivalent mammalian enzymes. Modelling served to identify specific features of the enzyme and key residues involved in catalysis. CONCLUSIONS The H. pylori XGPRTase is structurally similar to other phosphoribosyltransferase enzymes, but there were significant differences between the hood domain of H. pylori XGPRTase and other purine salvage phosphoribosyltransferases. Significant differences were found between the interactions of the H. pylori and human enzymes with a purine phosphoribosyltransferase inhibitor.
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Affiliation(s)
- Megan Duckworth
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
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Chen Q, Liang Y, Su X, Gu X, Zheng X, Luo M. Alternative IMP binding in feedback inhibition of hypoxanthine-guanine phosphoribosyltransferase from Thermoanaerobacter tengcongensis. J Mol Biol 2005; 348:1199-210. [PMID: 15854655 DOI: 10.1016/j.jmb.2005.02.064] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2005] [Revised: 02/23/2005] [Accepted: 02/25/2005] [Indexed: 10/25/2022]
Abstract
Crystal structures of Thermoanaerobacter tengcongensis hypoxanthine-guanine phosphoribosyltransferase (HGPRT) apoenzyme and the enzyme-inosine monophosphate (IMP) complex have been determined to 2.5A and 2.2A resolution, respectively. The active form of the enzyme was identified as a tetramer in solution and the K(i) value of IMP was measured to be 45 microM for alpha-D-phosphoribosyl-1-pyrophosphate (PRPP). Conformation of the flexible loop in T.tengcongensis HGPRT, which is involved in substrate PRPP binding, is different from that observed in phosphoribosyltransferases (PRTs). It contains a 3-10 helix, and a unique double serine repeat. This loop is ordered even in the apoenzyme and assumes a half-closed conformation. The primary magnesium ion is directly coordinated by side-chains of Glu101 and Asp102, and water molecules in the apoenzyme, suggesting a possible prerequisite role for substrate PRPP binding. Most interestingly, an alternative IMP binding mode is found in the structure of T.tengcongensis HGPRT-IMP complex. The 5'-phosphate of IMP occupies the PPi position usually seen in PRT-PRPP complexes. This new observation is consistent with the lower K(i) value of IMP and may suggest a mechanism involving multiple modes of interactions between IMP and T.tengcongensis HGPRT in product release and feedback inhibition. The structure of T.tengcongensis HGPRT is compared with those of mesophilic HPRTs, and several possible features contributing to its thermostability are elucidated. Overall, T.tengcongensis HGPRT appears to be more diverged from other PRTs.
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Affiliation(s)
- Qiang Chen
- Laboratory of Structural Biology, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China
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Duan J, Nilsson L, Lambert B. Structural and functional analysis of mutations at the human hypoxanthine phosphoribosyl transferase (HPRT1) locus. Hum Mutat 2004; 23:599-611. [PMID: 15146465 DOI: 10.1002/humu.20047] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Hypoxanthine phosphoribosyl transferase (HPRT, also known as HGPRT) is an often-used genetic marker in eukaryotic cells. The gene is conserved from bacteria to human, with retained catalytic activity, although substrate specificity may have changed, and the enzyme is essential in malaria-causing protozoans. Inherited mutations in the human HPRT1 gene result in three different phenotypes: Lesch-Nyhan syndrome (LNS or LND), LND variants, and HPRT-related hyperuricemia (HRH). In cultured cells, loss of HPRT activity gives rise to 6-thioguanine (6-TG) resistance. In general, cells from LND patients are also 6-TG resistant, whereas cells from HRH patients are not, with some interesting exceptions. Using modeling methods, we have studied the correlation between the mutable and nonmutated amino acid residues on one hand, and sequence conservation and predicted phenotypic effects on the other hand. Our results demonstrate that most of the mutations are explainable by the predicted effect on protein structure and function. They are also consistent with sequence conservation. Moreover, the mutational profiles of TG-resistant cells and LND overlap to a great extent, while most of the mutations in HRH are unique to that condition. We have also noticed a strong correlation between mutations in the tetramer interfaces and observed phenotypes, suggesting a functional role for a tetramer transition during catalysis.
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Affiliation(s)
- Jianxin Duan
- Department of Biosciences at Novum, Center for Structural Biochemistry, Karolinska Institutet, Huddinge, Sweden.
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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: 1.8] [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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