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Witek W, Sliwiak J, Rawski M, Ruszkowski M. Targeting imidazole-glycerol phosphate dehydratase in plants: novel approach for structural and functional studies, and inhibitor blueprinting. FRONTIERS IN PLANT SCIENCE 2024; 15:1343980. [PMID: 38559763 PMCID: PMC10978614 DOI: 10.3389/fpls.2024.1343980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024]
Abstract
The histidine biosynthetic pathway (HBP) is targeted for herbicide design with preliminary success only regarding imidazole-glycerol phosphate dehydratase (IGPD, EC 4.2.1.19), or HISN5, as referred to in plants. HISN5 catalyzes the sixth step of the HBP, in which imidazole-glycerol phosphate (IGP) is dehydrated to imidazole-acetol phosphate. In this work, we present high-resolution cryoEM and crystal structures of Medicago truncatula HISN5 (MtHISN5) in complexes with an inactive IGP diastereoisomer and with various other ligands. MtHISN5 can serve as a new model for plant HISN5 structural studies, as it enables resolving protein-ligand interactions at high (2.2 Å) resolution using cryoEM. We identified ligand-binding hotspots and characterized the features of plant HISN5 enzymes in the context of the HISN5-targeted inhibitor design. Virtual screening performed against millions of small molecules not only revealed candidate molecules but also identified linkers for fragments that were experimentally confirmed to bind. Based on experimental and computational approaches, this study provides guidelines for designing symmetric HISN5 inhibitors that can reach two neighboring active sites. Finally, we conducted analyses of sequence similarity networks revealing that plant HISN5 enzymes derive from cyanobacteria. We also adopted a new approach to measure MtHISN5 enzymatic activity using isothermal titration calorimetry and enzymatically synthesized IGP.
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Affiliation(s)
- Wojciech Witek
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Joanna Sliwiak
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Michal Rawski
- Cryo-EM Facility, SOLARIS National Synchrotron Radiation Centre, Krakow, Poland
| | - Milosz Ruszkowski
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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2
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The Role of Gene Elongation in the Evolution of Histidine Biosynthetic Genes. Microorganisms 2020; 8:microorganisms8050732. [PMID: 32414216 PMCID: PMC7284861 DOI: 10.3390/microorganisms8050732] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 11/29/2022] Open
Abstract
Gene elongation is a molecular mechanism consisting of an in-tandem duplication of a gene and divergence and fusion of the two copies, resulting in a gene constituted by two divergent paralogous modules. The aim of this work was to evaluate the importance of gene elongation in the evolution of histidine biosynthetic genes and to propose a possible evolutionary model for some of them. Concerning the genes hisA and hisF, which code for two homologous (β/α)8-barrels, it has been proposed that the two extant genes could be the result of a cascade of gene elongation/domain shuffling events starting from an ancestor gene coding for just one (β/α) module. A gene elongation event has also been proposed for the evolution of hisB and hisD; structural analyses revealed the possibility of an early elongation event, resulting in the repetition of modules. Furthermore, it is quite possible that the gene elongations responsible for the evolution of the four proteins occurred before the earliest phylogenetic divergence. In conclusion, gene elongation events seem to have played a crucial role in the evolution of the histidine biosynthetic pathway, and they may have shaped the structures of many genes during the first steps of their evolution.
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3
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Abstract
Histidine biosynthesis is a target for herbicide and antibacterial agents, with imidazoleglycerol-phosphate dehydratase (IGPD) a key enzyme within this pathway. As a result, IGPD is the focus of inhibitor design programs, with several potent herbicides in development. Interestingly, the lead inhibitor is more potent against yeast (Saccharomyces) compared with plant (Arabidopsis) IGPD. To understand this change, we have determined their structure by electron microscopy to reveal a possible mechanism behind differences in inhibitor potency, with Saccharomyces IGPD containing a 24-amino acid insert that forms an extended surface loop that stabilizes an inhibitor binding loop. This study provides insights into the IGPD family and demonstrates the power of using an electron microcopy approach to study inhibitor binding. Histidine biosynthesis is an essential process in plants and microorganisms, making it an attractive target for the development of herbicides and antibacterial agents. Imidazoleglycerol-phosphate dehydratase (IGPD), a key enzyme within this pathway, has been biochemically characterized in both Saccharomyces cerevisiae (Sc_IGPD) and Arabidopsis thaliana (At_IGPD). The plant enzyme, having been the focus of in-depth structural analysis as part of an inhibitor development program, has revealed details about the reaction mechanism of IGPD, whereas the yeast enzyme has proven intractable to crystallography studies. The structure–activity relationship of potent triazole-phosphonate inhibitors of IGPD has been determined in both homologs, revealing that the lead inhibitor (C348) is an order of magnitude more potent against Sc_IGPD than At_IGPD; however, the molecular basis of this difference has not been established. Here we have used single-particle electron microscopy (EM) to study structural differences between the At and Sc_IGPD homologs, which could influence the difference in inhibitor potency. The resulting EM maps at ∼3 Å are sufficient to de novo build the protein structure and identify the inhibitor binding site, which has been validated against the crystal structure of the At_IGPD/C348 complex. The structure of Sc_IGPD reveals that a 24-amino acid insertion forms an extended loop region on the enzyme surface that lies adjacent to the active site, forming interactions with the substrate/inhibitor binding loop that may influence inhibitor potency. Overall, this study provides insights into the IGPD family and demonstrates the power of using an EM approach to study inhibitor binding.
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4
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Chen XR, Wang XT, Hao MQ, Zhou YH, Cui WQ, Xing XX, Xu CG, Bai JW, Li YH. Homology Modeling and Virtual Screening to Discover Potent Inhibitors Targeting the Imidazole Glycerophosphate Dehydratase Protein in Staphylococcus xylosus. Front Chem 2017; 5:98. [PMID: 29177138 PMCID: PMC5686052 DOI: 10.3389/fchem.2017.00098] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/30/2017] [Indexed: 01/11/2023] Open
Abstract
The imidazole glycerophosphate dehydratase (IGPD) protein is a therapeutic target for herbicide discovery. It is also regarded as a possible target in Staphylococcus xylosus (S. xylosus) for solving mastitis in the dairy cow. The 3D structure of IGPD protein is essential for discovering novel inhibitors during high-throughput virtual screening. However, to date, the 3D structure of IGPD protein of S. xylosus has not been solved. In this study, a series of computational techniques including homology modeling, Ramachandran Plots, and Verify 3D were performed in order to construct an appropriate 3D model of IGPD protein of S. xylosus. Nine hits were identified from 2,500 compounds by docking studies. Then, these nine compounds were first tested in vitro in S. xylosus biofilm formation using crystal violet staining. One of the potential compounds, baicalin was shown to significantly inhibit S. xylosus biofilm formation. Finally, the baicalin was further evaluated, which showed better inhibition of biofilm formation capability in S. xylosus by scanning electron microscopy. Hence, we have predicted the structure of IGPD protein of S. xylosus using computational techniques. We further discovered the IGPD protein was targeted by baicalin compound which inhibited the biofilm formation in S. xylosus. Our findings here would provide implications for the further development of novel IGPD inhibitors for the treatment of dairy mastitis.
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Affiliation(s)
- Xing-Ru Chen
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Xiao-Ting Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Mei-Qi Hao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Yong-Hui Zhou
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Wen-Qiang Cui
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Xiao-Xu Xing
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Chang-Geng Xu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Jing-Wen Bai
- College of Science, Northeast Agricultural University, Harbin, China
| | - Yan-Hua Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
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5
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Bisson C, Britton KL, Sedelnikova SE, Rodgers HF, Eadsforth TC, Viner RC, Hawkes TR, Baker PJ, Rice DW. Mirror-Image Packing Provides a Molecular Basis for the Nanomolar Equipotency of Enantiomers of an Experimental Herbicide. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Claudine Bisson
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology; University of Sheffield; Firth Court Western Bank Sheffield S10 2TN UK
| | - K. Linda Britton
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology; University of Sheffield; Firth Court Western Bank Sheffield S10 2TN UK
| | - Svetlana E. Sedelnikova
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology; University of Sheffield; Firth Court Western Bank Sheffield S10 2TN UK
| | - H. Fiona Rodgers
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology; University of Sheffield; Firth Court Western Bank Sheffield S10 2TN UK
| | - Thomas C. Eadsforth
- Division of Biological Chemistry and Drug Discovery; Wellcome Trust Biocentre; University of Dundee; Dundee DD1 5EH UK
| | - Russell C. Viner
- Syngenta, Jealott's Hill International Research Station; Bracknell RG42 6EY UK
| | - Tim R. Hawkes
- Syngenta, Jealott's Hill International Research Station; Bracknell RG42 6EY UK
| | - Patrick J. Baker
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology; University of Sheffield; Firth Court Western Bank Sheffield S10 2TN UK
| | - David W. Rice
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology; University of Sheffield; Firth Court Western Bank Sheffield S10 2TN UK
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6
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Bisson C, Britton KL, Sedelnikova SE, Rodgers HF, Eadsforth TC, Viner RC, Hawkes TR, Baker PJ, Rice DW. Mirror-Image Packing Provides a Molecular Basis for the Nanomolar Equipotency of Enantiomers of an Experimental Herbicide. Angew Chem Int Ed Engl 2016; 55:13485-13489. [PMID: 27717128 PMCID: PMC5113775 DOI: 10.1002/anie.201607185] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Indexed: 11/26/2022]
Abstract
Programs of drug discovery generally exploit one enantiomer of a chiral compound for lead development following the principle that enantiomer recognition is central to biological specificity. However, chiral promiscuity has been identified for a number of enzyme families, which have shown that mirror-image packing can enable opposite enantiomers to be accommodated in an enzyme's active site. Reported here is a series of crystallographic studies of complexes between an enzyme and a potent experimental herbicide whose chiral center forms an essential part of the inhibitor pharmacophore. Initial studies with a racemate at 1.85 Å resolution failed to identify the chirality of the bound inhibitor, however, by extending the resolution to 1.1 Å and by analyzing high-resolution complexes with the enantiopure compounds, we determined that both enantiomers make equivalent pseudosymmetric interactions in the active site, thus mimicking an achiral reaction intermediate.
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Affiliation(s)
- Claudine Bisson
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - K Linda Britton
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Svetlana E Sedelnikova
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - H Fiona Rodgers
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Thomas C Eadsforth
- Division of Biological Chemistry and Drug Discovery, Wellcome Trust Biocentre, University of Dundee, Dundee, DD1 5EH, UK
| | - Russell C Viner
- Syngenta, Jealott's Hill International Research Station, Bracknell, RG42 6EY, UK
| | - Tim R Hawkes
- Syngenta, Jealott's Hill International Research Station, Bracknell, RG42 6EY, UK
| | - Patrick J Baker
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
| | - David W Rice
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
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7
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Yu H, Kago G, Yellman CM, Matouschek A. Ubiquitin-like domains can target to the proteasome but proteolysis requires a disordered region. EMBO J 2016; 35:1522-36. [PMID: 27234297 DOI: 10.15252/embj.201593147] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 04/27/2016] [Indexed: 11/09/2022] Open
Abstract
Ubiquitin and some of its homologues target proteins to the proteasome for degradation. Other ubiquitin-like domains are involved in cellular processes unrelated to the proteasome, and proteins containing these domains remain stable in the cell. We find that the 10 yeast ubiquitin-like domains tested bind to the proteasome, and that all 11 identified domains can target proteins for degradation. Their apparent proteasome affinities are not directly related to their stabilities or functions. That is, ubiquitin-like domains in proteins not part of the ubiquitin proteasome system may bind the proteasome more tightly than domains in proteins that are bona fide components. We propose that proteins with ubiquitin-like domains have properties other than proteasome binding that confer stability. We show that one of these properties is the absence of accessible disordered regions that allow the proteasome to initiate degradation. In support of this model, we find that Mdy2 is degraded in yeast when a disordered region in the protein becomes exposed and that the attachment of a disordered region to Ubp6 leads to its degradation.
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Affiliation(s)
- Houqing Yu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Grace Kago
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Christopher M Yellman
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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8
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Yu H, Singh Gautam AK, Wilmington SR, Wylie D, Martinez-Fonts K, Kago G, Warburton M, Chavali S, Inobe T, Finkelstein IJ, Babu MM, Matouschek A. Conserved Sequence Preferences Contribute to Substrate Recognition by the Proteasome. J Biol Chem 2016; 291:14526-39. [PMID: 27226608 PMCID: PMC4938175 DOI: 10.1074/jbc.m116.727578] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Indexed: 11/23/2022] Open
Abstract
The proteasome has pronounced preferences for the amino acid sequence of its substrates at the site where it initiates degradation. Here, we report that modulating these sequences can tune the steady-state abundance of proteins over 2 orders of magnitude in cells. This is the same dynamic range as seen for inducing ubiquitination through a classic N-end rule degron. The stability and abundance of His3 constructs dictated by the initiation site affect survival of yeast cells and show that variation in proteasomal initiation can affect fitness. The proteasome's sequence preferences are linked directly to the affinity of the initiation sites to their receptor on the proteasome and are conserved between Saccharomyces cerevisiae, Schizosaccharomyces pombe, and human cells. These findings establish that the sequence composition of unstructured initiation sites influences protein abundance in vivo in an evolutionarily conserved manner and can affect phenotype and fitness.
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Affiliation(s)
- Houqing Yu
- From the Department of Molecular Biosciences and the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | | | - Shameika R Wilmington
- From the Department of Molecular Biosciences and the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Dennis Wylie
- the Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas 78712
| | - Kirby Martinez-Fonts
- From the Department of Molecular Biosciences and the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208
| | - Grace Kago
- From the Department of Molecular Biosciences and
| | | | - Sreenivas Chavali
- the Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom, and
| | - Tomonao Inobe
- Frontier Research Core for Life Sciences, University of Toyama, 3190 Gofuku, Toyama-shi, Toyama 930-8555, Japan
| | | | - M Madan Babu
- the Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom, and
| | - Andreas Matouschek
- From the Department of Molecular Biosciences and the Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208,
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9
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Nasir N, Anant A, Vyas R, Biswal BK. Crystal structures of Mycobacterium tuberculosis HspAT and ArAT reveal structural basis of their distinct substrate specificities. Sci Rep 2016; 6:18880. [PMID: 26738801 PMCID: PMC4703992 DOI: 10.1038/srep18880] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 11/30/2015] [Indexed: 01/07/2023] Open
Abstract
Aminotransferases of subfamily Iβ, which include histidinol phosphate aminotransferases (HspATs) and aromatic amino acid aminotransferases (ArATs), are structurally similar but possess distinct substrate specificities. This study, encompassing structural and biochemical characterisation of HspAT and ArAT from Mycobacterium tuberculosis demonstrates that the residues lining the substrate binding pocket and N-terminal lid are the primary determinants of their substrate specificities. In mHspAT, hydrophilic residues in the substrate binding pocket and N-terminal lid allow the entry and binding of its preferential substrate, Hsp. On the other hand, the hydrophobic nature of both the substrate binding pocket and the N-terminal lid of mArAT is responsible for the discrimination of a polar substrate such as Hsp, while facilitating the binding of Phe and other aromatic residues such as Tyr and Trp. In addition, the present study delineates the ligand induced conformational rearrangements, providing insights into the plasticity of aminotransferases. Furthermore, the study also demonstrates that the adventitiously bound ligand 2-(N-morpholino)ethanesulfonic acid (MES) is indeed a specific inhibitor of HspAT. These results suggest that previously untapped morpholine-ring scaffold compounds could be explored for the design of new anti-TB agents.
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Affiliation(s)
- Nazia Nasir
- Protein Crystallography Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Avishek Anant
- Protein Crystallography Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Rajan Vyas
- Protein Crystallography Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India
| | - Bichitra Kumar Biswal
- Protein Crystallography Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India,
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10
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Bisson C, Britton KL, Sedelnikova SE, Rodgers HF, Eadsforth TC, Viner RC, Hawkes TR, Baker PJ, Rice DW. Crystal Structures Reveal that the Reaction Mechanism of Imidazoleglycerol-Phosphate Dehydratase Is Controlled by Switching Mn(II) Coordination. Structure 2015; 23:1236-45. [PMID: 26095028 PMCID: PMC4509728 DOI: 10.1016/j.str.2015.05.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/01/2015] [Accepted: 05/02/2015] [Indexed: 12/18/2022]
Abstract
Imidazoleglycerol-phosphate dehydratase (IGPD) catalyzes the Mn(II)-dependent dehydration of imidazoleglycerol phosphate (IGP) to 3-(1H-imidazol-4-yl)-2-oxopropyl dihydrogen phosphate during biosynthesis of histidine. As part of a program of herbicide design, we have determined a series of high-resolution crystal structures of an inactive mutant of IGPD2 from Arabidopsis thaliana in complex with IGP. The structures represent snapshots of the enzyme trapped at different stages of the catalytic cycle and show how substrate binding triggers a switch in the coordination state of an active site Mn(II) between six- and five-coordinate species. This switch is critical to prime the active site for catalysis, by facilitating the formation of a high-energy imidazolate intermediate. This work not only provides evidence for the molecular processes that dominate catalysis in IGPD, but also describes how the manipulation of metal coordination can be linked to discrete steps in catalysis, demonstrating one way that metalloenzymes exploit the unique properties of metal ions to diversify their chemistry.
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Affiliation(s)
- Claudine Bisson
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - K Linda Britton
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Svetlana E Sedelnikova
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - H Fiona Rodgers
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Thomas C Eadsforth
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Russell C Viner
- Syngenta, Jealott's Hill International Research Station, Bracknell RG42 6EY, UK
| | - Tim R Hawkes
- Syngenta, Jealott's Hill International Research Station, Bracknell RG42 6EY, UK
| | - Patrick J Baker
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
| | - David W Rice
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
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11
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Sanna D, Pecoraro VL, Micera G, Garribba E. Application of DFT methods to the study of the coordination environment of the VO2+ ion in V proteins. J Biol Inorg Chem 2012; 17:773-90. [PMID: 22526563 DOI: 10.1007/s00775-012-0895-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 03/18/2012] [Indexed: 11/24/2022]
Abstract
Density functional theory (DFT) methods were used to simulate the environment of vanadium in several V proteins, such as vanadyl-substituted carboxypeptidase (sites A and B), vanadyl-substituted chloroplast F(1)-ATPase (CF(1); site 3), the reduced inactive form of vanadium bromoperoxidase (VBrPO; low- and high-pH sites), and vanadyl-substituted imidazole glycerol phosphate dehydratase (IGPD; sites α, β, and γ). Structural, electron paramagnetic resonance, and electron spin echo envelope modulation parameters were calculated and compared with the experimental values. All the simulations were performed in water within the framework of the polarizable continuum model. The angular dependence of [Formula: see text] and [Formula: see text] on the dihedral angle θ between the V=O and N-C bonds and on the angle φ between the V=O and V-N bonds, where N is the coordinated aromatic nitrogen atom, was also found. From the results it emerges that it is possible to model the active site of a vanadium protein through DFT methods and determine its structure through the comparison between the calculated and experimental spectroscopic parameters. The calculations confirm that the donor sets of sites B and A of vanadyl-substituted carboxypeptidase are [[Formula: see text], H(2)O, H(2)O, H(2)O] and [N(His)(||), N(His)(⊥), [Formula: see text], H(2)O], and that the donor set of site 3 of CF(1)-ATPase is [[Formula: see text], OH(Thr), H(2)O, H(2)O, [Formula: see text]]. For VBrPO, the coordination modes [N(His)(||), N(His)(∠), OH(Ser), H(2)O, H(2)O(ax)] for the low-pH site and [N(His)(||), N(His)(∠), OH(Ser), OH(-), H(2)O(ax)] or [N(His)(||), N(His)(∠), [Formula: see text], H(2)O] for the high-pH site, with an imidazole ring of histidine strongly displaced from the equatorial plane, can be proposed. Finally, for sites α, β, and γ of IGPD, the subsequent deprotonation of one, two, and three imidazole rings of histidine and the participation of a carboxylate group of a glutamate residue ([N(His)(||), [Formula: see text], H(2)O, H(2)O], [N(His)(||), N(His)(||), [Formula: see text], H(2)O], and [N(His)(||), N(His)(||), [Formula: see text], OH(-), [Formula: see text]], respectively) seems to be the most plausible hypothesis.
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Affiliation(s)
- Daniele Sanna
- Istituto CNR di Chimica Biomolecolare, Trav. La Crucca 3, 07040, Sassari, Italy
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12
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Bayliak M, Gospodaryov D, Semchyshyn H, Lushchak V. Inhibition of catalase by aminotriazole in vivo results in reduction of glucose-6-phosphate dehydrogenase activity in Saccharomyces cerevisiae cells. BIOCHEMISTRY (MOSCOW) 2008; 73:420-6. [PMID: 18457571 DOI: 10.1134/s0006297908040068] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The inhibitor of catalase 3-amino-1,2,4-triazole (AMT) was used to study the physiological role of catalase in the yeast Saccharomyces cerevisiae under starvation. It was shown that AMT at the concentration of 10 mM did not affect the growth of the yeast. In vivo and in vitro the degree of catalase inhibition by AMT was concentration- and time-dependent. Peroxisomal catalase in bakers' yeast was more sensitive to AMT than the cytosolic one. In vivo inhibition of catalase by AMT in S. cerevisiae caused a simultaneous decrease in glucose-6-phosphate dehydrogenase activity and an increase in glutathione reductase activity. At the same time, the level of protein carbonyls, a marker of oxidative modification, was not affected. Possible mechanisms compensating the negative effects caused by AMT inhibition of catalase are discussed.
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Affiliation(s)
- M Bayliak
- Department of Biochemistry, Vassyl Stefanyk Precarpathian National University, Ivano-Frankivsk 76025, Ukraine
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13
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Lee HS, Cho Y, Lee JH, Kang SG. Novel monofunctional histidinol-phosphate phosphatase of the DDDD superfamily of phosphohydrolases. J Bacteriol 2008; 190:2629-32. [PMID: 18223080 PMCID: PMC2293174 DOI: 10.1128/jb.01722-07] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2007] [Accepted: 01/11/2008] [Indexed: 11/20/2022] Open
Abstract
The TON_0887 gene was identified as the missing histidinol-phosphate phosphatase (HolPase) in the hyperthermophilic archaeon "Thermococcus onnurineus" NA1. The protein contained conserved motifs of the DDDD superfamily of phosphohydrolase, and the recombinantly expressed protein exhibited strong HolPase activity. In this study, we functionally assessed for the first time the monofunctional DDDD-type HolPase, which is organized in the gene cluster.
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Affiliation(s)
- Hyun Sook Lee
- Korea Ocean Research & Development Institute, Ansan P.O. Box 29, Seoul 425-600, Republic of Korea
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Glynn SE, Baker PJ, Sedelnikova SE, Davies CL, Eadsforth TC, Levy CW, Rodgers HF, Blackburn GM, Hawkes TR, Viner R, Rice DW. Structure and mechanism of imidazoleglycerol-phosphate dehydratase. Structure 2006; 13:1809-17. [PMID: 16338409 DOI: 10.1016/j.str.2005.08.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Revised: 08/18/2005] [Accepted: 08/18/2005] [Indexed: 10/25/2022]
Abstract
The structure of A. thaliana imidazoleglycerol-phosphate dehydratase, an enzyme of histidine biosynthesis and a target for the triazole phosphonate herbicides, has been determined to 3.0 A resolution. The structure is composed of 24 identical subunits arranged in 432 symmetry and shows how the formation of a novel dimanganese cluster is crucial to the assembly of the active 24-mer from an inactive trimeric precursor and to the formation of the active site of the enzyme. Molecular modeling suggests that the substrate is bound to the manganese cluster as an imidazolate moiety that subsequently collapses to yield a diazafulvene intermediate. The mode of imidazolate recognition exploits pseudosymmetry at the active site arising from a combination of the assembly of the particle and the pseudosymmetry present in each subunit as a result of gene duplication. This provides an intriguing example of the role of evolution in the design of Nature's catalysts.
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Affiliation(s)
- Steven E Glynn
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom
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15
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Glynn SE, Baker PJ, Sedelnikova SE, Levy CW, Rodgers HF, Blank J, Hawkes TR, Rice DW. Purification, crystallization and preliminary crystallographic analysis of Arabidopsis thaliana imidazoleglycerol-phosphate dehydratase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:776-8. [PMID: 16511155 PMCID: PMC1952351 DOI: 10.1107/s1744309105022451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2005] [Accepted: 07/12/2005] [Indexed: 11/10/2022]
Abstract
Imidazoleglycerol-phosphate dehydratase catalyses the sixth step of the histidine-biosynthesis pathway in plants and microorganisms and has been identified as a possible target for the development of novel herbicides. Arabidopsis thaliana IGPD has been cloned and overexpressed in Escherichia coli, purified and subsequently crystallized in the presence of manganese. Under these conditions, the inactive trimeric form of the metal-free enzyme is assembled into a fully active species consisting of a 24-mer exhibiting 432 symmetry. X-ray diffraction data have been collected to 3.0 A resolution from a single crystal at 293 K. The crystal belongs to space group R3, with approximate unit-cell parameters a = b = 157.9, c = 480.0 A, alpha = beta = 90, gamma = 120 degrees and with either 16 or 24 subunits in the asymmetric unit. A full structure determination is under way in order to provide insights into the mode of subunit assembly and to initiate a programme of rational herbicide design.
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Affiliation(s)
- Steven E Glynn
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, England
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16
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Sinha SC, Chaudhuri BN, Burgner JW, Yakovleva G, Davisson VJ, Smith JL. Crystal Structure of Imidazole Glycerol-phosphate Dehydratase. J Biol Chem 2004; 279:15491-8. [PMID: 14724278 DOI: 10.1074/jbc.m312733200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Imidazole glycerol-phosphate dehydratase (IGPD) catalyzes the sixth step of histidine biosynthesis. The enzyme is of fundamental biochemical interest, because it catalyzes removal of a non-acidic hydrogen atom in the dehydration reaction. It is also a potential target for development of herbicides. IGPD is a metalloenzyme in which transition metals induce aggregation and are required for catalysis. Addition of 1 equivalent of Mn(2+)/subunit is shown by analytical ultracentrifugation to induce the formation of 24-mers from trimeric IGPD. Two histidine-rich motifs may participate in metal binding and aggregation. The 2.3-A crystal structure of metal-free trimeric IGPD from the fungus Filobasidiella neoformans reveals a novel fold containing an internal repeat, apparently the result of gene duplication. The 95-residue alpha/beta half-domain occurs in a few other proteins, including the GHMP kinase superfamily (galacto-homoserine-mevalonate-phosphomevalonate), but duplication to form a compact domain has not been seen elsewhere. Conserved residues cluster at two types of sites in the trimer, each site containing a conserved histidine-rich motif. A model is proposed for the intact, active 24-mer in which all highly conserved residues, including the histidine-rich motifs in both the N- and C-terminal halves of the polypeptide, cluster at a common site between trimers. This site is a candidate for the active site and also for metal binding leading to aggregation of trimers. The structure provides a basis for further studies of enzyme function and mechanism and for development of more potent and specific herbicides.
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Affiliation(s)
- Sangita C Sinha
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
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17
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Petersen J, Hawkes TR, Lowe DJ. Oxo-vanadium as a spin probe for the investigation of the metal coordination environment of imidazole glycerol phosphate dehydratase. J Inorg Biochem 2000; 80:161-8. [PMID: 10885480 DOI: 10.1016/s0162-0134(00)00025-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Imidazole glycerol phosphate dehydratase (IGPD) catalyses the dehydration of imidazole glycerol phosphate to imidazole acetol phosphate, an important late step in the biosynthesis of histidine. IGPD, isolated as a low molecular weight and inactive apo-form, assembles with specific divalent metal cations to form a catalytically active high molecular weight metalloenzyme. Oxo-vanadium ions also assemble the protein into, apparently, the same high molecular weight form but, uniquely, yield a protein without catalytic activity. The VO2+ derivative of IGPD has been investigated by electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM) spectroscopy. The spin Hamiltonian parameters indicate the presence of multiple 14N nuclei in the inner coordination sphere of VO2+ which is corroborated by ENDOR and ESEEM spectra showing resonances attributable to interactions with 14N nuclei. The isotropic superhyperfine coupling component of about 7 MHz determined by ENDOR is consistent with a nitrogen of coordinated histidine imidazole(s). The ESEEM Fourier-transform spectra further support the notion that the VO2+ substituted enzyme contains inner-sphere nitrogen ligands. The isotropic and anisotropic 14N superhyperfine coupling components are similar to those reported for other equatorially coordinated enzymatic histidine imidazole systems. ESEEM resonances from axial 14N ligands are discussed.
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Affiliation(s)
- J Petersen
- Nitrogen Fixation Laboratory, John Innes Centre, Norwich, UK
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18
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Chittur SV, Chen Y, Davisson VJ. Expression and purification of imidazole glycerol phosphate synthase from Saccharomyces cerevisiae. Protein Expr Purif 2000; 18:366-77. [PMID: 10733892 DOI: 10.1006/prep.2000.1207] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Imidazole glycerol phosphate (IGP) synthase is a glutamine amidotransferase that catalyzes the formation of IGP and 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) from N(1)-[(5'-phosphoribulosyl)formimino]-5-aminoimidazole-4-car boxamide ribonucleotide (PRFAR). This enzyme represents a junction between histidine biosynthesis and de novo purine biosynthesis. The recent characterization of the HIS7 gene in the yeast Saccharomyces cerevisiae IGP synthase established that this protein is bifunctional, representing a fusion between the N-terminal HisH domain and a C-terminal HisF domain. Catalytically active yeast HIS7 was expressed in a bacterial system under the control of T7 polymerase promoter. The recombinant enzyme was purified to homogeneity and the native molecular weight and steady-state kinetic constants were determined. The yeast enzyme is distinguished from the Escherichia coli IGP synthase in its utilization of ammonia as a substrate. HIS7 displays a higher K(m) for glutamine and a lower turnover in the ammonia-dependent IGP synthase activity. As observed with the E. coli IGP synthase, HIS7 shows a low basal level glutaminase activity that can be enhanced 1000-fold in the presence of a nucleotide substrate or analog. The purification and characterization of the S. cerevisiae enzyme will enable a more detailed investigation of the biochemical mechanisms that mediate the ammonia-transfer process. The fused structural feature of the HIS7 protein and the development of a high-level production system for the active enzyme elevate the potential for determination of its three-dimensional structure through X-ray crystallography.
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Affiliation(s)
- S V Chittur
- Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana, 47907, USA
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Cox JM, Hawkes TR, Bellini P, Ellis RM, Barrett R, Swanborough JJ, Russell SE, Walker PA, Barnes NJ, Knee AJ, Lewis T, Davies PR. The Design and Synthesis of Inhibitors of Imidazoleglycerol Phosphate Dehydratase as Potential Herbicides. ACTA ACUST UNITED AC 1999. [DOI: 10.1002/(sici)1096-9063(199708)50:4<297::aid-ps592>3.0.co;2-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Petersen J, Hawkes TR, Lowe DJ. Nitrogen Coordination in VO2+-Substituted Imidazole Glycerol Phosphate Dehydratase Studied by Electron Spin−Echo Envelope Modulation Spectroscopy. J Am Chem Soc 1998. [DOI: 10.1021/ja9814220] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jan Petersen
- Nitrogen Fixation Laboratory, John Innes Centre Colney Lane, Norwich NR4 7UH, U.K. Zeneca Agrochemicals Department of Exploratory Plant Sciences Jealott's Hill Research Station, Bracknell RG42 6EY, U.K
| | - Timothy R. Hawkes
- Nitrogen Fixation Laboratory, John Innes Centre Colney Lane, Norwich NR4 7UH, U.K. Zeneca Agrochemicals Department of Exploratory Plant Sciences Jealott's Hill Research Station, Bracknell RG42 6EY, U.K
| | - David J. Lowe
- Nitrogen Fixation Laboratory, John Innes Centre Colney Lane, Norwich NR4 7UH, U.K. Zeneca Agrochemicals Department of Exploratory Plant Sciences Jealott's Hill Research Station, Bracknell RG42 6EY, U.K
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Gohda K, Kimura Y, Mori I, Ohta D, Kikuchi T. Theoretical evidence of the existence of a diazafulvene intermediate in the reaction pathway of imidazoleglycerol phosphate dehydratase: design of a novel and potent heterocycle structure for the inhibitor on the basis of the electronic structure-activity relationship study. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1385:107-14. [PMID: 9630553 DOI: 10.1016/s0167-4838(98)00049-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reaction mechanism of imidazoleglycerol phosphate dehydratase has not yet been clearly revealed. Structural comparison between inhibitors and the substrate IGP implicates that the reaction involves a diazafulvene intermediate. Here, we present evidence to support this hypothesis by investigating the electronic structure-enzyme inhibitory activity relationship on inhibitors with different heterocycles using 6-31G** level theory of the ab initio molecular orbital method. The calculation results showed that potent inhibitors can be distinguished from weak ones by the atomic charge density and by the energy levels of the highest occupied lone-pair orbital on the nitrogen atoms in the heterocycles. Furthermore, very good correlations (r2=0.8-0.9) were found between the charge density on the nitrogen atom and the inhibitory activity. It was also revealed that the diazafulvene is electronically similar to the potent inhibitors. Thus, these results strongly suggest the existence of the diazafulvene as an intermediate possessing tight-binding affinity to the enzyme. Based on the electronic structural similarity between the potent inhibitors and the proposed intermediate, a novel heterocycle was designed and predicted its inhibitory activity prior to the synthesis. Then, activity of synthesized inhibitors showed excellent agreement with this prediction. Hence, from the theoretical studies and experimental results, we conclude to obtain evidence of the hypothesis that the enzyme reaction proceeds via the diazafulvene intermediate.
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Affiliation(s)
- K Gohda
- Computer Chemistry Unit, International Research Laboratories, CIBA-GEIGY Japan, P.O. Box 1, Takarazuka, Hyogo 665, Japan.
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