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Elucidating the structural basis for differing enzyme inhibitor potency by cryo-EM.

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Rawson S, Bisson C, Hurdiss DL, Fazal A, McPhillie MJ, Sedelnikova SE, Baker PJ, Rice DW, Muench SP
OpenAccess logo Proc Natl Acad Sci U S A 115 1795-1800 (2018)
Cited: 13 times
EuropePMC logo PMID: 29434040

Abstract

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.

Articles - 6ezj mentioned but not cited (4)

  1. Elucidating the structural basis for differing enzyme inhibitor potency by cryo-EM. Rawson S, Bisson C, Hurdiss DL, Fazal A, McPhillie MJ, Sedelnikova SE, Baker PJ, Rice DW, Muench SP. Proc Natl Acad Sci U S A 115 1795-1800 (2018)
  2. MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry. Terashi G, Kagaya Y, Kihara D. J Chem Inf Model 60 2634-2643 (2020)
  3. The Role of Gene Elongation in the Evolution of Histidine Biosynthetic Genes. Del Duca S, Chioccioli S, Vassallo A, Castronovo LM, Fani R. Microorganisms 8 E732 (2020)
  4. Targeting imidazole-glycerol phosphate dehydratase in plants: novel approach for structural and functional studies, and inhibitor blueprinting. Witek W, Sliwiak J, Rawski M, Ruszkowski M. Front Plant Sci 15 1343980 (2024)


Reviews citing this publication (1)

  1. Interpretation of medium resolution cryoEM maps of multi-protein complexes. Casañal A, Shakeel S, Passmore LA. Curr Opin Struct Biol 58 166-174 (2019)

Articles citing this publication (8)

  1. Collection, pre-processing and on-the-fly analysis of data for high-resolution, single-particle cryo-electron microscopy. Thompson RF, Iadanza MG, Hesketh EL, Rawson S, Ranson NA. Nat Protoc 14 100-118 (2019)
  2. In vitro activity and In vivo efficacy of Isoliquiritigenin against Staphylococcus xylosus ATCC 700404 by IGPD target. Qu Q, Wang J, Cui W, Zhou Y, Xing X, Che R, Liu X, Chen X, Bello-Onaghise G, Dong C, Li Z, Li X, Li Y. PLoS One 14 e0226260 (2019)
  3. An Investigation of Atomic Structures Derived from X-ray Crystallography and Cryo-Electron Microscopy Using Distal Blocks of Side-Chains. Chen L, He J, Sazzed S, Walker R. Molecules 23 E610 (2018)
  4. Rutin, A Natural Inhibitor of IGPD Protein, Partially Inhibits Biofilm Formation in Staphylococcus xylosus ATCC700404 in vitro and in vivo. Qu Q, Cui W, Xing X, Zou R, Huang X, Wang X, Wu T, Bello-Onaghise G, Yuan S, Li Y. Front Pharmacol 12 728354 (2021)
  5. A Visualization Tool for Cryo-EM Protein Validation with an Unsupervised Machine Learning Model in Chimera Platform. Chen L, Baker B, Santos E, Sheep M, Daftarian D. Medicines (Basel) 6 E86 (2019)
  6. A Histogram-based Outlier Profile for Atomic Structures Derived from Cryo-Electron Microscopy. Chen L, He J. ACM BCB 2019 586-591 (2019)
  7. Recombinant l-glutaminase obtained from Geobacillus thermodenitrificans DSM-465: characterization and in silico elucidation of conserved structural domains. Shah L, Nadeem MS, Khan JA, Zeyadi MA, Zamzami MA, Mohammed K. RSC Adv 9 4258-4267 (2019)
  8. Structure-Based Protein Assembly Simulations Including Various Binding Sites and Conformations. Walter LJ, Quoika PK, Zacharias M. J Chem Inf Model 64 3465-3476 (2024)


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