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TitleElucidating the structural basis for differing enzyme inhibitor potency by cryo-EM.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 115, Issue 8, Page 1795-1800, Year 2018
Publish dateFeb 20, 2018
AuthorsShaun Rawson / Claudine Bisson / Daniel L Hurdiss / Asif Fazal / Martin J McPhillie / Svetlana E Sedelnikova / Patrick J Baker / David W Rice / Stephen P Muench /
PubMed AbstractHistidine biosynthesis is an essential process in plants and microorganisms, making it an attractive target for the development of herbicides and antibacterial agents. Imidazoleglycerol-phosphate ...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 (IGPD) and (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 IGPD than 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 and 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 IGPD/C348 complex. The structure of _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.
External linksProc Natl Acad Sci U S A / PubMed:29434040 / PubMed Central
MethodsEM (single particle)
Resolution3.1 - 3.2 Å
Structure data

3999

6ezj

EMDB-3999, PDB-6ezj:
Imidazoleglycerol-phosphate dehydratase
Method: EM (single particle) / Resolution: 3.1 Å

4160

6ezm

EMDB-4160, PDB-6ezm:
Imidazoleglycerol-phosphate dehydratase from Saccharomyces cerevisiae
Method: EM (single particle) / Resolution: 3.2 Å

Chemicals

ChemComp-MN:
Unknown entry

ChemComp-5LD:
[(2R)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]phosphonic acid

Source
  • arabidopsis thaliana (thale cress)
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
KeywordsLYASE / Inhibitor / histidine biosynthesis / complex

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