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Structure paper

TitleTargeting imidazole-glycerol phosphate dehydratase in plants: novel approach for structural and functional studies, and inhibitor blueprinting.
Journal, issue, pagesFront Plant Sci, Vol. 15, Page 1343980, Year 2024
Publish dateMar 15, 2024
AuthorsWojciech Witek / Joanna Sliwiak / Michal Rawski / Milosz Ruszkowski /
PubMed AbstractThe 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 ...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 HISN5 (HISN5) in complexes with an inactive IGP diastereoisomer and with various other ligands. HISN5 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 HISN5 enzymatic activity using isothermal titration calorimetry and enzymatically synthesized IGP.
External linksFront Plant Sci / PubMed:38559763 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.55 - 2.23 Å
Structure data

18305

8qav

EMDB-18305, PDB-8qav:
Medicago truncatula HISN5 (IGPD) in complex with MN and IG2
Method: EM (single particle) / Resolution: 2.23 Å

PDB-8qaw:
Medicago truncatula HISN5 (IGPD) in complex with MN, IMD, EDO, FMT, GOL and TRS
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-8qax:
Medicago truncatula HISN5 (IGPD) in complex with MN, FMT, GOL and TRS
Method: X-RAY DIFFRACTION / Resolution: 1.69 Å

PDB-8qay:
Medicago truncatula HISN5 (IGPD) in complex with MN, FMT, ACT, CIT, EDO, SO4
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

Chemicals

ChemComp-MN:
Unknown entry

ChemComp-IG2:
(2S,3S)-2,3-dihydroxy-3-(1H-imidazol-5-yl)propyl dihydrogen phosphate

ChemComp-HOH:
WATER / Water

ChemComp-IMD:
IMIDAZOLE / Imidazole

ChemComp-FMT:
FORMIC ACID / Formic acid

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM / Tris

ChemComp-CL:
Unknown entry / Chloride

ChemComp-NA:
Unknown entry

ChemComp-CIT:
CITRIC ACID / Citric acid

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-ACT:
ACETATE ION / Acetate

Source
  • medicago truncatula (barrel medic)
KeywordsLYASE / Medicago truncatula HISN5 IGPD histidine / HISN5 / IGPD / histidine biosynthesis / Medicago truncatula

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