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Yorodumi- PDB-8qax: Medicago truncatula HISN5 (IGPD) in complex with MN, FMT, GOL and TRS -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qax | ||||||
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Title | Medicago truncatula HISN5 (IGPD) in complex with MN, FMT, GOL and TRS | ||||||
Components | Imidazoleglycerol-phosphate dehydratase | ||||||
Keywords | LYASE / HISN5 / IGPD / histidine biosynthesis | ||||||
Function / homology | Function and homology information imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / L-histidine biosynthetic process Similarity search - Function | ||||||
Biological species | Medicago truncatula (barrel medic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Witek, W. / Ruszkowski, M. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Front Plant Sci / Year: 2024 Title: Targeting imidazole-glycerol phosphate dehydratase in plants: novel approach for structural and functional studies, and inhibitor blueprinting. Authors: Wojciech Witek / Joanna Sliwiak / Michal Rawski / Milosz Ruszkowski / 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 ...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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 8qax.cif.gz | 458.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qax.ent.gz | 372.4 KB | Display | PDB format |
PDBx/mmJSON format | 8qax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qax_validation.pdf.gz | 505.7 KB | Display | wwPDB validaton report |
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Full document | 8qax_full_validation.pdf.gz | 514.7 KB | Display | |
Data in XML | 8qax_validation.xml.gz | 46.5 KB | Display | |
Data in CIF | 8qax_validation.cif.gz | 64.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/8qax ftp://data.pdbj.org/pub/pdb/validation_reports/qa/8qax | HTTPS FTP |
-Related structure data
Related structure data | 7oj5C 8qavC 8qawC 8qayC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.18150/XWLKP6 / Data set type: diffraction image data |
-Links
-Assembly
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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