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TitleCryo-EM structures of Mycobacterium tuberculosis imidazole glycerol phosphate dehydratase in the apo state and in the presence of small molecules.
Journal, issue, pagesActa Crystallogr F Struct Biol Commun, Vol. 81, Issue Pt 7, Page 297-305, Year 2025
Publish dateJul 1, 2025
AuthorsRahul Raina / Deepsikha Kar / Mohini Singla / Satish Tiwari / Swati Kumari / Sonanjali Aneja / Varun Kumar / Soumya Banerjee / Shivika Goyal / Ravi Kant Pal / Kutti R Vinothkumar / Bichitra Biswal /
PubMed AbstractUnlike humans, Mycobacterium tuberculosis (Mtb), the causative agent of human tuberculosis, has a de novo histidine-biosynthesis pathway. The enzyme imidazole glycerol phosphate dehydratase (IGPD), ...Unlike humans, Mycobacterium tuberculosis (Mtb), the causative agent of human tuberculosis, has a de novo histidine-biosynthesis pathway. The enzyme imidazole glycerol phosphate dehydratase (IGPD), which catalyses the conversion of imidazole glycerol phosphate to imidazole acetol phosphate, has been studied extensively from various organisms and has become a major target for the development of antibacterial, antiweed and antifungal small molecules. In our previous studies, we have shown that in crystals IGPD forms a 24-mer oligomeric state in which the monomers are arranged in 432 symmetry. In order to gain insights into the oligomeric state of Mtb IGPD in solution, we determined cryogenic sample electron microscopy (cryo-EM) structures of apo IGPD at 2.2 and 3.1 Å resolution. In addition, we also determined the cryo-EM structure of IGPD in the presence of 3-amino-1,2,4-triazole (ATZ) to 2.8 Å resolution. The results of this work, which corroborate those from the crystallographic studies, indicate that IGPD forms a homo-oligomeric structure in solution comprising of 24 subunits. ATZ binds in the active-site pocket of the enzyme, which is located at the interface of three monomers and tethers 24 ATZ molecules. The results of this study suggest that cryo-EM, in addition to being a rapidly evolving and complementary imaging technology for elucidating 3D structures of biological macromolecules, can be useful in pinpointing the mode of binding small molecules of low mass (here ∼85 Da) and mapping protein-ligand interactions, which could assist in the design of accurate (high-potency) inhibitors.
External linksActa Crystallogr F Struct Biol Commun / PubMed:40478632 / PubMed Central
MethodsEM (single particle)
Resolution2.2 - 3.1 Å
Structure data

63588

9m2p

EMDB-63588, PDB-9m2p:
Imidazole glycerol phosphate dehydratase from Mycobacterium tuberculosis, apo structure
Method: EM (single particle) / Resolution: 3.1 Å

63589

9m2q

EMDB-63589, PDB-9m2q:
Imidazole glycerol phosphate dehydratase from Mycobacterium tuberculosis, in complex with aminotriazole
Method: EM (single particle) / Resolution: 2.8 Å

63590

9m2r

EMDB-63590, PDB-9m2r:
Imidazole glycerol phosphate dehydratase from Mycobacterium tuberculosis, apo structure
Method: EM (single particle) / Resolution: 2.2 Å

Chemicals

ChemComp-MN:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-3TR:
3-AMINO-1,2,4-TRIAZOLE

Source
  • mycobacterium tuberculosis (bacteria)
KeywordsLYASE / histidine pathway / dehydratase / Mycobacterium tuberculosis

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