9F2K

Myo-inositol-1-phosphate synthase from Thermochaetoides thermophila in complex with NAD

Summary for 9F2K

• Entry DOI: 10.2210/pdb9f2k/pdb
• EMDB information: 50149
• Descriptor: inositol-3-phosphate synthase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE (2 entities in total)
• Functional Keywords: inositol metabolism, endogenous, conformational selection, isomerase
• Biological source: Thermochaetoides thermophila DSM 1495
• Total number of polymer chains: 1
• Total formula weight: 57398.90

Authors

Traeger, T.K.,Kyrilis, F.L.,Hamdi, F.,Kastritis, P.L. (deposition date: 2024-04-23, release date: 2024-08-14, Last modification date: 2024-08-28)

Primary citation

Trager, T.K.,Kyrilis, F.L.,Hamdi, F.,Tuting, C.,Alfes, M.,Hofmann, T.,Schmidt, C.,Kastritis, P.L.
Disorder-to-order active site capping regulates the rate-limiting step of the inositol pathway.
Proc.Natl.Acad.Sci.USA, 121:e2400912121-e2400912121, 2024

PubMed Abstract: Myo-inositol-1-phosphate synthase (MIPS) catalyzes the NAD-dependent isomerization of glucose-6-phosphate (G6P) into inositol-1-phosphate (IMP), controlling the rate-limiting step of the inositol pathway. Previous structural studies focused on the detailed molecular mechanism, neglecting large-scale conformational changes that drive the function of this 240 kDa homotetrameric complex. In this study, we identified the active, endogenous MIPS in cell extracts from the thermophilic fungus . By resolving the native structure at 2.48 Å (FSC = 0.143), we revealed a fully populated active site. Utilizing 3D variability analysis, we uncovered conformational states of MIPS, enabling us to directly visualize an order-to-disorder transition at its catalytic center. An acyclic intermediate of G6P occupied the active site in two out of the three conformational states, indicating a catalytic mechanism where electrostatic stabilization of high-energy intermediates plays a crucial role. Examination of all isomerases with known structures revealed similar fluctuations in secondary structure within their active sites. Based on these findings, we established a conformational selection model that governs substrate binding and eventually inositol availability. In particular, the ground state of MIPS demonstrates structural configurations regardless of substrate binding, a pattern observed across various isomerases. These findings contribute to the understanding of MIPS structure-based function, serving as a template for future studies targeting regulation and potential therapeutic applications.

PubMed: 39145930
DOI: 10.1073/pnas.2400912121

Experimental method

ELECTRON MICROSCOPY (2.48 Å)