9LJ9

Crystal structure of a bifunctional 3-hexulose-6-phosphate synthase/6-phospho-3-hexuloisomerase

Summary for 9LJ9

• Entry DOI: 10.2210/pdb9lj9/pdb
• Descriptor: 3-hexulose-6-phosphate synthase, MAGNESIUM ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: dimer, 3-hexulose-6-phosphate synthase, formaldehyde assimilation, ribulose monophosphate cycle, isomerase
• Biological source: Pyrococcus horikoshii OT3
• Total number of polymer chains: 2
• Total formula weight: 93611.36

Authors

Wang, H.,Feng, Y.,Liu, L.,Li, Y.X.,Ji, Y. (deposition date: 2025-01-14, release date: 2025-10-01)

Primary citation

Li, Y.,Liu, Y.,Ji, Y.,Xu, H.,Wang, H.,Feng, Y.,Liu, L.
Crystal Structure, Mutations, and Catalytic Properties of 3-Hexulose-6-phosphate Synthase from Pyrococcus horikoshii.
J.Agric.Food Chem., 73:17103-17113, 2025

PubMed Abstract: 3-Hexulose-6-phosphate synthase, a key enzyme in the ribulose monophosphate pathway, plays a central role in formaldehyde assimilation and detoxification, offering great potential for third-generation green biomanufacturing. In this study, we determined the crystal structure of HPS from at a 2.64 Å resolution. Combined approaches, including molecular docking, multiple sequence alignment, and alanine scanning, identified critical catalytic residues. Two variants, T136C and V186W, exhibited over 6-fold higher activity than the wild type. Molecular dynamics simulations indicated increased structural rigidity and enhanced stability upon substrate (d-ribulose-5-phosphate) binding, along with significantly improved binding energies. Furthermore, an enzyme cascade converting d-xylose and formaldehyde to d-fructose-6-phosphate was constructed to evaluate the HPS activity under optimized conditions. These findings provide insights into the catalytic mechanism of HPS and offer a basis for its application in one-carbon bioconversion.

PubMed: 40580126
DOI: 10.1021/acs.jafc.5c02365

Experimental method

X-RAY DIFFRACTION (2.64 Å)