Jul 2026· Biochemical and Biophysical Research Communications - BBRC· Vol 830, pp.
154274
· 0 citations· 45 references
Medicine
Abstract
Dihydroxyacetone kinase (DAK) catalyzes the ATP-dependent phosphorylation of dihydroxyacetone (DHA) and is an important enzyme in artificial starch synthesis. Here, we report the crystal structure of a methylotrophic yeast DAK from Komagataella phaffii (formly Pichia pastoris, PpDAK). ATP was observed at a non-canonical site distinct from the canonical bacterial ATP-binding pocket. Docking further suggested that the canonical pocket remains accessible, indicating flexibility in ATP recognition. Sequence and phylogenetic analyses show that PpDAK clusters within a distinct methylotrophic yeast lineage and that residues surrounding the non-canonical ATP-binding site are conserved among methylotrophic yeasts. In addition, Mg2+ ions were identified in some substrate-binding pockets and docking suggested substantial overlap between Mg2+ and the predicted DHA-binding position. Together, these findings provide structural insights into ATP recognition in fungal DAKs and a framework for future functional studies and enzyme engineering.
The crystal structure of Petunia hybrida BS is reported, which reveals an α2β2 heterotetrameric arrangement, establishing BS as a rare heterotetrameric plant SDR and demonstrating how subunit specialization and intersubunit arrangement enable function, providing principles for understanding and engineering multimeric e...
Jason O. Matos, Jihee Lee, Ramasamy P. Kumar et al.· Science Advances· 0 citations
Isoaspartate (isoAsp) formation is typically viewed as a “molecular clock” through nonenzymatic degradation of aspartate or asparagine during protein aging. Here we report a nearly universal enzymatic pathway for the formation of a conserved isoAsp in the bacterial ribosomal protein uS11. Proteome-wide protein-protein...
Yanqing Xue, Chandrima Majumdar, Salimat O. Sofela et al.· bioRxiv· 0 citations
It is concluded that the early emergence of the Rossmann fold reflects the chemical and physical constraints of protein folding, explaining both its profound antiquity and sustained longevity.
Koh Seya, Tatsuya Corlett, Hamza Giaffar et al.· bioRxiv· 0 citations
This systematic analysis of ATP-dependent diazotases from actinomycetes that catalyze the condensation of nitrite with aromatic amines establishes group 3 diazotases as promising, engineerable biocatalysts for selective and efficient diazo installation.
Jia-Yu Ning, Seiji Kawai, Y. Katsuyama et al.· Journal of the American Chem...· 0 citations
The sulfonamide-degrading monooxygenase sulX plays a dual role in bioremediation and antibiotic resistance, yet its molecular mechanism remains elusive. Here we report crystal structures of sulX in its ligand-free form, as an FMN-bound binary complex, and as ternary complexes with six distinct sulfonamides at resolutio...
Yu-Mei Hu, Wan-Huan Liu, Qi-Shan Zhang et al.· Journal of Hazardous Materia...· 0 citations
