26VK

Crystal structure of Dihydroxyacetone kinase from Komagataella pastoris

Summary for 26VK

• Entry DOI: 10.2210/pdb26vk/pdb
• Descriptor: Dihydroxyacetone kinase, MAGNESIUM ION, ADENOSINE-5'-TRIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: catalysis, biosynthetic protein
• Biological source: Komagataella pastoris
• Total number of polymer chains: 8
• Total formula weight: 523755.53

Authors

Wei, H.L.,Chen, Y.Y.,Li, Q.,Liu, W.D.,Cai, T. (deposition date: 2026-05-16, release date: 2026-07-22)

Primary citation

Wei, H.,Chen, Y.,Zhang, F.,Li, Q.,Liu, P.,Cai, T.,Liu, W.
Crystal structure of a fungal dihydroxyacetone kinase reveals a non-canonical ATP-binding site.
Biochem.Biophys.Res.Commun., 830:154274-154274, 2026

PubMed 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, Mg ions were identified in some substrate-binding pockets and docking suggested substantial overlap between Mg 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.

PubMed: 42442090
DOI: 10.1016/j.bbrc.2026.154274

Experimental method

X-RAY DIFFRACTION (2.88 Å)