Related Experiment Video
Updated: Jul 15, 2026

Direct Detection of the Acetate-forming Activity of the Enzyme Acetate Kinase
Published on: December 19, 2011
Crystal structure of a fungal dihydroxyacetone kinase reveals a non-canonical ATP-binding site
Hongli Wei1, Yangyang Chen1, Fan Zhang1
1National Engineering Research Center of Industrial Enzyme, National Center of Technology Innovation for Synthetic Biology and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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.
Related Concept Videos
ATP Synthase: Structure
Allosteric Proteins-ATCase
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...
ATP Synthase: Mechanism
ATP Driven Pumps III: V-type Pumps
The peripheral or cytosolic V1 domain with eight subunits is involved in ATP hydrolysis. The integral or transmembrane V0 domain containing at least five subunits...
ATP Driven Pumps I: An Overview
There are four main types of ATP-driven pumps - P-type, V-type, F-type, and ABC transporter. All these pumps are of varying complexities and are...
Ligand Binding and Linkage

