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Metabolically-resistant synthetic bioisostere overlaid on natural 5-InsP7  (left) and its co-crystal structure (right)
Metabolically-resistant synthetic bioisostere overlaid on natural 5-InsP7 (left) and its co-crystal structure (right)

Structural snapshots of protein/ligand complexes are crucial to gain insight into enzymatic reaction mechanisms. Diphospho-myo-inositol polyphosphates such as 5-InsP7 regulate immunity and phosphate homeostasis and are phosphatase substrates.

Data from a tripartite collaboration, between the Potter group within Oxford Pharmacology, the NIH and Freiburg University, “A structural exposé of noncanonical molecular reactivity within the protein tyrosine phosphatase WPD loop” just published in Nature Communications include the first multiple substrate/enzyme crystal complexes from a variety of pre-reactant-, reactant-, intermediate- and product-bound states for a Cys-based Arabidopsis thaliana protein tyrosine phosphate-phosphatase lacking a functional canonical catalytic acid.

These provide the first data-driven mechanism for a reaction cycle that does not utilize any amino-acid residue as a general acid, showing how the enzyme is optimized for regiospecific and rapid hydrolysis of the β-phosphate of its pyrophosphate substrate and how the latter can drive its own hydrolysis.

The work used a metabolically-resistant synthetic 5-InsP7 bioisostere (pink ligand), designed in the Potter group that replaces the scissile 5-β-phosphate of 5-InsP7 (grey) with a phosphonodifluoromethyl group. The co-crystallized ligand orientates like 5-InsP7 but with a gain-of-function interaction between one fluorine atom and a guanidinium group. Very notably the work also identifies crystallographically a highly elusive and reactive metaphosphate-like intermediate in the reaction cycle.

Read the paper: