Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures

Area of Science:

• Biochemistry
• Structural Biology
• Enzymology

Background:

• Inorganic polyphosphate is a linear biopolymer essential in cellular processes.
• Polyphosphate kinases family 2 (PPK2s) catalyze reversible phosphorylation using polyphosphate.
• PPK2s are significant targets for pharmaceuticals and biocatalysis, but their mechanism and substrate specificity are poorly understood.

Purpose of the Study:

• To elucidate the detailed mechanism of PPK2s.
• To define the molecular basis for substrate preference in different PPK2 classes.
• To provide insights for developing PPK2 inhibitors and engineered biocatalysts.

Main Methods:

• X-ray crystallography of class I and class III PPK2s complexed with substrates.
• Structural comparison of PPK2-substrate complexes.
• Biochemical analyses to complement structural data.

Main Results:

• High-resolution structures of PPK2s with polyphosphate and nucleotide substrates were determined.
• The molecular basis for nucleotide specificity in class I and class III PPK2s was defined.
• A Mg²⁺-catalyzed in-line phosphoryl transfer mechanism was proposed.

Conclusions:

• Structural and biochemical data reveal the mechanism of PPK2s and their substrate specificity.
• Findings will aid in designing PPK2 inhibitors for antibacterial applications.
• Insights enable the engineering of PPK2s for novel biocatalytic functions.