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

DOI: 10.1073/pnas.1710741115 DOI Help

Authors: Alice E. Parnell (University of Southampton) , Silja Mordhorst (Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg) , Florian Kemper (Institute of Biochemistry, Albert-Ludwigs-University Freiburg) , Mariacarmela Giurrandino (University of Southampton) , Josh P. Prince (University of Southampton) , Nikola J. Schwarzer (Institute of Biochemistry, Albert-Ludwigs-University Freiburg) , Alexandre Hofer (Organic Chemistry Institute, University of Zürich) , Daniel Wohlwend (Institute of Biochemistry, Albert-Ludwigs-University Freiburg) , Henning J. Jessen (Organic Chemistry Institute, University of Zürich) , Stefan Gerhardt (Institute of Biochemistry, Albert-Ludwigs-University Freiburg) , Oliver Einsle (Institute of Biochemistry, Albert-Ludwigs-University Freiburg) , Petra C. F. Oyston (Institute for Life Sciences, University of Southampton; Biomedical Sciences, Defence Science and Technology Laboratory Porton Down) , Jennifer N. Andexer (Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg) , Peter L. Roach (University of Southampton)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Proceedings Of The National Academy Of Sciences , VOL 265

State: Published (Approved)
Published: March 2018
Diamond Proposal Number(s): 8889

Abstract: Inorganic polyphosphate is a ubiquitous, linear biopolymer built of up to thousands of phosphate residues that are linked by energy-rich phosphoanhydride bonds. Polyphosphate kinases of the family 2 (PPK2) use polyphosphate to catalyze the reversible phosphorylation of nucleotide phosphates and are highly relevant as targets for new pharmaceutical compounds and as biocatalysts for cofactor regeneration. PPK2s can be classified based on their preference for nucleoside mono- or diphosphates or both. The detailed mechanism of PPK2s and the molecular basis for their substrate preference is unclear, which is mainly due to the lack of high-resolution structures with substrates or substrate analogs. Here, we report the structural analysis and comparison of a class I PPK2 (ADP-phosphorylating) and a class III PPK2 (AMP- and ADP-phosphorylating), both complexed with polyphosphate and/or nucleotide substrates. Together with complementary biochemical analyses, these define the molecular basis of nucleotide specificity and are consistent with a Mg2+ catalyzed in-line phosphoryl transfer mechanism. This mechanistic insight will guide the development of PPK2 inhibitors as potential antibacterials or genetically modified PPK2s that phosphorylate alternative substrates.

Journal Keywords: kinase; polyphosphate; enzyme; structure; kinetics

Subject Areas: Biology and Bio-materials, Medicine

Instruments: I04-1-Macromolecular Crystallography (fixed wavelength) , I04-Macromolecular Crystallography , I24-Microfocus Macromolecular Crystallography

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