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

  • Parnell AE Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom.
  • Mordhorst S Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.
  • Kemper F Institute of Biochemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.
  • Giurrandino M Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom.
  • Prince JP Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom.
  • Schwarzer NJ Institute of Biochemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.
  • Hofer A Organic Chemistry Institute, University of Zürich, 8057 Zürich, Switzerland.
  • Wohlwend D Institute of Biochemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.
  • Jessen HJ Organic Chemistry Institute, University of Zürich, 8057 Zürich, Switzerland.
  • Gerhardt S Institute of Biochemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.
  • Einsle O Institute of Biochemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.
  • Oyston PCF Institute for Life Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom.
  • Andexer JN Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; jennifer.andexer@pharmazie.uni-freiburg.de plr2@soton.ac.uk.
  • Roach PL Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom; jennifer.andexer@pharmazie.uni-freiburg.de plr2@soton.ac.uk.
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  • 2018-03-14
Published in:
  • Proceedings of the National Academy of Sciences of the United States of America. - 2018
enzyme structure
kinase
kinetics
polyphosphate
Crystallography, X-Ray
Deinococcus
Kinetics
Ligands
Phosphorylation
Phosphotransferases (Phosphate Group Acceptor)
Polyphosphates
Protein Conformation
Substrate Specificity
English 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.
Language
  • English
Open access status
bronze
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Persistent URL
https://sonar.ch/global/documents/191344
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