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

Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures
Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures
Inorganic polyphosphate is a ubiquitous, linear biopolymer built of up to thousands of phosphate residues that are linked by energyrich 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 detailedmechanism 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.
kinase, polyphosphate, enzyme structure, Kinetics
0027-8424
Parnell, Alice
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Mordhorst, Silja
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Kemper, Florian
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Giurrandino, Mariacarmela
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Prince, Josh, Phillip
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Schwarzer, Nikola J.
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Hofer, Alexandre
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Wohlwend, Daniel
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Jessen, Henning J.
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Gerhardt, Stefan
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Einsle, Oliver
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Oyston, Petra C.F.
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Andexer, Jennifer N.
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Roach, Peter L.
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Parnell, Alice
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Mordhorst, Silja
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Kemper, Florian
a9628737-3af8-481f-9050-eeae86abd985
Giurrandino, Mariacarmela
12ac7f41-687e-4b55-8142-707a157cf2ca
Prince, Josh, Phillip
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Schwarzer, Nikola J.
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Hofer, Alexandre
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Wohlwend, Daniel
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Jessen, Henning J.
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Gerhardt, Stefan
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Einsle, Oliver
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Oyston, Petra C.F.
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Andexer, Jennifer N.
4957cb6c-d5c1-41f2-af8a-3bda2e691f87
Roach, Peter L.
ca94060c-4443-482b-af3e-979243488ba9

Parnell, Alice, Mordhorst, Silja, Kemper, Florian, Giurrandino, Mariacarmela, Prince, Josh, Phillip, Schwarzer, Nikola J., Hofer, Alexandre, Wohlwend, Daniel, Jessen, Henning J., Gerhardt, Stefan, Einsle, Oliver, Oyston, Petra C.F., Andexer, Jennifer N. and Roach, Peter L. (2018) Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures. Proceedings of the National Academy of Sciences. (doi:10.1073/pnas.1710741115).

Record type: Article

Abstract

Inorganic polyphosphate is a ubiquitous, linear biopolymer built of up to thousands of phosphate residues that are linked by energyrich 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 detailedmechanism 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.

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Accepted/In Press date: 13 February 2018
e-pub ahead of print date: 12 March 2018
Keywords: kinase, polyphosphate, enzyme structure, Kinetics

Identifiers

Local EPrints ID: 418801
URI: https://eprints.soton.ac.uk/id/eprint/418801
ISSN: 0027-8424
PURE UUID: 749fa13c-9db5-4e0b-8e14-d32841d6dbf4
ORCID for Peter L. Roach: ORCID iD orcid.org/0000-0001-9880-2877

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Date deposited: 22 Mar 2018 17:30
Last modified: 14 Mar 2019 01:47

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Contributors

Author: Alice Parnell
Author: Silja Mordhorst
Author: Florian Kemper
Author: Mariacarmela Giurrandino
Author: Josh, Phillip Prince
Author: Nikola J. Schwarzer
Author: Alexandre Hofer
Author: Daniel Wohlwend
Author: Henning J. Jessen
Author: Stefan Gerhardt
Author: Oliver Einsle
Author: Petra C.F. Oyston
Author: Jennifer N. Andexer
Author: Peter L. Roach ORCID iD

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