Structural Insights into Substrate Selectivity and Activity of Bacterial Polyphosphate Kinases

Nocek, Boguslaw P.; Khusnutdinova, Anna N.; Ruszkowski, Milosz; Flick, Robert; Burda, Malgorzata; Batyrova, Khorcheska; Brown, Greg; Mucha, Artur; Joachimiak, Andrzej; Berlicki, Łukasz; Yakunin, Alexander F.

doi:10.1021/acscatal.8b03151

Title: Structural Insights into Substrate Selectivity and Activity of Bacterial Polyphosphate Kinases

Journal Article · 11 October 2018 · ACS Catalysis

DOI: https://doi.org/10.1021/acscatal.8b03151 · OSTI ID:1487282

Nocek, Boguslaw P. ^[1]; Khusnutdinova, Anna N. ^[2]; Ruszkowski, Milosz ^[3]; Flick, Robert ^[2]; Burda, Malgorzata ^[4]; Batyrova, Khorcheska ^[2]; Brown, Greg ^[2]; Mucha, Artur ^[4]; Joachimiak, Andrzej ^[1]; Berlicki, Łukasz ^[4];

^[2]

Argonne National Lab. (ANL), Argonne, IL (United States). Midwest Center for Structural Genomics and Structural Biology Center
Univ. of Toronto, ON (Canada)
National Cancer Institute, Argonne, IL (United States)
Wroclaw Univ. of Science and Technology, Wroclaw (Poland)

Polyphosphate (polyP) kinases are widely conserved enzymes with importance in basic bacterial metabolism and virulence in many pathogens. However, the molecular mechanisms of their substrate specificity and catalysis remain unknown. Here, we present the results of comprehensive biochemical and structural studies of three polyP kinases from different bacteria, which belong to different clusters of the PPK2 class III family. Purified PPK2 proteins catalyzed polyP-dependent phosphorylation of AMP, ADP, GMP, and GDP to corresponding nucleoside di- and triphosphates. Crystal structures of these proteins in complex with substrates, products, Mg²⁺, and inhibitors revealed the binding sites for the nucleotide and polyP substrates overlapping at the Walker A and B loops. The Walker A loop is involved in the binding of polyP and the Mg²⁺ ion, whereas the Walker B loop coordinates the nucleotide phosphate groups. Structure-based site-directed mutagenesis of CHU0107 from Cytophaga hutchinsonii demonstrated the critical role of several conserved residues from the PPK2 core and lid domains, involved in the coordination of both substrates and two Mg²⁺ ions. Additionally, a two-times higher activity was observed following deletion of the C-terminal tail in the CHU0107 mutant protein L285Stop. Crystal structures of PPK2 in complex with three aryl phosphonate inhibitors indicated the presence of at least two binding pockets for inhibitors located close to the Walker A loop and the catalytic residues Lys81 and Arg208. Our findings provide a molecular framework for understanding the molecular mechanisms of PPK2 kinases and have implications for future drug design and biocatalytic applications

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: National Institutes of Health (NIH); Natural Sciences and Engineering Research Council of Canada (NSERC); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1487282

Journal Information:: ACS Catalysis, Journal Name: ACS Catalysis Journal Issue: 11 Vol. 8; ISSN 2155-5435

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
ATP regeneration
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inorganic polyphosphate
polyphosphate kinase
site-directed mutagenesis

Title: Structural Insights into Substrate Selectivity and Activity of Bacterial Polyphosphate Kinases

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