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Phosphorylation and ATP-binding induced conformational changes in the PrkC, Ser/Thr kinase from B. subtilis

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Abstract

Recent studies on the PrkC, serine-threonine kinase show that that the enzyme is located at the inner membrane of endospores and is responsible for triggering spore germination. The activity of the protein increases considerably after phosphorylation of four threonine residues placed on the activation loop and one serine placed in the C-terminal lobe of the PrkC. The molecular relationship between phosphorylation of these residues and enzyme activity is not known. In this work molecular dynamics simulation is performed on four forms of the protein kinase PrkC from B. subtilis—phosphorylated or unphosphorylated; with or without ATP bound—in order to gain insight into phosphorylation and ATP binding on the conformational changes and functions of the protein kinase. Our results show how phosphorylation, as well as the presence of ATP, is important for the activity of the enzyme through its molecular interaction with the catalytic core residues. Three of four threonine residues were found to be involved in the interactions with conservative motifs important for the enzyme activity. Two of the threonine residues (T167 and T165) are involved in ionic interactions with an arginine cluster from αC-helix. The third residue (T163) plays a crucial role, interacting with His-Arg-Asp triad (HRD). Last of the threonine residues (T162), as well as the serine (S214), were indicated to play a role in the substrate recognition or dimerization of the enzyme. The presence of ATP in the unphosphorylated model induced conformational instability of the activation loop and Asp-Phe-Gly motif (DFG). Based on our calculations we put forward a hypothesis suggesting that the ATP binds after phosphorylation of the activation loop to create a fully active conformation in the closed position.

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Abbreviations

ATP:

Adenosine triphosphate

DFG-motif:

Asp-Phe-Gly conserved kinase motif

HRD-motif:

His-Arg-Asp conserved kinase motif

PASTA:

Penicillin-binding protein and serine/threonine kinase associated domain

PrkCc:

Catalytic domain of PrkC kinase

PrkCc-ATP:

Complex of PrkCc with ATP

pPrkCc:

Phosphorylated catalytic domain of PrkC kinase

pPrkCc-ATP:

Complex of pPrkCc with ATP

RMSd:

Root mean square deviation

RMSf:

Root mean square fluctuation

SAS:

Solvent-accessible surface

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Acknowledgments

We acknowledge Tiffany S. Han for critical reading of the manuscript. This work was partially supported by University of Gdańsk fund DS/B50A-4-162-8.

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Authors and Affiliations

  1. Faculty of Chemistry, University of Gdańsk, Sobieskiego 18/19, 80-952, Gdańsk, Poland

    Paweł Gruszczyński

  2. Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Kładki 24, 80-822, Gdańsk, Poland

    Paweł Gruszczyński & Rajmund Kaźmierkiewicz

  3. Department of Medical Biotechnology, Intercollegiate Faculty of Biotechnology, Medical University of Gdańsk, Dębinki 1, 80-811, Gdańsk, Poland

    Michał Obuchowski

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  1. Paweł Gruszczyński
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Correspondence to Paweł Gruszczyński.

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Gruszczyński, P., Obuchowski, M. & Kaźmierkiewicz, R. Phosphorylation and ATP-binding induced conformational changes in the PrkC, Ser/Thr kinase from B. subtilis . J Comput Aided Mol Des 24, 733–747 (2010). https://doi.org/10.1007/s10822-010-9370-4

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