Structure of McsB, a protein kinase for regulated arginine phosphorylation

Abstract

Protein phosphorylation regulates key processes in all organisms. In Gram-positive bacteria, protein arginine phosphorylation plays a central role in protein quality control by regulating transcription factors and marking aberrant proteins for degradation. Here, we report structural, biochemical, and in vivo data of the responsible kinase, McsB, the founding member of an arginine-specific class of protein kinases. McsB differs in structure and mechanism from protein kinases that act on serine, threonine, and tyrosine residues and instead has a catalytic domain related to that of phosphagen kinases (PhKs), metabolic enzymes that phosphorylate small guanidino compounds. In McsB, the PhK-like phosphotransferase domain is structurally adapted to target protein substrates and is accompanied by a novel phosphoarginine (pArg)-binding domain that allosterically controls protein kinase activity. The identification of distinct pArg reader domains in this study points to a remarkably complex signaling system, thus challenging simplistic views of bacterial protein phosphorylation.

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Fig. 1: Structure of the protein arginine kinase McsB.
Fig. 2: Catalytic mechanism and mutational analysis of McsB.
Fig. 3: Dimerization and putative negative cooperativity in McsB.
Fig. 4: The DD of McsB and the C-terminal domain of CtsR are pArg-binding domains.
Fig. 5: Allosteric stimulation of McsB by pArg binding.
Fig. 6: Organization of the McsB protein arginine kinase and the pArg signaling system.

Data availability

Atomic coordinates and structure factors have been deposited in the Protein Data Bank (PDB) under accession codes 6FH1 (McsB), 6FH2 (McsB–AMP-PN), 6FH3 (McsB-pArg), 6FH4 (Δ1–75 CtsR-pArg). All other source data are included in the paper or will be provided upon reasonable request.

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Acknowledgements

We thank R. Huber and all members of the Clausen group for remarks on the manuscript and discussions, J. Leodolter and M. Madalinski for support in preparing pArg-containing peptides, A. Schleiffer for help with bioinformatic analysis, A. Sedivy and P. Stolt-Bergner for assistance with CD spectroscopy measurements, N. Stanley-Wall (University of Dundee) for pMAD plasmid and advice on mutagenesis in B. subtilis, and staff of beamlines at ESRF (Grenoble), SLS (Villigen), and DESY (Hamburg) for excellent help during data collection. This work was supported by a grant from the European Research Council (AdG 694978, to T.C.). The IMP is supported by Boehringer Ingelheim.

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M.J.S. and T.C. designed and performed experiments, analyzed data, and wrote the paper with input from all authors; B.H., A.H. L.D.V., R.K., K.H., V.T., K.R., and A.M. helped with biochemical and structural analyses; R.B and K.M. with mass spectrometric measurements.

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Correspondence to Tim Clausen.

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Suskiewicz, M.J., Hajdusits, B., Beveridge, R. et al. Structure of McsB, a protein kinase for regulated arginine phosphorylation. Nat Chem Biol 15, 510–518 (2019). https://doi.org/10.1038/s41589-019-0265-y

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