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Imperfect coordination chemistry facilitates metal ion release in the Psa permease

Nature Chemical Biology volume 10, pages 35–41 (2014)Cite this article

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Abstract

The relative stability of divalent first-row transition metal ion complexes, as defined by the Irving-Williams series, poses a fundamental chemical challenge for selectivity in bacterial metal ion acquisition. Here we show that although the substrate-binding protein of Streptococcus pneumoniae, PsaA, is finely attuned to bind its physiological substrate manganese, it can also bind a broad range of other divalent transition metal cations. By combining high-resolution structural data, metal-binding assays and mutational analyses, we show that the inability of open-state PsaA to satisfy the preferred coordination chemistry of manganese enables the protein to undergo the conformational changes required for cargo release to the Psa permease. This is specific for manganese ions, whereas zinc ions remain bound to PsaA. Collectively, these findings suggest a new ligand binding and release mechanism for PsaA and related substrate-binding proteins that facilitate specificity for divalent cations during competition from zinc ions, which are more abundant in biological systems.

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Figure 1: Metal ion interaction with PsaA and accumulation by S. pneumoniae.
Figure 2: The structure of open, metal-free PsaA reveals an open metal-binding site.
Figure 3: Closing of PsaA is initiated by the interaction between Asp280 and manganese.
Figure 4: Location of introduced cysteine residues in Cys-PsaA and metal ion binding by the Cys-PsaA protein.
Figure 5: Proposed metal-binding mechanism for PsaA.

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Acknowledgements

This work was supported by the Australian Research Council (ARC) grants DP0986578 to A.G.M. and DP120103957 to C.A.M. and the National Health and Medical Research Council (NHMRC) project grant 1022240 to C.A.M. and program grant 565526 to J.C.P., A.G.M. and B.K. M.L.O. holds an ARC Discovery Early Career Researcher Award. B.K. is a NHMRC Senior Research Fellow. J.C.P. is a NHMRC Senior Principal Research Fellow. We thank A.E. Mark for discussions.

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  1. Rafael M Couñago and Miranda P Ween: These authors contributed equally to this work.

Authors and Affiliations

  1. School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Australia

    Rafael M Couñago, Megan L O'Mara, Alastair G McEwan & Bostjan Kobe

  2. Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia

    Rafael M Couñago, Megha Bajaj, Johannes Zuegg, Matthew A Cooper & Bostjan Kobe

  3. Research Centre for Infectious Diseases, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia

    Miranda P Ween, Stephanie L Begg, James C Paton & Christopher A McDevitt

  4. School of Mathematics and Physics, University of Queensland, Brisbane, Australia

    Megan L O'Mara

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Contributions

R.M.C. designed and executed the crystallographic experiments. M.P.W., S.L.B. and C.A.M. designed and executed all of the biochemical studies. M.B., J.Z. and M.L.O. executed the molecular dynamics experiments. R.M.C., M.P.W., M.L.O. and C.A.M. drafted the manuscript. All of the authors contributed to the design, analysis, discussion of the research and writing of the final manuscript.

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Correspondence to Bostjan Kobe or Christopher A McDevitt.

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Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Tables 1–4, Supplementary Movie Legend and Supplementary Figures 1–6. (PDF 4603 kb)

Supplementary Video

The movie shows the conformational changes in PsaA as the cognate physiological ligand Mn2+ binds the protein, as revealed by the crystal structures of metal-free, open-state PsaA (PDB code 3ZK7); open-state Mn2+-PsaAD280N (PDB code 3ZKA); and closed-state Mn2+-PsaA (PDB code 3ZTT). Changes in secondary structure and backbone hydrogen bonding that occur in the flexible ('spring') helix of PsaA during binding are highlighted. The movie also shows the conformational differences between closed-state Mn2+-PsaA (PDB code 3ZTT) and closed-state Zn2+-PsaA (PDB code 1PSZ) (MOV 22844 kb)

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Couñago, R., Ween, M., Begg, S. et al. Imperfect coordination chemistry facilitates metal ion release in the Psa permease. Nat Chem Biol 10, 35–41 (2014). https://doi.org/10.1038/nchembio.1382

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