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Structure of the Ni(II) complex of Escherichia coli peptide deformylase and suggestions on deformylase activities depending on different metal(II) centres

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Abstract

Crystal structures of polypeptide deformylase (PDF) of Escherichia coli with nickel(II) replacing the native iron(II) have been solved with chloride and formate as metal ligands. The chloro complex is a model for the correct protonation state of the hydrolytic hydroxo ligand and the protonated status of the Glu133 side chain as part of the hydrolytic mechanism. The ambiguity that recently some PDFs have been identified with Zn2+ ion as the active-site centre whereas others are only active with Fe2+ (or Co2+, Ni2+) is discussed with respect to Lewis acid criteria of the metal ion and substrate activation by the CD loop.

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Abbreviations

HEPES:

N-(2-Hydroxyethyl)piperazine-N′-ethanesulfonic acid

PDF:

Peptide deformylase

RMSD:

Root mean square deviation

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Acknowledgments

We thank Thomas Schweder (University of Greifswald) and his group for help in cloning E. coli PDF. Y.T.H.N. is grateful for a personal grant from the MOET, Vietnam, and financial support by DAAD, Germany.

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Author notes

  1. Ngo Thi Hai Yen

    Present address: Institute of Industrial Chemistry, Center for Pharmaceutical Chemistry, N2 Pham Ngu Lao Street, Hoan Kiem District, Hanoi, Vietnam

Authors and Affiliations

  1. Department of Molecular Structural Biology, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany

    Ngo Thi Hai Yen, Xenia Bogdanović, Gottfried J. Palm & Winfried Hinrichs

  2. Bioinorganic Research Group, Institute for Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany

    Olaf Kühl

Authors
  1. Ngo Thi Hai Yen
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  2. Xenia Bogdanović
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  3. Gottfried J. Palm
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  4. Olaf Kühl
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  5. Winfried Hinrichs
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Correspondence to Winfried Hinrichs.

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Yen, N.T.H., Bogdanović, X., Palm, G.J. et al. Structure of the Ni(II) complex of Escherichia coli peptide deformylase and suggestions on deformylase activities depending on different metal(II) centres. J Biol Inorg Chem 15, 195–201 (2010). https://doi.org/10.1007/s00775-009-0583-8

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  • DOI: https://doi.org/10.1007/s00775-009-0583-8

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