The reaction mechanism of type I phosphomannose isomerases: New information from inhibition and polarizable molecular mechanics studies

Authors

  • Céline Roux,

    1. Laboratoire de Chimie Bioorganique et Bioinorganique, ICMMO, Univ Paris-Sud, UMR 8182, Orsay F-91405, France
    2. CNRS, UMR 8182, Laboratoire de Chimie Bioorganique et Bioinorganique, ICMMO, Orsay, F-91405, France
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    • Current address: Département de Botanique et Biologie Végétale, Université de Genève, Sciences III, 30 quai E. Ansermet, CH-1211 Genève 4, Switzerland

  • Forum Bhatt,

    1. Laboratory for Molecular Biology, MC567, Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607
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    • Current address: Argonne National Laboratories, Biosciences division, 9700 S. Cass Avenue, Argonne, Illinois 60439

  • Johanna Foret,

    1. Laboratoire de Chimie Bioorganique et Bioinorganique, ICMMO, Univ Paris-Sud, UMR 8182, Orsay F-91405, France
    2. CNRS, UMR 8182, Laboratoire de Chimie Bioorganique et Bioinorganique, ICMMO, Orsay, F-91405, France
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  • Benoit de Courcy,

    1. UMR 7616, Laboratoire de Chimie Théorique, UPMC Univ Paris 06, F-75252, Paris Cedex 05, France
    2. CNRS, UMR 7616, Laboratoire de Chimie Théorique, F-75252, Paris Cedex 05, France
    3. Laboratoire de Chimie et Biochimie Pharmacologique et Toxicologique, CNRS UMR 8601, Univ Paris Descartes, F-75006, Paris, France
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  • Nohad Gresh,

    1. Laboratoire de Chimie et Biochimie Pharmacologique et Toxicologique, CNRS UMR 8601, Univ Paris Descartes, F-75006, Paris, France
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  • Jean-Philip Piquemal,

    1. UMR 7616, Laboratoire de Chimie Théorique, UPMC Univ Paris 06, F-75252, Paris Cedex 05, France
    2. CNRS, UMR 7616, Laboratoire de Chimie Théorique, F-75252, Paris Cedex 05, France
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  • Constance J. Jeffery,

    1. Laboratory for Molecular Biology, MC567, Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois 60607
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  • Laurent Salmon

    Corresponding author
    1. Laboratoire de Chimie Bioorganique et Bioinorganique, ICMMO, Univ Paris-Sud, UMR 8182, Orsay F-91405, France
    2. CNRS, UMR 8182, Laboratoire de Chimie Bioorganique et Bioinorganique, ICMMO, Orsay, F-91405, France
    • Université Paris-Sud, Laboratoire de Chimie Bioorganique et Bioinorganique, ICMMO, UMR 8182, bâtiment 420, 15 rue Georges Clemenceau, Orsay, F-91405, France
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Abstract

Type I phosphomannose isomerases (PMIs) are zinc-dependent metalloenzymes involved in the reversible isomerization of D-mannose 6-phosphate (M6P) and D-fructose 6-phosphate (F6P). 5-Phospho-D-arabinonohydroxamic acid (5PAH), an inhibitor endowed with nanomolar affinity for yeast (Type I) and Pseudomonas aeruginosa (Type II) PMIs (Roux et al., Biochemistry 2004; 43:2926–2934), strongly inhibits human (Type I) PMI (for which we report an improved expression and purification procedure), as well as Escherichia coli (Type I) PMI. Its K i value of 41 nM for human PMI is the lowest value ever reported for an inhibitor of PMI. 5-Phospho-D-arabinonhydrazide, a neutral analogue of the reaction intermediate 1,2-cis-enediol, is about 15 times less efficient at inhibiting both enzymes, in accord with the anionic nature of the postulated high-energy reaction intermediate. Using the polarizable molecular mechanics, sum of interactions between fragments ab initio computed (SIBFA) procedure, computed structures of the complexes between Candida albicans (Type I) PMI and the cyclic substrate β-D-mannopyranose 6-phosphate (β-M6P) and between the enzyme and the high-energy intermediate analogue inhibitor 5PAH are reported. Their analysis allows us to identify clearly the nature of each individual active site amino acid and to formulate a hypothesis for the overall mechanism of the reaction catalyzed by Type I PMIs, that is, the ring-opening and isomerization steps, respectively. Following enzyme-catalyzed ring-opening of β-M6P by zinc-coordinated water and Gln111 ligands, Lys136 is identified as the probable catalytic base involved in proton transfer between the two carbon atoms C1 and C2 of the substrate D-mannose 6-phosphate. Proteins 2010. © 2010 Wiley-Liss, Inc.

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