Nucleic Acids Research Advance Access originally published online on May 7, 2008
Nucleic Acids Research 2008 36(11):3620-3629; doi:10.1093/nar/gkn212
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Nucleic Acids Research, 2008, Vol. 36, No. 11 3620-3629
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
Molecular basis for the lack of enantioselectivity of human 3-phosphoglycerate kinase
1Centre d’études d’agents Pathogènes et Biotechnologies pour la Santé (CPBS), UMR 5236, CNRS–Universités Montpellier 1 et 2, Institut de Biologie, 4 bd Henri IV, CS69033, 34965 Montpellier cedex 2, 2Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS–Universités Montpellier 1 et 2, case courrier 1705, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier cedex 5, France, 3Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Karolina Strasse 29, H-1113 Budapest, Hungary, 4CNRS, UMR5048, Centre de Biochimie Structurale, 34090 Montpellier, 5INSERM, U554 and 6Universités Montpellier 1 et 2, 34090 Montpellier, France
*To whom correspondence should be addressed. Tel: +33 467 417 702; Fax: +33 467 417 913; Email: Stefan.Arold{at}cbs.cnrs.fr
Received January 25, 2008. Revised March 18, 2008. Accepted April 9, 2008.
Non-natural L-nucleoside analogues are increasingly used as therapeutic agents to treat cancer and viral infections. To be active, L-nucleosides need to be phosphorylated to their respective triphosphate metabolites. This stepwise phosphorylation relies on human enzymes capable of processing L-nucleoside enantiomers. We used crystallographic analysis to reveal the molecular basis for the low enantioselectivity and the broad specificity of human 3-phosphoglycerate kinase (hPGK), an enzyme responsible for the last step of phosphorylation of many nucleotide derivatives. Based on structures of hPGK in the absence of nucleotides, and bound to L and D forms of MgADP and MgCDP, we show that a non-specific hydrophobic clamp to the nucleotide base, as well as a water-filled cavity behind it, allows high flexibility in the interaction between PGK and the bases. This, combined with the dispensability of hydrogen bonds to the sugar moiety, and ionic interactions with the phosphate groups, results in the positioning of different nucleotides so to expose their diphosphate group in a position competent for catalysis. Since the third phosphorylation step is often rate limiting, our results are expected to alleviate in silico tailoring of L-type prodrugs to assure their efficient metabolic processing.