Nucleic Acids Research Advance Access originally published online on April 16, 2009
Nucleic Acids Research 2009 37(11):3714-3722; doi:10.1093/nar/gkp227
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Nucleic Acids Research, 2009, Vol. 37, No. 11 3714-3722
© 2009 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.
Nucleic Acids Enzymes |
Nucleotide analogs and molecular modeling studies reveal key interactions involved in substrate recognition by the yeast RNA triphosphatase
RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC, Canada J1H 5N4
*To whom correspondence should be addressed. Tel: +1 819 564 5287; Fax: +1 819 564 5340; Email: martin.bisaillon{at}usherbrooke.ca
Received January 13, 2009. Revised March 20, 2009. Accepted March 24, 2009.
RNA triphosphatases (RTPases) are involved in the addition of the distinctive cap structure found at the 5' ends of eukaryotic mRNAs. Fungi, protozoa and some DNA viruses possess an RTPase that belongs to the triphosphate tunnel metalloenzyme family of enzymes that can also hydrolyze nucleoside triphosphates. Previous crystallization studies revealed that the phosphohydrolase catalytic core is located in a hydrophilic tunnel composed of antiparallel β-strands. However, all past efforts to obtain structural information on the interaction between RTPases and their substrates were unsuccessful. In the present study, we used computational molecular docking to model the binding of a nucleotide substrate into the yeast RTPase active site. In order to confirm the docking model and to gain additional insights into the molecular determinants involved in substrate recognition, we also evaluated both the phosphohydrolysis and the inhibitory potential of an important number of nucleotide analogs. Our study highlights the importance of specific amino acids for the binding of the sugar, base and triphosphate moieties of the nucleotide substrate, and reveals both the structural flexibility and complexity of the active site. These data illustrate the functional features required for the interaction of an RTPase with a ligand and pave the way to the use of nucleotide analogs as potential inhibitors of RTPases of pathogenic importance.