ODCase active site yeast

Fig. 4 Schematic representation of the yeast ODCase active site, showing contacts formed between the enzyme and bound 6-hydroxyuridine 5 -phosphate (BMP). Hydrogen bonding distances were measured between electronegative atoms... 

Fig. 6 Schematic representation of the yeast ODCase active site, depicting the effects on transition state binding affinity of replacing individual active site residues with alanine. Free energy contributions (AAG) of individual interactions were calculated from the decrease in catalytic efficiency (/Ccat/ m) produced upon mutation to alanine. The sum of individual mutations totals more than 45 kcal/mol of binding free energy...

After the initial crystal structures of ODCase were reported, a modified 04 protonation mechanism was proposed [22]. In the original Lee-Houk proposal, the active-site residue Lys93 (yeast numbering, analogous to Lys72 in E, coli Fig. 4 and Table 2), which was experimentally shown to be catalyt-ically important, was assumed to be the species that protonated 04 [27, 32]. However, in the reported crystal structures this lysine does not reside near 04. It was therefore proposed that proton transfer from Lys93 to 04 might be mediated by an active site water molecule (see Fig. 7). The viability of this scenario has not yet been established, however. 

Fig. 5 Results of molecular docking simulations of UMP (upper left), BMP (lower left), OMP (lower right), and 2-thioOMP (upper right) at the active site of yeast ODCase, with reference to Lys93, using MOE...

How can a theoretical method decide between proposed mechanisms, and how can the origin of the enzymatic power be identified This review will try to answer these questions for one particular theoretical approach, the one where an active site model is treated by accurate quantum mechanical (QM) methods. The main idea in the QM active site approach is to make sure that the computational results have the required accuracy. During the last decade the accuracy of density functional methods (DFT) has been dramatically improved, and in particular the hybrid B3LYP functional has achieved a remarkable accuracy [8, 9]. The use of DFT has also made it possible to treat dramatically larger molecular systems than can be done with conventional wave-function methods of similar accuracy. In spite of this important development, DFT models have usually been limited to 50-60 atoms, but more recently systems with more than 100 atoms have been treated efficiently. Still, even 100 atoms is a very small part of the total number of 8,300 atoms in yeast ODCase, not counting hydrogens or surrounding water molecules. Thus a very severe selection has to be made when the enzyme model is set up, and an important task is to select the residues required to solve the mechanism and to analyze all important contributions. 

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