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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)

Probing the chemistries of the substrate and flavin ring system of p-hydroxybenzoate hydroxylase by raman difference spectroscopy.

Details of the substrate, p-hydroxybenzoate, and substrate analog, p-aminobenzoate, binding to p-hydroxybenzoate hydroxylase have been elicited by Raman difference spectroscopy. Deep red (752 nm) excitation was used to avoid interference from a fluorescence background. The Raman data provide information on changes in the ligand upon binding as well as changes in the flavin ring system of the enzyme in the enzyme-substrate complex. For p-aminobenzoate, its three most intense Raman features, due to a phenyl mode (1607 cm-1) and carboxylate stretching (1383 cm-1) and scissoring (863 cm-1) motions, are little perturbed upon binding and show no changes in the pH range 6.5-8. 5. However, changes in a number of spectral features associated with isoalloxazine modes in this pH range are evidence for a protonation/deprotonation event occurring in or near the active site. A feature in the difference spectrum of the complex at 1700 cm-1 is assigned to the stretch of the 4C&dbd;O group of the isoalloxazine; the relatively narrow profile of this feature is due to the ring being held in a rigid network of hydrogen bonds as demonstrated by the X-ray-derived structure [Schreuder, H. A., Prick, P. A. J., Wierenga, R. K., Vriend, G., Wilson, K. S., Hol, W. G. J., & Drenth, J. (1989) J. Mol. Biol. 208, 679-696]. The absence of a corresponding negative band in the spectrum near 1725 cm-1 shows that in the enzyme, in the absence of ligand, the 4C&dbd;O peak is "washed out" by a fluctuating series of hydrogen bonds to water molecules which penetrate to the flavin ring, resulting in a broad C&dbd;O stretching feature which escapes detection in the difference spectrum. For p-hydroxybenzoate, upon complexation, the -COO- symmetric stretch shifts 10 cm-1, which is ascribed to the formation of the salt bridge to the guanidinium of Arg 214, seen in the X-ray structure. This is in contrast with the results for the complex involving the p-amino analog where no shift in the carboxylate mode is detected and demonstrates an advantage of using vibrational spectroscopy as a fine probe of active site interactions, since the X-ray structures for the p-amino and p-hydroxy analog complexes indicate that the structures in the -COO- group guanidinium regions are the same. The Raman difference data for the substrate complex in the 1700 cm-1 region closely resemble those for the p-amino analog, indicating that in both cases the 4C&dbd;O group is participating in a rigid hydrogen bonding network in the complexes with ligand but is in a more dynamic hydrogen bonding environment involving water molecules in the unliganded enzyme. In order to measure the pKa of the -OH group in bound p-hydroxybenzoate, the substrate was labeled with 18O in both -COO- oxygen atoms. By subtracting the Raman spectrum of the complex with labeled substrate from that with unlabeled substrate, a simple difference spectrum was obtained with features involving the -COO- group alone. These features were used to measure the pKa of the ring hydroxyl group which was found to be 8. 3. The value determined from absorption spectroscopy is 7.4, and possible reasons for the discrepancy are discussed. Both methods are in accord, however, in that they show that the pKa of the bound substrate is substantially below that for the free, a device which assists in the hydroxylation at the 3-position.[1]


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