The molecular basis for sulfite oxidation in a bacterial sulfite dehydrogenase from Starkeya novella

Trevor Rapson (2009). The molecular basis for sulfite oxidation in a bacterial sulfite dehydrogenase from Starkeya novella PhD Thesis, School of Chemistry & Molecular Bioscience, The University of Queensland.

       
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Author Trevor Rapson
Thesis Title The molecular basis for sulfite oxidation in a bacterial sulfite dehydrogenase from Starkeya novella
School, Centre or Institute School of Chemistry & Molecular Bioscience
Institution The University of Queensland
Publication date 2009-12
Thesis type PhD Thesis
Supervisor Prof Paul Bernhardt
Dr Ulrike Kappler
Total pages 204
Total colour pages 23
Total black and white pages 181
Subjects 03 Chemical Sciences
Abstract/Summary Sulfite oxidising enzymes are found in all forms of life and play an important role in detoxification of sulfite produced through biochemical processes. All known sulfite oxidising enzymes share a common molybdenum active site. The sulfite dehydrogenase (SDH) from the soil bacterium Starkeya novella differs from the vertebrate sulfite oxidases (SO) in that the heme and Mo subunits are tightly associated rather than connected by a flexible hinge. This structural integrity makes SDH an ideal model enzyme for the study of enzymatic sulfite oxidation without the complications of structural changes underlying catalysis. In human sulfite oxidase (HSO) the substitution of a conserved active site amino acid residue, Arg-160 for Gln, results in a lethal disease. A number of independent studies have been carried out in order to understand the effects of this substitution on catalysis in both human (HSO) and chicken sulfite oxidising enzymes (CSO). The focus of this work is the analogous residue in SDH, Arg 55. A number of active site substitutions have been investigated, including SDHR55Q, an analogous substitution to the lethal mutation identified in humans. In addition, the properties of the Arg residue have also been probed using a substitution to a hydrophobic residue, Met (SDHR55M) and a substitution to the positively charged Lys (SDHR55K). A fourth active site substitution, SDHH57A, was also investigated as the crystal structure of this variant indicated that His-57 plays a role in stabilising the position of Arg-55 in SDH. It was of interest to determine the effect of the instability in the position of Arg-55 on the catalytic parameters of the SDHH57A. The kinetic properties of the substituted enzymes were investigated using steady-state assays with cytochrome c as an electron acceptor. When the positive charge was lost in the case of SDHR55M and SDHR55Q, a dramatic increase in the KM (sulfite - app) of 2 – 3 orders of magnitude resulted. This indicates that the positive charge on Arg-55 is important for substrate binding. All the Arg-55 variants studied were found to have lower turnover numbers than the wild type, in particular, SDHR55Q was found to have a reduced kcat (108 s-1 vs 345 s-1 for SDHWT at pH 8). The changes in the Mo centre underlying the altered kinetic properties were investigated in detail using EPR spectroscopy of the intermediate MoV oxidation state in SDHR55Q and SDHH57A. Similar to what has been noted for HSOR160Q, a sulfate blocked form was observed at pH 6 using pulsed EPR experiments, suggesting that this substitution causes an inhibition of the hydrolysis step required to release the reaction product, sulfate. This could be a further reason for the poor catalytic activity of SDHR55Q, in particular, a reason for the low turnover rate of this variant. Unlike what was noted in HSOR160Q, where the substituted enzyme showed a dramatic decrease in rate of intramolecular transfer by three orders of magnitude compared to HSOWT, the rate of electron transfer was found to be 3 times faster in SDHR55Q relative to the wild type enzyme. These results indicate that Arg-55 is not involved in the pathway of electron transfer between the Mo and heme centres, but rather assists with the the docking of the heme group in HSO. As this process is not required in SDH, our results suggest that intramolecular electron transfer (IET) in HSOR160Q decreases because it is crucial for docking of the heme domain. Through potentiometric redox titrations, the effect of the active site amino acid substitutions on both the Mo and Fe redox potentials was investigated. No significant change was determined for the MoVI/V redox potentials, however, the heme potentials for SDHWT and SDHR55K were 40 mV higher than those of the other variants, with the lowest potentials belonging to SDHR55M and SDHH57A. Of further interest was that the MoVI/V couple is significantly lower than the heme couple (175 mV vs 240 mV respectively) in SDHWT. It appears that the positive charge of the Arg is important in regulating the heme redox potentials and could thereby contribute to modulating enzymatic activity. When SDH was immobilised on a modified pyrolytic graphite electrode, stable and high catalytic currents were observed, indicating facile heterogeneous electron transfer between the enzyme and the electrode. This good electron transfer allowed the catalytic properties of SDH and its substituted enzymes to be investigated as a function of potential. A pH dependence ( 59 mV/pH) in the catalytic operating potential was noted for SDHWT and SDHR55K, which appears to follow the pH dependence of the MoVI/V couple. This catalytic potential is pH-independent in the R55M and H57A variants, where the catalytic operating potentials appeared to follow the FeIII/II redox couple. It is proposed that two distinct pathways of electron transfer from the Mo centre to the electrode are likely to exist. The first is direct transfer from the Mo centre to the electrode at lower potential (~ 175 mV) while the second proceeds via the heme group (320 mV). The pathway followed is determined by the oxidation state of the heme group. A slight difference in the electron transfer rates of these two processes was seen, with direct transfer (from Mo) being the faster, which accounts for the unusual peak shape noted in the voltammogram for SDHWT at high sulfite concentrations, where the rate of catalytic activity slows at a higher potentials despite the greater thermodynamic driving force. This work provides new insights into the mechanism of enzymatic sulfite oxidation. Arg-55 has been shown to play an important role in the catalytic functioning of SDH in both substrate affinity and product release. Unlike what has been previously proposed, Arg-55 does not play a part in the pathway of electron transfer, but is rather involved in the regulation of the redox potentials of the metal centres in the enzyme.
Keyword Molybdenum Enzyme
electrochemistry
electron paramagnetic resonance
laser flash photolysis
enzyme kinetics
Additional Notes 30,36,43,49,50,67,82,87,89,92,93,101,103,117,119,126,136,139,145,168,174,180,183

 
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