Student Abstracts: Biology at SLAC

Determination of the Chemical Structure of 3- Hydroxyisobutyrate Dehydrogenase (HIBADH) from Alcaligenes faecalis (Bacterium). RAJNESH NARAYAN (Contra Costa College, San Pablo, CA 94804) PAUL ELLIS (Stanford Linear Accelerator Center, Stanford, CA 94025) .
3- Hydroxyisobutyrate Dehydrogenase, commonly known as HIBADH, is a ubiquitous enzyme involved in valine catabolism. HIBADH is composed of approximately 300 amino acid residues, and has a molecular weight of 30,000. The organism from which the HIBADH being researched throughout this paper was extracted from a bacterium known as Alcaligenes faecalis. If the level of HIBADH in an organism is changed from its equilibrium, the process of valine catabolism is disturbed. Thus, leading to a fatality in an organism. This disturbance is not genetic. Rather, it is a spontaneous mutation. It would be of clinical and industrial advantage if the chemical structure of HIBADH could be determined. The chemical structure may give an understanding of how to overcome disturbance in the process of valine catabolism. While performing crystallization of an impure sample of Arsenite Oxidase from Alcaligenes faecalis, one HIBADH crystal was grown out of pure luck. Diffraction data was collected using this crystal. An electron density map from the data was calculated. Using the XtalView- Xfit program, amino acid residues making up the HIBADH structure were fit into their corresponding electron densities. The built HIBADH structure was refined for several cycles. Appropriate adjustments were made to the structure. The R factor decreased from a value of 36% to 34%. Because of the use of 2Å data, we would have expected to get a final R factor value of 20%. However, possible errors might have occurred leading towards this very high R factor value after refinement. Considerations might be an error in the unit cell symmetry, or possibly the fact that 1/10 of the structure was not accounted for.