Evaluation of the Active Site of Phenylalanine Dehydrogenase Isolated from Bacillus badius using Homology Based Modeling

The enzyme, Phenylalanine dehydrogenase (L-phe DH; NAD oxidoreductase, deaminating; EC 1.4.1.20) belongs to the amino acid dehydrogenase family of enzymes which catalyzes the reversible oxidative deamination reaction of L-phenylalanine to their respective α- ketoacids. An assay technique with a high sensitivity for blood L-phenylalanine level, an important marker for the screening of Phenylketonuria (PKU), has been established by means of PheDH. This enzyme is being used as a commercial and valuable biocatalyst in medical and pharmaceutical industries. The enzymes of this family are closely related in structure and function. Swiss-Pdb Viewer used for analysis and Rhodococcus sp. M4 was chosen because of the availability of several crystal structures with bound substrates and its high specific activity. Rhodococcus sp. M4 and B. badius PheDHs are very different from each other on a sequence level, sharing only %32 identity and %50 similarity. Coming from the same structural sub-family, they share a much stronger correlation in their folding motifs. Since there currently is no crystal structure available for the B. badius PheDH, the sequence was folded over the 1BW9 crystal structure and superimposedover the original scaffold using SuperPose.