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

Abstract

Introduction: 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.
Methods: 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.
Results: 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.
Conclusions: Since there currently is no crystal structure available for the B. badius PheDH, the sequence was folded over the 1BW9 crystal structure and superimposed over the original scaffold using SuperPose.