    1.2.1.26 | more |
molecular docking simulations of AbKGSADH with 2-oxoglutaric semialdehyde (alpha-KGSA) and succinate semialdehyde (SSA). Molecular docking simulations reveal that these two substrates fit well into the somewhat positively charged substrate binding pocket. The aldehyde-groups of these substrates, which are the sites of enzyme reaction, are located in the same place around the catalytic residues. The aldehyde-group of alpha-KGSA is stabilized by Gln160 and Arg163 through hydrogen bonds, and two catalytic residues, Glu253 and Cys287, also assist the binding of the molecule. The 4'-oxo-group of alpha-KGSA is stabilized by hydrogen bonds with Arg281, and the carboxyl-group of the molecule is stabilized by Glu106 and Gln160. The substrate binding pocket is also formed by several hydrophobic residues, such as Phe156, Val286, Ile288, Pro444, and Phe450, which seem to contribute to the stabilization of the hydrophobic part of alpha-KGSA. The binding of SSA is similar to that of alpha-KGSA, however, the stabilization of the carboxyl-group of SSA is quite different. Arg281, a residue that is involved in the stabilization of the 4'-oxo-group of alpha-KGSA, forms a hydrogen bond with the carboxyl-group of SSA instead. These observations explain how AbKGSADH can accommodate both alpha-KGSA and SSA as real substrates |
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