Gamma glutamyl semialdehyde dehydrogenase: Simulations on native and mutant forms support the importance of outer shell lysines

Our computer simulations of gamma glutamyl semialdehyde dehydrogenase (GGSALDH, pyrroline 5-carboxylate dehydrogenase, ALDH4) were initiated from the Thermus thermophilus crystal structures in an effort to understand the effects of a seemingly subtle mutation. In humans, a natural S352L mutation gives rise to type II hyperprolinemia (mental retardation). The mutation occurs in what might be a priori considered the outer shell of the active site, affecting a residue of no obvious significance. In another member of the superfamily (ALDH3) this serine residue is an aspartate, which tethers the “distal” Lys. It has been our hypothesis that in ALDH3 this is a beneficial interaction, enabling the “proximal” Lys to interact with the carbonyl oxygen of the peptide bond with the catalytic Cys, allowing the Cys amide N to transiently protonate the tetrahedral intermediate. That the role of this Asp is significant is proved by a natural Asp-to-Asn mutation that abolishes activity.The Ser-to-Leu exchange in GGSALDH might be expected to alter the water structure at the site of mutation, and the MM simulations clearly support this. It was our hypothesis, based on initial static models of the mutation, that the leucyl side chain would block the direct or indirect interaction of the distal Lys with the active site. Our simulations indicate that this lysine residue is indeed important in explaining the molecular pathology of the mutation. Through small rotations of its C–C bonds, the Lys ɛ-amino group comes into H-bonding distance with Ser-326, the equivalent of human Ser-352. In the S326L mutant, this interaction is not possible, while the water network from this residue to the target main-chain carbonyl oxygen is disturbed as well.