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enzyme D-ManDH2 forms many hydrogen bonds with the 2-ketoacid moiety of AOA in the ternary complex structure, involving Asn105, Lys187, Asn191, Asn195 and Ser260, substrate binding structures in binary and tertiary complexes, structure and structure-function analysis, overview. The substrate binding induces a shear motion of the N-terminal domain along the C-terminal domain, following the hinge motion induced by the NADH binding, and allows the bound NADH molecule to form favorable interactions with a 2-oxoacid substrate. D-ManDH possesses a sufficiently wide pocket that accommodates the C3 branched side chains of substrates like KPR, but unlike the pocket of KPR, the pocket of D-ManDH comprises an entirely hydrophobic surface and an expanded space, in which the AOA benzene is accommodated. The expanded space mostly comprises a mobile loop structure, which likely modulates the shape and size of the space depending on the substrate. D-ManDH2 undergoes the opening and closing motion in the entrance area of the substrate binding pocket, which comprises mostly Met128, Thr130 and Ile254, between the binary and ternary complexes. Lys187 is actually the acid/base catalyst of the enzyme |
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