Molecular Mechanism of Allosteric Substrate Activation in a Thiamine Diphosphate-dependent Decarboxylase

Abstract

Thiamine diphosphate-dependent enzymes are involved in a wide variety of metabolic pathways. The molecular mechanism behind active site communication and substrate activation, observed in some of these enzymes, has since long been an area of debate. Here, we report the crystal structures of a phenylpyruvate decarboxylase in complex with its substrates and a covalent reaction intermediate analogue. These structures reveal the regulatory site and unveil the mechanism of allosteric substrate activation. This signal transduction relies on quaternary structure reorganizations, domain rotations, and a pathway of local conformational changes that are relayed from the regulatory site to the active site. The current findings thus uncover the molecular mechanism by which the binding of a substrate in the regulatory site is linked to the mounting of the catalytic machinery in the active site in this thiamine diphosphate-dependent enzyme.

Production of Aromatic Compounds by Metabolically Engineered Escherichia coli with an Expanded Shikimate Pathway

“…The enzyme encoded by the ipdC gene derived from Azospirillum brasilense has been extensively investigated, and its threedimensional structure has been published (35,42). The enzyme acts not only on PP but also on 4HPP to produce the corresponding aldehydes.…”

Progress in the experimental observation of thiamin diphosphate-bound intermediates on enzymes and mechanistic information derived from these observations

“…By virtue of the neutral ring in place of the positively charged thiazolium ring, the authors suggested that this would serve as an electrostatic mimic of the carbene [57,58]. Later the thiazolium ring was replaced by a triazole ring in yet a different mimic of a neutral 5-membered ring [59].…”

“…The 3-deazaThDP synthesized by the Leeper group enabled observation of the MM complex with substrates in a E1p from Geobacillus stearothermophilus [57] and in indolepyruvate decarboxylase [58] and the residues important in maintaining the MM complex. On L. plantarum POX, there was significant concentration of LThDP found in the active centers [41] after acidification and precipitation of protein.…”

Auxin and Plant-Microbe Interactions

“…In A. brasilense, the decarboxylase can use both indole-3-pyruvate and phenylpyruvate as substrates ). In addition, the crystal structure of both indole-3-pyruvate decarboxylases has been determined (Schütz et al 2003b;Versées et al 2007a;Versées et al 2007b). …”