Mechanism of Sugar Ring Contraction and Closure Catalyzed by UDP-d-apiose/UDP-d-xylose Synthase (UAXS)

Abstract

Uridine diphosphate (UDP)-apiose/UDP-xylose synthase (UAXS) is a member of the short-chain dehydrogenase/reductase superfamily (SDR), which catalyzes the ring contraction and closure of UDP-d-glucuronic acid (UDP-GlcA), affording UDP-apiose and UDP-xylose. UAXS is a special enzyme that integrates ring-opening, decarboxylation, rearrangement, and ring closure/contraction in a single active site. Recently, the ternary complex structure of UAXS was crystallized from Arabidopsis thaliana. In this work, to gain insights into the detailed formation mechanism of UDP-apiose and UDP-xylose, an enzyme–substrate reactant model has been constructed and quantum mechanical/molecular mechanical (QM/MM) calculations have been performed. Our calculation results reveal that the reaction starts from the C4–OH oxidation, which is accompanied by the conformational transformation of the sugar ring from chair type to boat type. The sugar ring-opening is prior to decarboxylation, and the deprotonation of the C2–OH group is the prerequisite for sugar ring-opening. Moreover, the keto–enol tautomerization of the decarboxylated intermediate is a necessary step for ring closure/contraction. Based on our calculation results, more UDP-apiose product was expected, which is in line with the experimental observation. Three titratable residues, Tyr185, Cys100, and Cys140, steer the reaction by proton transfer from or to UDP-GlcA, and Arg182, Glu141, and D337 constitute a proton conduit for sugar C2–OH deprotonation. Although Thr139 and Tyr105 are not directly involved in the enzymatic reaction, they are responsible for promoting the catalysis by forming hydrogen-bonding interactions with GlcA. Our calculations may provide useful information for understanding the catalysis of the SDR family.

Multiscale QM/MM modelling of catalytic systems with ChemShell

“…117 While most recent ChemShell protein studies have targeted metalloenzymes, QM/MM simulations are equally applicable to other types of enzymes. [118][119][120][121][122][123][124][125][126] Cantu ´Reinhard et al investigated the case of nogalamycin monoxygenase (NMO), which, unlike most other monooxygenases, is able to catalyse the oxidation of a substrate without either a metal or organic cofactor. QM/MM calculations revealed paths for activation of the substrate by triplet O 2 , giving insight into the NMO reaction mechanism.…”

Catalytic Mechanism of Pyridoxal 5′-Phosphate-Dependent Aminodeoxychorismate Lyase: A Computational QM/MM Study

“…In this work, the detailed mechanism was further investigated by performing quantum mechanics and molecular mechanics (QM/MM) calculations. The QM/MM method has been successfully applied in exploring the enzymatic mechanisms in past years. − Based on our calculations, the reaction details, including the transamination reaction of PLP, the release of pyruvate, and the recovery of the initial PLP internal aldimine with the lysine, were all given, which contain 11 elementary steps. Besides, ADCL is one of the most complex PLP-dependent enzymes, and thus, this study may provide a reactant template for understanding the catalysis of PLP-dependent enzymes.…”