D-Apiose is a C-branched pentose sugar important for plant cell wall development. Its biosynthesis as UDP-D-apiose involves decarboxylation of the UDP-D-glucuronic acid precursor coupled to pyranosyl-to-furanosyl sugar ring contraction. This unusual multistep reaction is catalyzed within a single active site by UDP-D-apiose/UDP-D-xylose synthase (UAXS). Here, we decipher the UAXS catalytic mechanism based on crystal structures of the enzyme from Arabidopsis thaliana, molecular dynamics simulations expanded by QM/MM calculations, and mutational-mechanistic analyses. Our studies show how UAXS uniquely integrates a classical catalytic cycle of oxidation and reduction by a tightly bound nicotinamide coenzyme with retro-aldol/aldol chemistry for the sugar ring contraction. They further demonstrate that decarboxylation occurs only after the sugar ring opening and identify the thiol group of Cys100 in steering the sugar skeleton rearrangement by proton transfer to and from the C3'. The mechanistic features of UAXS highlight the evolutionary expansion of the basic catalytic apparatus of short-chain dehydrogenases/reductases for functional versatility in sugar biosynthesis.

中文翻译：

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破译UDP-apiose生物合成中糖环收缩的酶促机制。

D-Apiose 是一种对植物细胞壁发育很重要的 C 支化戊糖。其作为 UDP-D-apiose 的生物合成涉及 UDP-D-葡萄糖醛酸前体的脱羧与吡喃糖基到呋喃糖基糖环收缩偶联。这种不寻常的多步反应由 UDP-D-apiose/UDP-D-木糖合酶 (UAXS) 在单个活性位点内催化。在这里，我们根据拟南芥酶的晶体结构、通过 QM/MM 计算扩展的分子动力学模拟和突变机制分析来破译 UAXS 催化机制。我们的研究表明，UAXS 如何通过紧密结合的烟酰胺辅酶独特地整合经典的氧化和还原催化循环，以及用于糖环收缩的逆醛醇/醛醇化学。他们进一步证明了脱羧仅在糖开环后发生，并确定了 Cys100 的硫醇基团通过质子转移到 C3' 和从 C3' 转移来控制糖骨架重排。UAXS 的机制特征突出了短链脱氢酶/还原酶的基本催化装置的进化扩展，以实现糖生物合成中的多功能性。