Crystal Structure of a Zinc-dependent d-Serine Dehydratase from Chicken Kidney*
Crystal Structure of a Zinc-dependent d-Serine Dehydratase from Chicken Kidney*
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鸡肾锌依赖性 d-丝氨酸脱水酶的晶体结构*
DOI：
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发表时间：
2011
影响因子：
4.8
通讯作者：
K. Horiike
中科院分区：
文献类型：
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作者：
Hiroyuki Tanaka;M. Senda;Nagarajan Venugopalan;A. Yamamoto;T. Senda;T. Ishida;K. Horiike
d-丝氨酸是 N-甲基-d-天冬氨酸受体的生理学共激动剂。它调节兴奋性神经传递，这对于脊椎动物的高级大脑功能很重要。在哺乳动物大脑中，d-氨基酸氧化酶降解 d-丝氨酸。然而，我们最近发现，鸡脑中不表达氧化酶，而是用 d-丝氨酸脱水酶降解 d-丝氨酸。该酶的一级结构与金属激活的 d-苏氨酸醛缩酶显着相似，后者是折叠型 III 吡哆醛 5'-磷酸 (PLP) 依赖性酶，表明它是一类新型 d-丝氨酸脱水酶。在本研究中，我们通过生化和 X 射线晶体学对鸡酶进行了表征。 EDTA 处理后 d-丝氨酸的酶活性降低了 20 倍，添加 Zn2+ 后几乎完全恢复。在超过 6000 次脱水催化循环期间，没有检测到 PLP-d-丝氨酸席夫碱副反应所预期的反应产物，这表明反应特异性很高。我们以 1.9 Å 的分辨率确定了 d-丝氨酸脱水酶的第一个晶体结构。在活性位点袋中，协调 His347 和 Cys349 的锌离子位于 PLP-Lys45 希夫碱附近。酶-d-丝氨酸复合物的理论模型表明，d-丝氨酸的羟基直接与锌离子配位，并且Lys45的ε-NH2基团与底物Cα原子的距离很短。 Lys45 从 d-丝氨酸中夺取 α-质子并消除羟基似乎是在锌离子的帮助下发生的，从而产生了严格的反应特异性。
d-Serine is a physiological co-agonist of the N-methyl-d-aspartate receptor. It regulates excitatory neurotransmission, which is important for higher brain functions in vertebrates. In mammalian brains, d-amino acid oxidase degrades d-serine. However, we have found recently that in chicken brains the oxidase is not expressed and instead a d-serine dehydratase degrades d-serine. The primary structure of the enzyme shows significant similarities to those of metal-activated d-threonine aldolases, which are fold-type III pyridoxal 5′-phosphate (PLP)-dependent enzymes, suggesting that it is a novel class of d-serine dehydratase. In the present study, we characterized the chicken enzyme biochemically and also by x-ray crystallography. The enzyme activity on d-serine decreased 20-fold by EDTA treatment and recovered nearly completely by the addition of Zn2+. None of the reaction products that would be expected from side reactions of the PLP-d-serine Schiff base were detected during the >6000 catalytic cycles of dehydration, indicating high reaction specificity. We have determined the first crystal structure of the d-serine dehydratase at 1.9 Å resolution. In the active site pocket, a zinc ion that coordinates His347 and Cys349 is located near the PLP-Lys45 Schiff base. A theoretical model of the enzyme-d-serine complex suggested that the hydroxyl group of d-serine directly coordinates the zinc ion, and that the ϵ-NH2 group of Lys45 is a short distance from the substrate Cα atom. The α-proton abstraction from d-serine by Lys45 and the elimination of the hydroxyl group seem to occur with the assistance of the zinc ion, resulting in the strict reaction specificity.