Midwest Center for Structural Genomics and Structural Biology Center, Argonne National Laboratory, Argonne, IL 60439, USA.
J Mol Biol. 2010 Apr 2;397(3):617-26. doi: 10.1016/j.jmb.2010.01.062. Epub 2010 Feb 4.
Biosynthesis of lysine and meso-diaminopimelic acid in bacteria provides essential components for protein synthesis and construction of the bacterial peptidoglycan cell wall. The dapE operon enzymes synthesize both meso-diaminopimelic acid and lysine and, therefore, represent potential targets for novel antibacterials. The dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase functions in a late step of the pathway and converts N-succinyl-L,L-diaminopimelic acid to L,L-diaminopimelic acid and succinate. Deletion of the dapE gene is lethal to Helicobacter pylori and Mycobacterium smegmatis, indicating that DapE's are essential for cell growth and proliferation. Since there are no similar pathways in humans, inhibitors that target DapE may have selective toxicity against only bacteria. A major limitation in developing antimicrobial agents that target DapE has been the lack of structural information. Herein, we report the high-resolution X-ray crystal structures of the DapE from Haemophilus influenzae with one and two zinc ions bound in the active site, respectively. These two forms show different activity. Based on these newly determined structures, we propose a revised catalytic mechanism of peptide bond cleavage by DapE enzymes. These structures provide important insight into catalytic mechanism of DapE enzymes as well as a structural foundation that is critical for the rational design of DapE inhibitors.
细菌中赖氨酸和中-二氨基庚二酸的生物合成为蛋白质合成和细菌肽聚糖细胞壁的构建提供了必需的成分。dapE 操纵子酶合成中-二氨基庚二酸和赖氨酸，因此代表了新型抗菌药物的潜在靶标。dapE 编码的 N-琥珀酰基-L,L-二氨基庚二酸脱琥珀酰基酶在该途径的后期步骤中发挥作用，将 N-琥珀酰基-L,L-二氨基庚二酸转化为 L,L-二氨基庚二酸和琥珀酸。dapE 基因的缺失对幽门螺杆菌和耻垢分枝杆菌是致命的，表明 DapE 对细胞生长和增殖是必需的。由于人类没有类似的途径，因此针对 DapE 的抑制剂可能对细菌具有选择性毒性。开发针对 DapE 的抗菌药物的主要限制是缺乏结构信息。在此，我们报告了分别与一个和两个锌离子结合在活性部位的流感嗜血杆菌 DapE 的高分辨率 X 射线晶体结构。这两种形式显示出不同的活性。基于这些新确定的结构，我们提出了 DapE 酶肽键裂解的修订催化机制。这些结构为 DapE 酶的催化机制提供了重要的见解，以及对 DapE 抑制剂的合理设计至关重要的结构基础。
