Protein degradation by aminopeptidases is involved in bacterial responses to stress. Escherichia coli produces two metal‐dependent M17 family leucine aminopeptidases (LAPs), aminopeptidase A (PepA) and aminopeptidase B (PepB). Several structures have been solved for PepA as well as other bacterial M17 peptidases. Herein, we report the first structures of a PepB M17 peptidase. The E. coli PepB protein structure was determined at a resolution of 2.05 and 2.6 Å. One structure has both Zn²⁺ and Mn²⁺, while the second structure has two Zn²⁺ ions bound to the active site. A 2.75 Å apo structure is also reported for PepB from Yersinia pestis . Both proteins form homohexamers, similar to the overall arrangement of PepA and other M17 peptidases. However, the divergent N‐terminal domain in PepB is much larger resulting in a tertiary structure that is more expanded. Modeling of a dipeptide substrate into the C‐terminal LAP domain reveals contacts that account for PepB to uniquely cleave after aspartate.

中文翻译：

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大肠杆菌和鼠疫耶尔森氏菌氨基肽酶B蛋白的金属结合和未结合结构比较。

氨基肽酶引起的蛋白质降解与细菌对压力的反应有关。大肠杆菌产生两种金属依赖性的M17家族亮氨酸氨基肽酶（LAPs），氨基肽酶A（PepA）和氨基肽酶B（PepB）。PepA以及其他细菌M17肽酶的几种结构均已解决。在这里，我们报告PepB M17肽酶的第一个结构。将大肠杆菌在2.05和2.6埃的分辨率测定PepB蛋白质结构。一种结构同时具有Zn ²⁺和Mn ²⁺，而第二种结构具有与活性位点结合的两个Zn ²⁺离子。还报道了鼠疫耶尔森菌的PepB具有2.75Åapo结构。两种蛋白质均形成同型六聚体，类似于PepA和其他M17肽酶的总体排列。但是，PepB中不同的N末端结构域要大得多，从而导致三级结构进一步扩展。将二肽底物建模到C末端LAP结构域中，揭示了导致PepB在天冬氨酸后独特裂解的接触。