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首页> 外文期刊>Journal of Molecular Biology >Specific structural features of the N-acetylmuramoyl-L-alanine amidase AmiD from Escherichia coli and mechanistic implications for enzymes of this family.
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Specific structural features of the N-acetylmuramoyl-L-alanine amidase AmiD from Escherichia coli and mechanistic implications for enzymes of this family.

机译：来自大肠杆菌的N-乙酰基村酰基-L-丙氨酸酰胺酶AmiD的特定结构特征及其对该酶家族的影响。

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摘要

AmiD is the fifth identified N-acetylmuramoyl-L-alanine zinc amidase of Escherichia coli. This periplasmic lipoprotein is anchored in the outer membrane and has a broad specificity. AmiD is capable of cleaving the intact peptidoglycan (PG) as well as soluble fragments containing N-acetylmuramic acid regardless of the presence of an anhydro form or not, unlike the four other amidases, AmiA, AmiB, AmiC, and AmpD, which have some specificity. AmiD function is, however, not clearly established but it could be part of the enzymatic machinery involved in the PG turnover in E. coli. We solved three structures of the E. coli zinc amidase AmiD devoid of its lipidic anchorage: the holoenzyme, the apoenzyme in complex with the substrate anhydro-N-acetylmuramic-acid-L-Ala-gamma-d-Glu-L-Lys, and the holoenzyme in complex with the L-Ala-gamma-D-Glu-L-Lys peptide, the product of the hydrolysis of this substrate by AmiD. The AmiD structure shows a relatively flexible N-terminal extension that allows an easy reach of the PG by the enzyme inserted into the outer membrane. The C-terminal domain provides a potential extended geometrical complementarity to the substrate. AmiD shares a common fold with AmpD, the bacteriophage T7 lysozyme, and the PG recognition proteins, which are receptor proteins involved in the innate immune responses of a wide range of organisms. Analysis of the different structures reveals the similarity between the catalytic mechanism of zinc amidases of the AmiD family and the thermolysin-related zinc peptidases.
机译：AmiD是大肠杆菌中第五个鉴定出的N-乙酰基muramoyl-L-丙氨酸锌酰胺酶。这种周质脂蛋白锚定在外膜中，具有广泛的特异性。不论是否存在脱水形式，AmiD都能裂解完整的肽聚糖（PG）以及含有N-乙酰基山酰胺酸的可溶性片段，这与其他四个酰胺酶AmiA，AmiB，AmiC和AmpD不同，它们具有一些特异性。然而，AmiD功能尚未明确建立，但可能是参与大肠杆菌PG转化的酶促机制的一部分。我们解决了无脂锚定的大肠杆菌锌酰胺酶AmiD的三种结构：全酶，脱辅酶与基质脱水N-乙酰基村酰胺酸-L-Ala-γ-d-Glu-L-Lys复合，以及与L-Ala-γ-D-Glu-L-Lys肽复合的全酶，这是AmiD水解该底物的产物。 AmiD结构显示相对灵活的N端延伸，可通过插入外膜的酶轻松到达PG。 C末端结构域为底物提供了潜在的扩展的几何互补性。 AmiD与AmpD，噬菌体T7溶菌酶和PG识别蛋白具有相同的折叠，后者是参与多种生物体固有免疫应答的受体蛋白。对不同结构的分析揭示了AmiD家族的锌酰胺酶的催化机理与与嗜热菌蛋白酶相关的锌肽酶的相似性。

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