The crystal structure of human Atg4b, a processing and de-conjugating enzyme for autophagosome-forming modifiers
The crystal structure of human Atg4b, a processing and de-conjugating enzyme for autophagosome-forming modifiers
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DOI：
10.1016/j.jmb.2005.11.018
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发表时间：
2006-01-27
影响因子：
5.6
通讯作者：
Yamane, T
中科院分区：
文献类型：
--
作者：
Kumanomidou, T;Mizushima, T;Yamane, T
自噬是一种进化上保守的途径，其中细胞质和细胞器被吞噬在称为自噬体的双膜囊泡中，以进行这些细胞成分的周转和再循环。酵母at8及其人类同源物，如LC3和GABARAP，具有独特的特征，它们与磷脂共价结合，不同于泛素和其他泛素样修饰剂，它们只附着在蛋白质底物上。脂化的at8和LC3定位于自噬体膜，对自噬体的成熟起着不可或缺的作用。在自噬体形成完成后，脂化的at8和LC3的一些种群被降解以进行再循环。Atg4b是LC3和GABARAP的特异性蛋白酶，可催化LC3和GABARAP前体的加工反应和磷脂修饰剂的解偶联反应。Atg4b是一种独特的酶，其初级结构不同于任何其他作为泛素和泛素样修饰物加工和/或脱偶联酶的蛋白酶。然而，底物的三级结构除了n端附加结构域外，与泛素相当相似。本文利用x射线晶体学技术在2.0埃分辨率下测定了人Atg4b的晶体结构，表明Atg4b是一种半胱氨酸蛋白酶，其活性催化位点由Cys74、His280和Asp278组成。该结构由一个左叶和一个小的右叶组成，分别称为“蛋白酶结构域”和“辅助结构域”。虽然Atg4b的蛋白酶结构域与木瓜蛋白酶超家族半胱氨酸蛋白酶的结构域相匹配，但辅助结构域包含一个独特的结构域，其功能尚不清楚。我们认为Atg4b中的R229和W142残基对于识别底物和催化磷脂前体加工和解偶联是特别重要的。(c) 2005 Elsevier Ltd版权所有。
Autophagy is an evolutionarily conserved pathway in which the cytoplasm and organelles are engulfed within double-membrane vesicles, termed autophagosomes, for the turnover and recycling of these cellular constituents. The yeast Atg8 and its human orthologs, such as LC3 and GABARAP, have a unique feature as they conjugate covalently to phospholipids, differing from ubiquitin and other ubiquitin-like modifiers that attach only to protein substrates. The lipidated Atg8 and LC3 localize to autophagosomal membranes and play indispensable roles for maturation of autophagosomes. Upon completion of autophagosome formation, some populations of lipidated Atg8 and LC3 are delipidated for recycling. Atg4b, a specific protease for LC3 and GABARAP, catalyzes the processing reaction of LC3 and GABARAP precursors to mature forms and de-conjugating reaction of the modifiers from phospholipids. Atg4b is a unique enzyme whose primary structure differs from that of any other proteases that function as processing and/or de-conjugating enzymes of ubiquitin and ubiquitin-like modifiers. However, the tertiary structures of the substrates considerably resemble that of ubiquitin except for the N-terminal additional domain. Here we determined the crystal structure of human Atg4b by X-ray crystallography at 2.0 angstrom resolution, and show that Atg4b is a cysteine protease whose active catalytic triad site consists of Cys74, His280 and Asp278. The structure is comprised of a left lobe and a small right lobe, designated the "protease domain" and the "auxiliary domain", respectively. Whereas the protease domain structure of Atg4b matches that of papain superfamily cysteine proteinases, the auxiliary domain contains a unique structure with yet-unknown function. We propose that the R229 and W142 residues in Atg4b are specifically essential for recognition of substrates and catalysis of both precursor processing and de-conjugation of phospholipids. (c) 2005 Elsevier Ltd. All rights reserved.