Crystal structures of γ-glutamylmethylamide synthetase provide insight into bacterial metabolism of oceanic monomethylamine.
Crystal structures of γ-glutamylmethylamide synthetase provide insight into bacterial metabolism of oceanic monomethylamine.
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γ-谷氨酰甲基酰胺合成酶的晶体结构提供了对海洋一甲胺的细菌代谢的深入了解。
DOI：
10.1074/jbc.ra120.015952
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发表时间：
2021-01
期刊：
影响因子：
--
通讯作者：
Li CY
中科院分区：
文献类型：
--
作者：
Wang N;Chen XL;Gao C;Peng M;Wang P;Zhang N;Li F;Yang GP;Shen QT;Li S;Chen Y;Zhang YZ;Li CY
单甲胺(MMA)是一种重要的海洋痕量气候气体，广泛存在于海洋中。γ-谷氨酰甲酰胺合成酶(GMAS)催化甲基丙烯酸甲酯转化为γ-谷氨酰甲酰胺，这是许多海洋细菌代谢的第一步。∼基因存在于海洋表层23%的微生物基因组中，是检测利用甲基丙烯酸甲酯细菌的有效生物标志物。然而，由于缺乏结构信息，GMAs的催化机理还没有得到研究。在这里，从红假单胞菌中分离到了GMA。对12E13(RhGmaS)进行了表征，解析了apo-RhGmaS和不同配体的RhGmaS在五种状态下的晶体结构。结合结构分析和生化分析，对RhGmaS的催化机理进行了解释。ATP首先与RhGmaS结合，导致一个柔性环(Lys287-Ile305)的构象变化，这对随后的谷氨酸结合是必不可少的。在RhGmaS的催化过程中，Arg312残基参与极化三磷酸腺苷的γ-磷酸，稳定γ-谷氨酰磷酸中间体；Asp177负责甲基丙烯酸甲酯的去质子化，协助甲基丙烯酸甲酯攻击γ-谷氨酰磷酸生成四面体中间体；Glu186作为催化碱从四面体中间体中提取质子，最终生成谷氨酰胺。序列分析表明，本研究提出的RhGmaS的催化机制在含GMAs的细菌中具有普遍意义。我们的结果为MMA代谢提供了新的见解，有助于更好地理解MMA在全球碳和氮循环中的分解代谢。
Monomethylamine (MMA) is an important climate-active oceanic trace gas and ubiquitous in the oceans. γ-Glutamylmethylamide synthetase (GmaS) catalyzes the conversion of MMA to γ-glutamylmethylamide, the first step in MMA metabolism in many marine bacteria. The gmaS gene occurs in ∼23% of microbial genomes in the surface ocean and is a validated biomarker to detect MMA-utilizing bacteria. However, the catalytic mechanism of GmaS has not been studied because of the lack of structural information. Here, the GmaS from Rhodovulum sp. 12E13 (RhGmaS) was characterized, and the crystal structures of apo-RhGmaS and RhGmaS with different ligands in five states were solved. Based on structural and biochemical analyses, the catalytic mechanism of RhGmaS was explained. ATP is first bound in RhGmaS, leading to a conformational change of a flexible loop (Lys287-Ile305), which is essential for the subsequent binding of glutamate. During the catalysis of RhGmaS, the residue Arg312 participates in polarizing the γ-phosphate of ATP and in stabilizing the γ-glutamyl phosphate intermediate; Asp177 is responsible for the deprotonation of MMA, assisting the attack of MMA on γ-glutamyl phosphate to produce a tetrahedral intermediate; and Glu186 acts as a catalytic base to abstract a proton from the tetrahedral intermediate to finally generate glutamylmethylamide. Sequence analysis suggested that the catalytic mechanism of RhGmaS proposed in this study has universal significance in bacteria containing GmaS. Our results provide novel insights into MMA metabolism, contributing to a better understanding of MMA catabolism in global carbon and nitrogen cycles.