Department of Chemistry, University of Konstanz, Konstanz, 78457, Germany.
Konstanz Research School Chemical Biology (KoRS-CB), Konstanz, 78457, Germany.
Nat Commun. 2018 Nov 29;9(1):5071. doi: 10.1038/s41467-018-07563-6.
Lysine degradation has remained elusive in many organisms including Escherichia coli. Here we report catabolism of lysine to succinate in E. coli involving glutarate and L-2-hydroxyglutarate as intermediates. We show that CsiD acts as an α-ketoglutarate-dependent dioxygenase catalysing hydroxylation of glutarate to L-2-hydroxyglutarate. CsiD is found widespread in bacteria. We present crystal structures of CsiD in complex with glutarate, succinate, and the inhibitor N-oxalyl-glycine, demonstrating strong discrimination between the structurally related ligands. We show that L-2-hydroxyglutarate is converted to α-ketoglutarate by LhgO acting as a membrane-bound, ubiquinone-linked dehydrogenase. Lysine enters the pathway via 5-aminovalerate by the promiscuous enzymes GabT and GabD. We demonstrate that repression of the pathway by CsiR is relieved upon glutarate binding. In conclusion, lysine degradation provides an important link in central metabolism. Our results imply the gut microbiome as a potential source of glutarate and L-2-hydroxyglutarate associated with human diseases such as cancer and organic acidurias.
赖氨酸降解在包括大肠杆菌在内的许多生物体中仍然难以捉摸。在这里，我们报告了大肠杆菌中赖氨酸分解为琥珀酸的过程，涉及戊二酸和 L-2-羟基戊二酸作为中间产物。我们表明 CsiD 作为一种依赖α-酮戊二酸的双加氧酶，催化戊二酸的羟化生成 L-2-羟基戊二酸。CsiD 在细菌中广泛存在。我们展示了 CsiD 与戊二酸、琥珀酸和抑制剂 N-草酰基甘氨酸复合物的晶体结构，证明了对结构相关配体的强烈区分。我们表明，L-2-羟基戊二酸通过 LhgO 转化为α-酮戊二酸，LhgO 作为一种膜结合的、与泛醌相连的脱氢酶。赖氨酸通过混杂酶 GabT 和 GabD 进入途径通过 5-氨基戊酸。我们证明，CsiR 对途径的阻遏作用在戊二酸结合时得到缓解。总之，赖氨酸降解为中心代谢提供了一个重要的联系。我们的结果表明肠道微生物组可能是与癌症和有机酸血症等人类疾病相关的戊二酸和 L-2-羟基戊二酸的潜在来源。
