State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China.
School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China.
Nat Commun. 2023 Oct 20;14(1):6638. doi: 10.1038/s41467-023-42456-3.
Mammalian lactate dehydrogenase D (LDHD) catalyzes the oxidation of D-lactate to pyruvate. LDHD mutations identified in patients with D-lactic acidosis lead to deficient LDHD activity. Here, we perform a systematic biochemical study of mouse LDHD (mLDHD) and determine the crystal structures of mLDHD in FAD-bound form and in complexes with FAD, Mn and a series of substrates or products. We demonstrate that mLDHD is an Mn-dependent general dehydrogenase which exhibits catalytic activity for D-lactate and other D-2-hydroxyacids containing hydrophobic moieties, but no activity for their L-isomers or D-2-hydroxyacids containing hydrophilic moieties. The substrate-binding site contains a positively charged pocket to bind the common glycolate moiety and a hydrophobic pocket with some elasticity to bind the varied hydrophobic moieties of substrates. The structural and biochemical data together reveal the molecular basis for the substrate specificity and catalytic mechanism of LDHD, and the functional roles of mutations in the pathogenesis of D-lactic acidosis.
哺乳动物乳酸脱氢酶 D（LDHD）催化 D-乳酸氧化为丙酮酸。在 D-乳酸酸中毒患者中鉴定的 LDHD 突变导致 LDHD 活性不足。在这里，我们对小鼠 LDHD（mLDHD）进行了系统的生化研究，并确定了 FAD 结合形式和与 FAD、Mn 以及一系列底物或产物结合的 mLDHD 的晶体结构。我们证明 mLDHD 是一种依赖 Mn 的一般脱氢酶，它对 D-乳酸和其他含有疏水性部分的 D-2-羟基酸表现出催化活性，但对其 L-异构体或含有亲水性部分的 D-2-羟基酸没有活性。底物结合位点包含一个带正电荷的口袋以结合常见的乙醇酸部分和一个具有一定弹性的疏水性口袋以结合底物的不同疏水性部分。结构和生化数据共同揭示了 LDHD 的底物特异性和催化机制的分子基础，以及突变在 D-乳酸酸中毒发病机制中的功能作用。
