Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
Department of Chemical Sciences, University of Padua, Padova, Italy.
Nat Commun. 2024 Apr 13;15(1):3199. doi: 10.1038/s41467-024-47466-3.
The increasing availability of experimental and computational protein structures entices their use for function prediction. Here we develop an automated procedure to identify enzymes involved in metabolic reactions by assessing substrate conformations docked to a library of protein structures. By screening AlphaFold-modeled vitamin B6-dependent enzymes, we find that a metric based on catalytically favorable conformations at the enzyme active site performs best (AUROC Score=0.84) in identifying genes associated with known reactions. Applying this procedure, we identify the mammalian gene encoding hydroxytrimethyllysine aldolase (HTMLA), the second enzyme of carnitine biosynthesis. Upon experimental validation, we find that the top-ranked candidates, serine hydroxymethyl transferase (SHMT) 1 and 2, catalyze the HTMLA reaction. However, a mouse protein absent in humans (threonine aldolase; Tha1) catalyzes the reaction more efficiently. Tha1 did not rank highest based on the AlphaFold model, but its rank improved to second place using the experimental crystal structure we determined at 2.26 Å resolution. Our findings suggest that humans have lost a gene involved in carnitine biosynthesis, with HTMLA activity of SHMT partially compensating for its function.
越来越多的实验和计算蛋白质结构可供使用，这诱使人们利用它们进行功能预测。在这里，我们开发了一种自动程序，通过评估与蛋白质结构库对接的底物构象来识别参与代谢反应的酶。通过筛选 AlphaFold 建模的维生素 B6 依赖性酶，我们发现基于酶活性位点处催化有利构象的度量标准在识别与已知反应相关的基因方面表现最佳（AUROC 评分=0.84）。应用此程序，我们鉴定出编码羟甲基三赖氨酸醛缩酶 (HTMLA) 的哺乳动物基因，这是肉碱生物合成的第二个酶。经过实验验证，我们发现排名最高的候选酶丝氨酸羟甲基转移酶 (SHMT)1 和 2 催化 HTMLA 反应。然而，一种在人类中不存在的小鼠蛋白（苏氨酸醛缩酶；Tha1）更有效地催化该反应。Tha1 不是基于 AlphaFold 模型排名最高的，但使用我们以 2.26 Å 分辨率确定的实验晶体结构，其排名提高到第二位。我们的研究结果表明，人类已经失去了一个参与肉碱生物合成的基因，SHMT 的 HTMLA 活性部分补偿了其功能。
