Rational Engineering of AKR13B3 from Devosia A6-243 for Enhanced Aflatoxin B1 Degradation: A Dual Mechanism of Substrate Polarization and Tunnel Remodeling

Abstract

Aflatoxin B1 (AFB1) is one of the most toxic mycotoxins, widely contaminating agricultural products and posing a serious threat to food safety and human health. Enzymatic degradation is considered a promising detoxification strategy due to its high efficiency, strong specificity, and lack of secondary pollution. AKR13B3, a member of the aldo-keto reductase family, possesses intrinsic catalytic activity for AFB1 degradation; however, its low natural activity severely limits practical application. In this study, the binding mode of the AKR13B3-NADPH complex with AFB1 was first determined using AlphaFold 3.0 and AutoDock Vina. Through interaction analysis, Trp102 and Asp41 were identified as key targets for enhancing catalytic activity. Following site-directed mutagenesis screening, two mutants, D41H and D41T, with significantly improved catalytic activity were obtained, exhibiting 52.32% and 46.44% higher activity than the wild-type enzyme, respectively. Three-dimensional structural simulation revealed that D41H and D41T form stable interactions with the carbonyl group on the lactone ring of AFB1, thereby polarizing the carbonyl group and reducing the activation energy of the reaction, ultimately enhancing catalytic activity. Substrate channel analysis demonstrated that, compared with the wild-type, the D41H and D41T mutants significantly increased the bottleneck radius of the substrate channel (by 25% and 22%, respectively) and shortened the channel length (by 23% and 33%, respectively), thereby partially relieving steric hindrance and diffusion limitations and improving catalytic efficiency. In summary, this study elucidates the molecular basis by which D41H and D41T enhance the catalytic activity of AKR13B3 toward AFB1 through the dual mechanisms of external/hydrogen bond catalysis and channel remodeling, providing an important theoretical foundation for the rational design and directed engineering of AFB1-degrading enzymes.