Homology Modeling of Cu/Zn Superoxide Dismutase in Sweet Potato (Ipomoea batatas)

Abstract

Superoxide dismutase (SOD) is a ubiquitous antioxidant enzyme essential for protecting cells from damage caused by reactive oxygen species. While the role of SOD in plant stress tolerance, particularly in crops like Ipomoea batatas (Sweet Potato), is well-established but high-resolution experimental structure for its isoenzymes is still lacking. This study aimed to predict the three-dimensional structure of the Cu/Zn SOD in I. batatas using the homology modelling method. Here, we focus on Cu/Zn SOD because it is the dominant isoform in photosynthetically active tissues and provides the fastest catalytic efficiency, making it the primary defence against reactive oxygen species (ROS) in plant. The target sequence was retrieved from the NCBI database, and a suitable template was identified via sequence alignment with 88.16% sequence identity. The model was generated using SWISS-MODEL and subsequently validated using established tools, including Ramachandran analysis, MolProbity, global model evaluation and local model evaluation including GMQE (Global Model Quality Estimate) QMEANDisCo global score and QMEAN Z-score analysis. The structural models provided insights into key functional regions, including the metal-binding active sites. The Cu/Zn active site displayed a distorted tetrahedral geometry, which is essential for superoxide detoxification. Evaluation of the model generated confirmed that it exhibits high reliability, high stereochemical quality, correct folding and strong suitability. These findings provide valuable insights into the action and regulation Cu/Zn SOD of I. batatas and a foundation for guiding targeted enzyme engineering, enhancing our molecular understanding of stress resilience in sweet potato, and supporting future agrobiotechnology efforts. Understanding the structural features of Cu/Zn SOD enables identification of stability-enhancing or activity-boosting residues that can be targeted through gene editing or molecular breeding. Such insights support the development of sweet potato varieties with improved oxidative stress tolerance, higher resilience in changing climates, and better overall crop performance.