<p>Apples (<i>Malus domestica</i>) are one of the most widely-produced fruits globally and possess significant economic and nutritional value. The plant U-box (PUB) type E3 ubiquitin ligase plays a crucial role in the ubiquitination modification process in plants. MdPUB17 has been newly identified as an E3 ubiquitin ligase in apple fruit. This study presents a preliminary analysis of the gene and amino acid structure and properties of MdPUB17. Furthermore, by constructing an overexpression plasmid for MdPUB17 and genetically transforming apple callus tissue, we employed transcriptome sequencing technology to investigate the effects of MdPUB17 overexpression (MdPUB17-OE) on the expression of genes involved in various metabolic pathways in apples. The results indicate that MdPUB17-OE significantly modified the metabolic pathways of apple callus by influencing the expression levels of multiple differentially expressed genes associated with phenylpropanoid biosynthesis, terpenoid backbone biosynthesis, γ-aminobutyric acid biosynthesis, and ascorbate biosynthesis. These findings provide important insights into the regulatory role of MdPUB17 in the metabolic pathways of apple fruit.</p> Graphical abstract <p></p>