Analyse in silico d’allantoinase d’Actinopolyspora saharensis

Abstract

Allantoinase (EC 3.5.2.5) is an enzyme belonging to the amidohydrolase family. It is involved in the purine catabolism by hydrolyzing the amide bond between N3 and C4 of allantoin, converting it into allantoate. This reaction constitutes a key step in the biosynthesis and degradation of purines as well as nitrogen recycling in many organisms, including bacteria, fungi, and plants. However, this enzyme is absent in humans, in whom purine metabolism terminates at the formation of uric acid. However, allantoinase remains poorly characterized, particularly in Actinopolyspora saharensis. This study therefore aimed to determine its physicochemical properties, subcellular localization, and 3D structure using bioinformatics approaches. These analyses revealed the acidic nature, stability, and hydrophilicity of this enzyme, as well as its cytoplasmic localization. Secondary structure prediction, performed using the SOPMA tool, revealed a predominance of loops (50.33%), followed by α-helices (27.79%) and β-sheets (21.88%). The AlphaFold tool generated the most reliable 3D structure model compared to other tools, including SWISS-Model, Phyre2, I-TASSER, and trRosetta. This protein model was validated using PROCHECK, ERRAT, and Verify 3D. Analysis of protein–protein interactions identified aspartate carbamoyltransferase as a major partner (confidence score: 0.999). Functional analysis using CD Search identified L-hydantoinase and allantoinase as conserved domains (E-value equal to 0). To assess the biotechnological potential of this enzyme, molecular docking was performed. Interesting results were obtained regarding the degradation of herbicides, with the best result observed for Nicosulfuron, which exhibited a binding energy of -8.2 kcal/mol, highlighting its potential for bioremediation applications. However, these findings are computational and require experimental validation.