Theoretical study of the arabinan hydrolysis by an inverting GH43 arabinanase

The endo-1,5--L-arabinanases (ABNases) belong to the glycoside hydrolase family 43 (GH43) and hydrolyse -1,5-arabinofuranosidic bonds in arabinose-containing polysaccharides by aninverting mechanism. ABNases are key enzymes involved in hemicellulose degradation with various applications in food technology, organic synthesis and biofuel production. Here, the reaction mechanism of the Geobacillus stearothermophilus GH43 ABNases has been investigated using density functional theory method. To probe the role of the pKa modulators (Ser164 and Tyr229) in the reaction, two different orientations of a catalytic acid (Glu201) with respect to the position of these residues are considered. The results show that the orientation involving a hydrogen bond network (Ser164 center dot center dot center dot Glu201 center dot center dot center dot Tyr229) is energetically more favourable, compared to the other one (Ser164 center dot center dot center dot Glu201), with a barrier of 13.6kcalmol(-1), consistent with the experimental data. Our calculations also give support to a single displacement mechanism proposed in the literature where the protonation of glycosidic bond and a nucleophilic attack by a catalytic water occur in a concerted but asynchronous manner.