Structural-mechanistic insights and performance engineering of chitinase MpChit35 for tailored chito-oligosaccharide production

Chitinase-catalysed synthesis offers a promising biotechnological route for converting chitin-rich waste into value-added chito-oligosaccharides, whose biological activity depends on their degree of polymerization and acetylation, highlighting the need for precise enzymatic tools to tailor their structures. This study investigates the structural-functional determinants of the chitinase MpChit35 from Metschnikowia pulcherrima, which mainly produces di-acetyl-chitobiose ((GlcNAc)2) and to a lesser extent tri-acetyl-chitotriose ((GlcNAc)3) from chitin. Here the MpChit35 structure was solved at 2.55 Å and structural analysis combined with site-directed mutagenesis enabled the identification of key residues involved in substrate binding and catalysis. Thus, the L253R mutation significantly increased the protein catalytic efficiency and promoted near-exclusive production of (GlcNAc)2 from chitin and oligomeric substrates, underscoring the role of polar interactions in defining the enzyme specificity and processivity. In contrast, the multiple-mutation A107D/D151N/A181S/M279A favoured the release of (GlcNAc)3 and tetra-acetyl-chitotetraose. Furthermore, residue Trp73 contributed to an unusual distal substrate-binding platform and Ala107 resulted a key determinant for the product specificity. These findings provide mechanistic insights into chitinase function and support the rational design of enzymes with tailored cleavage patterns. This work contributes to the development of efficient biocatalysts for sustainable chitin valorisation and the industrial production of custom chito-oligosaccharides.