A chitinase, from Pyrococcus furiosus, is a hyperthermophilic glycosidase that effectively hydrolyses both α and β crystalline chitin. This chitinase has unique structural features; it contains two catalytic domains (AD1 and AD2) and two chitin-binding domains (ChBD1 and ChBD2). We have determined the structure of ChBD1, which significantly enhances the activity of the catalytic domains, by nuclear magnetic resonance spectroscopy. The overall structure of ChBD1 had a compact and globular architecture consisting of three anti-parallel β-strands, similar to those of other proteins classified into carbohydrate-binding module (CBM) family 5. A mutagenesis experiment suggested three solvent-exposed aromatic residues (Tyr112, Trp113 and Tyr123) as the chitin-binding sites. The involvement of Tyr123 or the corresponding aromatic residues in other CBMs, has been demonstrated for the first time. This result indicates that the binding mode may be different from those of other chitin-binding domains in CBM family 5. In addition, the binding affinities of ChBD1 and ChBD2 were quite different, suggesting that the two ChBDs each play a different role in efficiently increasing the activities of AD1 and AD2.
Keywords: CBM family 5; Chitinase; carbohydrate-binding module; chitin-binding domain.