Gene cloning and enzymatic characteristics of a novel γ-cyclodextrin-specific cyclodextrinase from alkalophilic Bacillus clarkii 7364

A new gene, cda, was found in the downstream region of the cgt gene encoding cyclodextrin (CD) glucanotransferase from Bacillus clarkii 7364. Cda encoded by the cda was a cyclodextrinase that has extremely high specificity for γ-CD. The rates of hydrolysis toward α- and β-CD, maltooctaose and polysaccharides were less than 4% of that toward γ-CD. Cda also has a transglycosylation activity, by which the maltotriose moiety was transferred from maltohexaose and maltopentaose. The comparison of the amino acid sequences between Cda and CD-degrading enzymes revealed the sequence of Cda has unique features. One of them is Gly247 next to the catalytic nucleophile Asp246. Most enzymes in GH family 13 have more bulky amino acids at this position. Other features in Cda are the lack of the N-domain in CD-degrading enzymes involving in the dimerization contributing to the preference of CDs and the existence of a long extra sequence in the C-terminus. Despite the lack of N-domain, Cda showed a dodecameric structure. The long extra sequence in the C-terminus might contribute to the oligomerization of Cda through a new mechanism. These unique features indicate that Cda is a novel type of CD-degrading enzyme.