A recombinant cyclodextrin glycosyltransferase (CGTase) gene fused with thioredoxin (Trx), hexa-histidine (His6) and S-protein (S) at the N terminus and a proline-rich peptide (PRP) at the C terminus, was constructed using the wild-type gene from Paenibacillus sp. A11, the pET-32a vector and Escherichia coli BL21(DE3) as the host cell. The expression levels and enzyme characteristics of the Trx-His6-CGTase-PRP fusion protein, the recombinant CGTase without fusion peptides, and the wild-type CGTase were compared. The maximum specific activity for the Trx-His6-CGTase-PRP fusion enzyme was 2.7 fold higher than that of the non-fusion form at the optimal IPTG concentration. The Trx-His6-CGTase-PRP fusion protein was purified to homogeneity by starch adsorption and Ni-NTA affinity chromatography, with a specific activity of 2,268 units/mg protein at a 61% yield. The ease of purification and the higher enzyme yield were obtained with the fusion form when compared to the non-fusion and wild-type enzymes. The fusion enzyme was superior than its wild-type counterpart in terms of stability against high temperature and organic solvents. Moreover, the fusion enzyme could catalyze the synthesis of cyclodextrins in 20% (v/v) dimethylformamide with a higher product yield of CD7 and CD8 compared to that of the wild-type enzyme in the same buffer-solvent system. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.