Abstract Highly specific dockerin–cohesin interaction intrinsically involved in the cellulosome formation in Clostridium josui was applied for the construction of an affinity tag purification system. Amino acid substitutions were introduced into the dockerin domain of C. josui Cel8A at positions 11, 12, 44, and 45 and mutant dockerin domains were examined for their ability as an affinity tag: mutant dockerin-tagged proteins were adsorbed onto a cohesin (Coh2)-coupled Sepharose in the presence of Ca 2+ and desorbed from the protein and Coh2-Sepharose complex by the addition of a chelating agent, EGTA. Single-step purification tests showed that substitution of glycine or serine for isoleucine at position 45 markedly improved the recovery of the recombinant proteins from the proteins and Coh2-Sepharose complex. Surface plasmon resonance analysis of the interaction between the I45G mutant and Coh2 indicated that the mutation decreased binding rate and increased dissociation rate, resulting in decrease in dissociation constant. When model proteins such as JNK3, MAP2K3, IL-8, and pro-IL-18 were expressed as I45G dockerin-tagged proteins in the baculovirus expression system and purified by the single-step purification, purity of all the I45G dockerin-tagged proteins tested was higher than 90%. Furthermore, insertion of a thrombin cleavage site between the dockerin tag and target proteins enabled rapid removal of the tag from the target proteins by thrombin protease. This system, named the Dock tag purification system, can be widely utilized and contributes to various fields in academic and application researches.