We developed a strategy for finding out the adapted variants of enzymes, and we applied it to an enzyme, dihydrofolate reductase (DHFR), in terms of its catalytic activity so that we successfully obtained several hyperactive cysteine-and methionine-free variants of DHFR in which all five methionyl and two cysteinyl residues were replaced by other amino acid residues. Among them, a variant (M1A/ M16N/M20L/M42Y/C85A/M92F/C152S), named as ANLYF, has an approximately seven times higher k cat value than wild type DHFR. Enzyme kinetics and crystal structures of the variant were investigated for elucidating the mechanism of the hyperactivity. Steady-state and transient binding kinetics of the variant indicated that the kinetic scheme of the catalytic cycle of ANLYF was essentially the same as that of wild type, showing that the hyperactivity was brought about by an increase of the dissociation rate constants of tetrahydrofolate from the enzyme-NADPH-tetrahydrofolate ternary complex. The crystal structure of the variant, solved and refined to an R factor of 0.205 at 1.9-Å resolution, indicated that an increased structural flexibility of the variant and an increased size of the N-(p-aminobenzoyl)-L-glutamate binding cleft induced the increase of the dissociation constant. This was consistent with a large compressibility (volume fluctuation) of the variant. A comparison of folding kinetics between wild type and the variant showed that the folding of these two enzymes was similar to each other, suggesting that the activity enhancement of the enzyme can be attained without drastic changes of the folding mechanism.To freely design enzymes with desired properties is the ultimate dream for protein engineers. Because the "protein folding problem," namely how an amino acid sequence determines its tertiary folded structure, has not completely been solved at atomic resolution, the rational design approach is still limited, even for improvement of enzymes from natural sources. Alternatively, protein design can be thought of as a process of "picking up" from all the possible amino acid sequences (i.e. sequence space) until a protein with the desired properties is found, because the structure and function of a protein is determined by its amino acid sequence (1). When we set the goal of protein design "to create a protein of a desired property consisting of a given number of amino acid residues n," the solution can be obtained by the complete search of all the possible amino acid sequences with "n" amino acid residues, the total number reaching 20 n . Therefore, the protein design problem can be reduced to a searching problem in sequence space of polypeptides with n amino acid residues. The solution to this searching problem should include a reliable process that can be performed within a realistic time span, otherwise it is of no use in practical protein design. In this regard, the size of sequence space to be searched is a critical factor (2). The size of the sequence space of a polypeptide with amino acids even as small as 100 is ...