A critical survey of average distances between catalytic carboxyl groups in glycoside hydrolases

Published X-ray crystallographic structures for glycoside hydrolases (GHs) from 39 different families are surveyed according to some rigorous selection criteria, and the distances separating 208 pairs of catalytic carboxyl groups (20 alpha-retaining, 87 beta-retaining, 38 alpha-inverting, and 63 beta-inverting) are analyzed. First, the average of all four inter-catboxyl O center dot center dot center dot O distances for each pair is determined; second, the mean of all the pair averages within each GH family is determined; third, means are determined for groups of GH families. No significant differences are found for free structures compared with those complexed with a ligand in the active site of the enzyme, nor for alpha-GHs as compared with beta-GHs. The mean and standard deviation (1 sigma) of the unimodal distribution of average O center dot center dot center dot O distances for all families of inverting GHs is 8 +/- 2 angstrom, with a very wide range from 5 angstrom (GH82) to nearly 13 angstrom (GH46). The distribution of average O center dot center dot center dot O distances for all families for retaining GHs appears to be bimodal: the means and standard deviations of the two groups are 4.8 +/- 0.3 angstrom and 6.4 +/- 0.6 angstrom. These average values are more representative, and more likely to be meaningful, than the often-quoted literature values, which are based on a very small sample of structures. The newly-updated average values proposed here may alter perceptions about what separations between catalytic residues are normal or abnormal for GHs.