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 α-retaining, 87 β-retaining, 38 α-inverting, and 63 β-inverting) are analyzed. First, the average of all four inter-carboxyl O…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 α-GHs as compared with β-GHs. The mean and standard deviation (1σ) of the unimodal distribution of average O…O distances for all families of inverting GHs is 8 ± 2Å, with a very wide range from 5Å (GH82) to nearly 13Å (GH46). The distribution of average O…O distances for all families of retaining GHs appears to be bimodal: the means and standard deviations of the two groups are 4.8 ± 0.3Å and 6.4 ± 0.6Å. 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.
Discipline of Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
Ndumiso N
NN
Mhlongo
Adam A
AA
Skelton
Gert
G
Kruger
Mahmoud E S
ME
Soliman
Ian H
IH
Williams
D000595:Amino Acid Sequence; D050260:Carbohydrate Metabolism; D002245:Carbon Dioxide / Q000737:chemistry; D020134:Catalytic Domain / Q000502:physiology*; D018360:Crystallography, X-Ray; D006026:Glycoside Hydrolases / Q000737:chemistry* / Q000648:ultrastructure*; D008958:Models, Molecular
D002245:Carbon Dioxide; C041069:carboxyl radical; D006026:Glycoside Hydrolases
glycoside hydrolases (GHs); inter-carboxyl separation; structural analysis