Systematic comparison of catalytic mechanisms of hydrolysis and transfer reactions classified in the EzCatDB database

Abstract

Catalytic mechanisms of 270 enzymes from 131 superfamilies, mainly hydrolases and transferases, were analyzed based on their enzyme structures. A method of systematic comparison and classification of the catalytic reactions was developed. Hydrolysis and transfer reactions closely resemble one another, displaying common mechanisms, single displacement, and double displacement. These displacement mechanisms might be further subclassified according to the type of catalytic factors and nucleophilic substitution involved. Several types of catalytic factors exist: nucleophile, acid, base, stabilizer, modulator, cofactors. Nucleophilic substitution might be categorized as S(N)1/S(N)2 (or dissociative/associative) reactions. The classification indicates that some mechanisms favor particular types of catalytic factors. In hydrolyses of amide bonds and phosphoric ester bonds, mechanisms with single displacement tend to use inorganic cofactors such as zinc and magnesium ions as important catalysts, whereas those with double displacement frequently do not use such cofactors. In contrast, hydrolyses of O-glycoside bond rarely use such cofactors, with one exception. The trypsin-like hydrolytic reaction, which is catalyzed by the classic catalytic triad comprising serine/histidine/aspartate, can be considered as a "super-reaction" because it is observed in at least three nonhomologous enzymes, whereas most reactions are singlets without any nonhomologous enzymes. By dividing complex reactions into several reactions, correlations between active site structures and catalytic functions can be suggested. This classification method is applicable to other reactions such as elimination and isomerization. Furthermore, it will facilitate annotation of enzyme functions from 3D patterns of enzyme active sites. The classification is available at http://mbs.cbrc.jp/EzCatDB/RLCP/index.html.

Geometric Attributes of Retaining Glycosyltransferase Enzymes Favor an Orthogonal Mechanism

“…The double displacement mechanism has strong precedent for enzymes that do not use metallic co-factors (reviewed in [34]) such as glycoside hydrolases, in which covalent glycosyl-enzyme intermediates have been trapped in crystal structures by using fluoridated substrates ( e.g. [63], [64]).…”

“…No partially inverted products have ever been described for a retaining glycosyltransferases. Enzymes that do involve dissociative character are hydrolases or transferases that do not transfer stereocenters (reviewed in [34]). Thus proposed dissociative pathways also require that steric hindrance is provided by the enzyme to force the generation of retained product ( Fig.…”

Integrating Bioinformatics and Computational Biology: Perspectives and Possibilities for In Silico Network Reconstruction in Molecular Systems Biology

“…Kinetic information can also be found for example in KDBI [320]. EzCatDB [321,322] and MaCie [323,324] include information regarding catalytic mechanisms. ProTherm provides thermodynamics data for mutant proteins [325].…”

Metric learning for enzyme active-site search

“…Nagano (2005) analyzed the catalytic mechanisms of 270 enzymes (mainly hydrolases and transferases) from 131 superfamilies, which are manually compiled in the enzyme reaction database, EzCatDB. Analysis of the enzyme reactions has revealed several analogous reactions that are observed in non-homologous enzymes (Nagano et al , 2007). EzCatDB also provides a hierarchic classification of enzyme reactions, RLCP, which clusters the same reaction types together based on basic Reaction (R), Ligand group involved in catalysis (L), type of Catalytic mechanism (C), and residue/cofactors located on Proteins (P) (Nagano, 2005).…”