BACKGROUND Carbohydrate-binding domains are usually small and physically separate from the catalytic domains of hydrolytic enzymes. Glucoamylase 1 (G1) from Aspergillus niger, an enzyme used widely in the food and brewing industries, contains a granular starch binding domain (SBD) which is separated from the catalytic domain by a semi-rigid linker. The aim of this study was to determine how the...

Pseudomonas acidovorans has been studied by laser pulse, flash photolysis. Previous studies demonstrated that saturation of the catalytic and allosteric sites of the enzyme by L-tryptophan resulted in a 28-fold increase in the equilibrium constant for carboxyenzyme complex formation (MAENO, H., AND FEIGELSON, P. (1968) J. Biol. Chem. 243, 301-305). The present studies have shown that the predom...

Escherichia coli endonuclease VIII (Endo VIII) is a DNA glycosylase with substrate specificity for a wide range of oxidatively damaged pyrimidine bases. Endo VIII catalyzes hydrolysis of the N-glycosidic bond and β, δ-elimination of 3'- and 5'-phosphate groups of an apurinic/apyrimidinic site. Single mutants of Endo VIII L70S, L70W, Y71W, F121W, F230W, and P253W were analyzed here with the aim ...

MOTIVATION The identification of catalytic residues is a key step in understanding the function of enzymes. While a variety of computational methods have been developed for this task, accuracies have remained fairly low. The best existing method exploits information from sequence and structure to achieve a precision (the fraction of predicted catalytic residues that are catalytic) of 18.5% at a...

Treatment of the catalytic subunit of aspartate transcarbamylase from Escherichia coli with either Dor Lbromosuccinate at pH 8.5 results in a loss of catalytic activity. Succinate, an analog of the substrate L-aspartate, affords some protection against inactivation, while the putative transition state analogN-(phosphonacetyl)-L-aspartate provides complete protection. The substrate carbamyl phos...

In many catalytic reactions lateral interactions between adsorbates are believed to have a strong influence on the reaction rates. We apply a microkinetic model to explore the effect of lateral interactions and how to efficiently take them into account in a simple catalytic reaction. Three different approximations are investigated: site, mean-field, and quasichemical approximations. The obtaine...

Enzymes are complex macromolecules that catalyze chemical reactions at their active sites. Important information about catalytic interactions is commonly gathered by perturbation or mutation of active site residues that directly contact substrates. However, active sites are engaged in intricate networks of interactions within the overall structure of the macromolecule, and there is a growing bo...

The EzCatDB (Enzyme Catalytic-mechanism Database) specifically includes catalytic mechanisms of enzymes in terms of sequences and tertiary structures of enzymes, and proposed catalytic mechanisms, along with ligand structures. The EzCatDB groups enzyme data in the Protein Data Bank (PDB) and the SWISS-PROT database with identical domain compositions, Enzyme Commission (EC) numbers and catalytic...

Proton transfer reactions are ubiquitous in enzymes and utilize active site residues as general acids and bases. Crystal structures and site-directed mutagenesis are routinely used to identify these residues, but assessment of their catalytic contribution remains a major challenge. In principle, effective molarity measurements, in which exogenous acids/bases rescue the reaction in mutants lacki...