Biocatalysis: Database Tools

Abstract

Industrial biotechnology increasingly depends on the use of enzymes to carry out desired biotransformation reactions. The reactions have traditionally been used to produce specialty chemicals. Now, enzymic catalysis is being used to manufacture commodity chemicals and fuels. Thousands of enzymes are available commercially; millions are produced by microorganisms in nature. Applications of enzyme catalysis are based on using the best enzyme and optimizing metabolic pathways. Databases are crucial to this effort. Enzyme databases contain information on enzyme characteristics and substrate specificity. Gene sequence databases provide information crucial for cloning and expressing key enzymes. Metabolism databases reveal how enzymes interact in specific organisms to catalyze consecutive reactions. Microorganism databases provide information about the history and availability of individual strains. Chemical substance databases provide key compound information; solubility, reactivity, and biological activity. Commodity‐scale chemical substances that are substrates for industrial enzymes include sugars (glucose isomerase), sugar polymers (cellulase), nitriles (nitrile hydratase and nitrilase), proteins (rennin), and β‐lactam antibiotics (penicillin acylase). Databases will play a prominent role in synthetic biology, using biological tools to engineer novel enzymes and metabolic pathways for industrial biotechnology.