ERC Researchers Construct Large Database Used Globally to Study Enzymes

Achievement date: 
2014
Outcome/accomplishment: 

Researchers at the Center for Biorenewable Chemicals (CBiRC), an NSF-funded Engineering Research Center (ERC) headquartered at Iowa State University, have constructed an open-source database  known as ThYme (Thioester-active EnzYmes), which contains huge amounts of information about amino acid sequences and three- dimensional structures of fatty acid- and polyketide-producing enzymes.

Impact/benefits: 

The database is designed to be used by CBiRC researchers, members, and by the general public. ThYme is a prime example of enzyme databases that tabulate sequences and structures and have links to other databases, thereby allowing many researchers to find in central locations data on enzymes that are not easily gathered from the published literature.

 

Explanation/Background: 

With the advent of methods to easily and  cheaply sequence whole DNA contents of all organisms, researchers have been overwhelmed with DNA sequences of organisms and their proteins as well as amino acid sequences of thousands of enzymes that catalyze thousands of different reactions. The difficulty has been in finding the human and computational resources to make sense of this deluge. To address this problem, researchers in many organizations around the world have constructed databases on enzymes, nucleic acids, and other organic molecules for the benefit of all.

The ThYme database comprises 300,000 amino acid sequences and 1,300 three-dimensional structures of enzymes that produce fatty acids and polyketides (see figure). ThYme is used by many CBiRC researchers and members at all levels to identify, obtain data, and study fatty acid- and polyketide-producing enzymes. It is also used each month by an average of 200 individual researchers from around the world.