Predicting Protein Function

By adapting a technique normally used for drug discovery, researchers have determined the function of an enzyme whose activity previously had been unknown (Nature, DOI: 10.1038/nature05981). The method could help in cases where a protein of unknown function has no analogs of known function for comparison. Brian K. Shoichet of the University of California, San Francisco, and colleagues extracted the enzyme, dubbed Tm0936, from the Thermotoga maritima bacterium. Using a computer program, the researchers simulated docking of the enzyme with transition states of thousands of potential substrates. The compounds that best fit the enzyme's active site were adenosine analogs undergoing deamination. Frank M. Raushel's group at Texas A&M University tested four of the best substrates, and three of them showed substantial activity with Tm0936. Steven C. Almo's group at Albert Einstein College of Medicine determined the crystal structure of the enzyme bound to the reaction product of the S-adenosylhomocysteine substrate (transition state shown), confirming Tm0936's role as an S-adenosylhomocysteine deaminase.