Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods

A novel protein superfamily with over 600 members was discovered by iterati ve profile searches and analyzed with powerful bioinformatics and informati on visualization methods. Evidence exists that these proteins generate a ra dical species by reductive cleavage of S-adenosylmethionine (SAM) through a n unusual Fe-S center. The superfamily (named here Radical SAM) provides ev idence that radical-based catalysis is important in a number of previously well-studied but unresolved biochemical pathways and reflects an ancient co nserved mechanistic approach to difficult chemistries. Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulfur insertion, ring formation, anaerobic oxidation and protein radical formation, They function in DNA precursor, vitamin, cofactor, antibiotic an d herbicide biosynthesis and in biodegradation pathways, One eukaryotic mem ber is interferon-inducible and is considered a candidate drug target for o steoporosis; another is observed to bind the neuronal Cdk5 activator protei n. Five defining members not previously recognized as homologs are lysine 2 ,3-aminomutase, biotin synthase, lipoic acid synthase and the activating en zymes for pyruvate formate-lyase and anaerobic ribonucleotide reductase. Tw o functional predictions for unknown proteins are made based on integrating other data types such as motif, domain, operon and biochemical pathway int o an organized view of similarity relationships.