Snapshots of radical enzyme catalysis : the crystal structures of biotin synthase and lysine 5,6-aminomutase

Abstract

(cont.) in the same pathway. To further probe the relationship of the adenosylmethionine and adenosylcobalamin-dependent radical enzymes, the crystal structure of lysine 5,6-aminomutase was determined to 2.8 [angstroms] resolution. Like biotin synthase, the structure of lysine-5,6-aminomutase adheres to the general theme of barrels or barrel-like structures for enzymes that utilize 5'-deoxyadenosyl radicals in catalysis. Additionally, the structure of lysine-5,6-aminomutase implicates pyridoxal phosphate in a novel role, acting as a lock to prevent the formation of aberrant radicals in the absence of substrate.

"AdoMet radical" enzymes utilize a 4Fe-4S cluster and S-adenosylmethionine, in conjunction with a reducing system, to catalyze reactions that proceed through organic radical intermediates. Genomics studies suggest that at least 600 such enzymes exist across the archaea, bacteria, and eukaryotes, though few have been purified and characterized. AdoMet radical enzymes participate in several biomedically important processes, such as DNA biosynthesis and repair, cofactor biosynthesis, and bacterial pathogenesis. To gain insight into this enzyme family, the crystal structure biotin synthase from Escherichia coli, in complex with its substrate dethiobiotin, was determined to 3.4 [angstrom] resolution. Biotin synthase catalyzes a remarkable reaction, the insertion of sulfur into dethiobiotin to form biotin (vitamin B₈). The structure of biotin synthase indicates that adenosylmethionine is coordinated to a unique Fe of the 4Fe-4S cluster, in agreement with spectroscopic investigations from other laboratories. Additionally, the structure reveals that the active site, located in the core of an (α/β)₈ barrel, contains a unique 2Fe-2S cluster, in addition to the 4Fe-4S cluster, adenosylmethionine, and dethiobiotin. Multiple lines of evidence suggest that in the AdoMet radical enzymes, adenosylmethionine is a source of 5'-deoxyadenosyl radical, an intermediate that is historically associated with the adenosylcobalamin-dependent radical enzymes. Interestingly, some of the adenosylcobalamin radical enzymes catalyze reactions that are very similar to those of AdoMet radical enzymes. One such example is adenosylcobalamin-dependent lysine 5,6-aminomutase, which is analogous to lysine 2,3-aminomutase, an AdoMet radical enzyme that is found