Spectroscopic investigations into the active site structure and the mechanisms of radical SAM enzymes

Abstract

The radical S-adenosyl-L-methionine (SAM) superfamily of enzymes carry out diverse and complex reactions through generation of a 5'-deoxyadenosyl (5'-dAdo·) radical followed by transfer to substrate. These enzymes contain a [4Fe-4S] cluster which binds and transfers an electron to SAM. The exact mechanism of 5-dAdo· generation is unknown and the studies herein provide further investigation into pyruvate formate lyase activating enzyme (PFL-AE) and lysine 2,3-aminomutase (LAM) pre and post SAM cleavage. To understand the active site of PFL-AE prior to SAM cleavage, cation and small molecule effects were examined by electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) spectroscopies. Previously, PFL-AE had been observed to contain a valence localized cluster in the presence of small molecules and this work used EPR and ENDOR spectroscopy to further probe the effects of these molecules. These studies determined that these molecules do not directly bind the cluster but rather an H xO species occupies the unique Fe site. The crystal structure of PFL-AE revealed a cation site and to probe this site, EPR and ENDOR spectroscopies were employed. Monovalent cations stimulated PFL-AE activity, with the greatest activity in the presence of potassium. The identity of the cation perturbed the EPR signal of PFL-AE which was more pronounced in the presence of SAM. ENDOR spectroscopy determined that SAM coordination differed depending on the monovalent cation. Due to its high reactivity, 5'-dAdo· has never been spectroscopically observed. In order to examine any intermediate states, a SAM analog and rapid freeze quench (RFQ) techniques were employed in conjunction with EPR and ENDOR spectroscopies. LAM can cleave the SAM analog, S-3',4'-anhydroadenosyl-L-methionine, to produce a stable allylic radical which was coupled with isotopically labeled lysine for ENDOR analysis. It was determined that radical generation is highly controlled with little movement towards its substrate upon 5'-dAdo· production. During RFQ techniques on PFL-AE, an organometallic intermediate species was observed. To probe this intermediate, isotopically labeled SAM and an 57Fe labeled cluster were coupled with the unknown paramagnetic species. It was determined that this intermediate was an unprecedented organometallic Fe-adenosyl bound species post SAM cleavage.