Cluster-selective 57Fe labeling of a Twitch-domain-containing radical SAM enzyme

Abstract

⁵⁷Fe-specific techniques such as Mössbauer spectroscopy are invaluable tools in mechanistic studies of Fe–S proteins. However, they remain underutilized for proteins that bind multiple Fe–S clusters because such proteins are typically uniformly enriched with ⁵⁷Fe. As a result, it can be unclear which spectroscopic responses derive from which cluster, and this in turn obscures the chemistry that takes place at each cluster. Herein, we report a facile method for cluster-selective ⁵⁷Fe enrichment based on exchange between the protein's Fe–S clusters and exogenous Fe ions. Through a combination of inductively coupled plasma mass spectrometric and ⁵⁷Fe Mössbauer spectroscopic analysis, we show that, of the two [Fe₄S₄] clusters in BtrN (a Twitch-domain-containing radical S-adenosyl-L-methionine (SAM) enzyme), the Fe ions in the SAM-binding cluster undergo faster exchange with exogenous Fe²⁺; the auxiliary cluster is essentially inert under the reaction conditions. Exploiting this rate difference allows for either of the two [Fe₄S₄] clusters to be selectively labeled: the SAM-binding cluster can be labeled by exchanging unlabeled BtrN with ⁵⁷Fe²⁺, or the auxiliary cluster can be labeled by exchanging fully labeled BtrN with natural abundance Fe²⁺. The labeling selectivity likely originates primarily from differences in the clusters' accessibility to small molecules, with secondary contributions from the different redox properties of the clusters. This method for cluster-selective isotopic labeling could in principle be applied to any protein that binds multiple Fe–S clusters so long as the clusters undergo exchange with exogenous Fe ions at sufficiently different rates.