EF-Hand Binding Order and Conformational Control of Lanthanide Ion Binding in M. extorquens Lanmodulin

Abstract Biomolecular chelators have emerged recently as potential alternatives to conventional, energy-intensive methods for the challenging separation of rare earth elements (REEs), including the lanthanide (LnIII) ions. Lanmodulin (LanM) from Methylobacterium extorquens is the archetype for highly selective biological REE chelation and has been applied for recovery and separations of REEs. LanM’s high affinity and selectivity are driven by a large disorder-to-order conformational transition in response to cooperative binding of LnIII ions to three of its EF-hand motifs, with one site being more labile than the other two. Definition of the order of LnIII ion binding and the structural interactions contributing to cooperativity has been elusive but is essential for engineering of LanM and other REE-binding proteins. Here, we use a combination of mutagenesis and spectroscopic methods (UV absorbance, circular dichroism, luminescence, and NMR spectroscopies) to achieve both aims. We identify a salt bridge (K93-D56) between LanM’s two primary helices, disruption of which inactivates one of the metal-binding sites. Together, our results suggest, contrary to previous hypotheses, that EF1 and EF2 are the tightest sites, which are sufficient to organize most of the protein’s tertiary structure; EF3 is the labile, third binding site; and REEs, circumneutral pH, and the salt bridge are all essential for LanM’s full conformational change. These results help to define the conformational landscape underlying LanM’s selective REE recognition and provide design principles for engineering REE-binding proteins for recovery and separation applications.