8FNR

X-ray crystal structure of Hansschlegelia quercus lanmodulin (LanM) with dysprosium (III) bound at pH 7

Summary for 8FNR

• Entry DOI: 10.2210/pdb8fnr/pdb
• Descriptor: EF-hand domain-containing protein, DYSPROSIUM ION (3 entities in total)
• Functional Keywords: methanol dehydrogenase, metal binding protein
• Biological source: Hansschlegelia quercus
• Total number of polymer chains: 4
• Total formula weight: 49968.20

Authors

Jung, J.J.,Lin, C.-Y.,Boal, A.K. (deposition date: 2022-12-28, release date: 2023-06-07, Last modification date: 2024-05-22)

Primary citation

Mattocks, J.A.,Jung, J.J.,Lin, C.Y.,Dong, Z.,Yennawar, N.H.,Featherston, E.R.,Kang-Yun, C.S.,Hamilton, T.A.,Park, D.M.,Boal, A.K.,Cotruvo Jr., J.A.
Enhanced rare-earth separation with a metal-sensitive lanmodulin dimer.
Nature, 618:87-93, 2023

PubMed Abstract: Technologically critical rare-earth elements are notoriously difficult to separate, owing to their subtle differences in ionic radius and coordination number. The natural lanthanide-binding protein lanmodulin (LanM) is a sustainable alternative to conventional solvent-extraction-based separation. Here we characterize a new LanM, from Hansschlegelia quercus (Hans-LanM), with an oligomeric state sensitive to rare-earth ionic radius, the lanthanum(III)-induced dimer being >100-fold tighter than the dysprosium(III)-induced dimer. X-ray crystal structures illustrate how picometre-scale differences in radius between lanthanum(III) and dysprosium(III) are propagated to Hans-LanM's quaternary structure through a carboxylate shift that rearranges a second-sphere hydrogen-bonding network. Comparison to the prototypal LanM from Methylorubrum extorquens reveals distinct metal coordination strategies, rationalizing Hans-LanM's greater selectivity within the rare-earth elements. Finally, structure-guided mutagenesis of a key residue at the Hans-LanM dimer interface modulates dimerization in solution and enables single-stage, column-based separation of a neodymium(III)/dysprosium(III) mixture to >98% individual element purities. This work showcases the natural diversity of selective lanthanide recognition motifs, and it reveals rare-earth-sensitive dimerization as a biological principle by which to tune the performance of biomolecule-based separation processes.

PubMed: 37259003
DOI: 10.1038/s41586-023-05945-5

Experimental method

X-RAY DIFFRACTION (1.4 Å)