8FNS image
Deposition Date 2022-12-28
Release Date 2023-06-07
Last Version Date 2024-05-22
Entry Detail
PDB ID:
8FNS
Title:
X-ray crystal structure of Methylorubrum extorquens AM1 lanmodulin (LanM) with neodymium (III) bound at pH 7
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.01 Å
R-Value Free:
0.15
R-Value Work:
0.14
R-Value Observed:
0.14
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:EF-hand domain-containing protein
Gene (Uniprot):lanM
Chain IDs:A
Chain Length:105
Number of Molecules:1
Biological Source:Methylorubrum extorquens AM1
Ligand Molecules
Primary Citation
Enhanced rare-earth separation with a metal-sensitive lanmodulin dimer.
Nature 618 87 93 (2023)
PMID: 37259003 DOI: 10.1038/s41586-023-05945-5

Abstact

Technologically critical rare-earth elements are notoriously difficult to separate, owing to their subtle differences in ionic radius and coordination number1-3. The natural lanthanide-binding protein lanmodulin (LanM)4,5 is a sustainable alternative to conventional solvent-extraction-based separation6. 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.

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Primary Citation of related structures