9C90 image
Entry Detail
PDB ID:
9C90
Title:
X-ray crystal structure of Methylorubrum extorquens Ho(III)-bound LanD
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2024-06-13
Release Date:
2024-10-16
Method Details:
Experimental Method:
Resolution:
1.38 Å
R-Value Free:
0.22
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
I 21 3
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:landiscernin
Chain IDs:A
Chain Length:61
Number of Molecules:1
Biological Source:Methylorubrum extorquens
Ligand Molecules
Primary Citation
Modulating metal-centered dimerization of a lanthanide chaperone protein for separation of light lanthanides.
Proc.Natl.Acad.Sci.USA 121 e2410926121 e2410926121 (2024)
PMID: 39467132 DOI: 10.1073/pnas.2410926121

Abstact

Elucidating details of biology's selective uptake and trafficking of rare earth elements, particularly the lanthanides, has the potential to inspire sustainable biomolecular separations of these essential metals for myriad modern technologies. Here, we biochemically and structurally characterize Methylobacterium (Methylorubrum) extorquens LanD, a periplasmic protein from a bacterial gene cluster for lanthanide uptake. This protein provides only four ligands at its surface-exposed lanthanide-binding site, allowing for metal-centered protein dimerization that favors the largest lanthanide, LaIII. However, the monomer prefers NdIII and SmIII, which are disfavored lanthanides for cellular utilization. Structure-guided mutagenesis of a metal-ligand and an outer-sphere residue weakens metal binding to the LanD monomer and enhances dimerization for PrIII and NdIII by 100-fold. Selective dimerization enriches high-value PrIII and NdIII relative to low-value LaIII and CeIII in an all-aqueous process, achieving higher separation factors than lanmodulins and comparable or better separation factors than common industrial extractants. Finally, we show that LanD interacts with lanmodulin (LanM), a previously characterized periplasmic protein that shares LanD's preference for NdIII and SmIII. Our results suggest that LanD's unusual metal-binding site transfers less-desirable lanthanides to LanM to siphon them away from the pathway for cytosolic import. The properties of LanD show how relatively weak chelators can achieve high selectivity, and they form the basis for the design of protein dimers for separation of adjacent lanthanide pairs and other metal ions.

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