8BBZ image
Deposition Date 2022-10-14
Release Date 2023-10-25
Last Version Date 2025-05-07
Entry Detail
PDB ID:
8BBZ
Title:
Crystal Structure of SilF (apo form)
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.20 Å
R-Value Free:
0.25
R-Value Work:
0.21
Space Group:
P 65 2 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:SilF
Chain IDs:A (auth: AAA), B (auth: CCC), C (auth: BBB)
Chain Length:119
Number of Molecules:3
Biological Source:Escherichia coli
Ligand Molecules
Primary Citation
The adaptability of the ion-binding site by the Ag(I)/Cu(I) periplasmic chaperone SilF.
J.Biol.Chem. 299 105331 105331 (2023)
PMID: 37820867 DOI: 10.1016/j.jbc.2023.105331

Abstact

The periplasmic chaperone SilF has been identified as part of an Ag(I) detoxification system in Gram-negative bacteria. Sil proteins also bind Cu(I) but with reported weaker affinity, therefore leading to the designation of a specific detoxification system for Ag(I). Using isothermal titration calorimetry, we show that binding of both ions is not only tighter than previously thought but of very similar affinities. We investigated the structural origins of ion binding using molecular dynamics and QM/MM simulations underpinned by structural and biophysical experiments. The results of this analysis showed that the binding site adapts to accommodate either ion, with key interactions with the solvent in the case of Cu(I). The implications of this are that Gram-negative bacteria do not appear to have evolved a specific Ag(I) efflux system but take advantage of the existing Cu(I) detoxification system. Therefore, there are consequences for how we define a particular metal resistance mechanism and understand its evolution in the environment.

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Primary Citation of related structures