8BBZ

Crystal Structure of SilF (apo form)

This is a non-PDB format compatible entry.

Summary for 8BBZ

• Entry DOI: 10.2210/pdb8bbz/pdb
• Descriptor: SilF, ZINC ION (3 entities in total)
• Functional Keywords: silver, copper, metallochaperone, chaperone., metal binding protein
• Biological source: Escherichia coli
• Total number of polymer chains: 3
• Total formula weight: 38361.17

Authors

Lithgo, R.M.,Carr, S.B.,Quigley, A.M.,Scott, D.J. (deposition date: 2022-10-14, release date: 2023-10-25, Last modification date: 2025-05-07)

Primary citation

Lithgo, R.M.,Hanzevacki, M.,Harris, G.,Kamps, J.J.A.G.,Holden, E.,Gianga, T.M.,Benesch, J.L.P.,Jager, C.M.,Croft, A.K.,Hussain, R.,Hobman, J.L.,Orville, A.M.,Quigley, A.,Carr, S.B.,Scott, D.J.
The adaptability of the ion-binding site by the Ag(I)/Cu(I) periplasmic chaperone SilF.
J.Biol.Chem., 299:105331-105331, 2023

PubMed Abstract: 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.

PubMed: 37820867
DOI: 10.1016/j.jbc.2023.105331

Experimental method

X-RAY DIFFRACTION (2.2 Å)