5A4G

NMR structure of a 180 residue construct encompassing the N-terminal metal-binding site and the membrane proximal domain of SilB from Cupriavidus metallidurans CH34


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 20 
  • Selection Criteria: TOTAL ENERGY 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Structural and Functional Investigation of the Ag+/Cu+-Binding Domains of the Periplasmic Adaptor Protein Silb from Cupriavidus Metallidurans Ch34.

Urbina, P.Bersch, B.De Angelis, F.Derfoufi, K.Prevost, M.Goormaghtigh, E.Vandenbussche, G.

(2016) Biochemistry 55: 2883

  • DOI: https://doi.org/10.1021/acs.biochem.6b00022
  • Primary Citation of Related Structures:  
    5A4G

  • PubMed Abstract: 

    Silver ion resistance in bacteria mainly relies on efflux systems, and notably on tripartite efflux complexes involving a transporter from the resistance-nodulation-cell division (RND) superfamily, such as the SilCBA system from Cupriavidus metallidurans CH34. The periplasmic adaptor protein SilB hosts two specific metal coordination sites, located in the N-terminal and C-terminal domains, respectively, that are believed to play a different role in the efflux mechanism and the trafficking of metal ions from the periplasm to the RND transporter. On the basis of the known domain structure of periplasmic adaptor proteins, we designed different protein constructs derived from SilB domains with either one or two metal binding sites per protein chain. ITC data acquired on proteins with single metal sites suggest a slightly higher affinity of Ag(+) for the N-terminal metal site, compared to that for the C-terminal one. Remarkably, via the study of a protein construct featuring both metal sites, nuclear magnetic resonance (NMR) and fluorescence spectroscopies concordantly show that the C-terminal site is saturated prior to the N-terminal one. The C-terminal binding site is supposed to transfer the metal ions to the RND protein, while the transport driven by this latter is activated upon binding of the metal ion to the N-terminal site. Our results suggest that the filling of the C-terminal metal site is a key prerequisite for preventing futile activation of the transport system. Exhaustive NMR studies reveal for the first time the structure and dynamics of the functionally important N-terminal domain connected to the membrane proximal domain as well as of its Ag(+) binding site.


  • Organizational Affiliation

    Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles , B-1050 Bruxelles, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SILB, SILVER EFFLUX PROTEIN, MFP COMPONENT OF THE THREE COMPONENTS PROTON ANTIPORTER METAL EFFLUX SYSTEM180Cupriavidus metallidurans CH34Mutation(s): 0 
UniProt
Find proteins for Q58AF3 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34))
Explore Q58AF3 
Go to UniProtKB:  Q58AF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58AF3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AG
Query on AG

Download Ideal Coordinates CCD File 
B [auth A]SILVER ION
Ag
FOIXSVOLVBLSDH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 20 
  • Selection Criteria: TOTAL ENERGY 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Database references
  • Version 2.0: 2019-10-23
    Changes: Atomic model, Data collection, Other
  • Version 2.1: 2023-06-14
    Changes: Database references, Derived calculations, Other
  • Version 2.2: 2024-06-19
    Changes: Data collection, Database references