6HUI

The structure of Dps from Listeria innocua soaked with zinc

• PDB DOI:  https://doi.org/10.2210/pdb6HUI/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Listeria innocua
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-08 Released: 2019-09-04 
• Deposition Author(s): Zeth, K., Okuda, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.284 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 

Literature

Metal Positions and Translocation Pathways of the Dodecameric Ferritin-like Protein Dps.

Zeth, K., Sancho-Vaello, E., Okuda, M.

(2019) Inorg Chem 58: 11351-11363

• PubMed: 31433627 
• DOI: https://doi.org/10.1021/acs.inorgchem.9b00301
• Primary Citation of Related Structures:  
  6HUI, 6HV1, 6HVQ, 6HX2, 6SEV


• PubMed Abstract: 
  

Iron storage in biology is carried out by cage-shaped proteins of the ferritin superfamily, one of which is the dodecameric protein Dps. In Dps, four distinct steps lead to the formation of metal nanoparticles: attraction of ion-aquo complexes to the protein matrix, passage of these complexes through translocation pores, oxidation of these complexes at ferroxidase centers, and, ultimately, nanoparticle formation. In this study, we investigated Dps from Listeria innocua to structurally characterize these steps for Co ²⁺ , Zn ²⁺ , and La ³⁺ ions. The structures reveal that differences in their ion coordination chemistry determine alternative metal ion-binding sites on the areas of the surface surrounding the translocation pore that captures nine La ³⁺ , three Co ²⁺ , or three Zn ²⁺ ions as aquo clusters and passes them on for translocation. Inside these pores, ion-selective conformational changes at key residues occur before a gating residue to actively move ions through the constriction zone. Ions upstream of the Asp130 gate residue are typically hydrated, while ions downstream directly interact with the protein matrix. Inside the cavity, ions move along negatively charged residues to the ferroxidase center, where seven main residues adapt to the three different ions by dynamically changing their conformations. In total, we observed more than 20 metal-binding sites per Dps monomer, which clearly highlights the metal-binding capacity of this protein family. Collectively, our results provide a detailed structural description of the preparative steps for amino acid-assisted biomineralization in Dps proteins, demonstrating unexpected protein matrix plasticity.

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Organizational Affiliation: 

IKERBASQUE , Basque Foundation for Science , 48011 Bilbao , Basque Country , Spain.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (3D View)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 112.48 kDa 
• Atom Count: 7,398 
• Modelled Residue Count: 901 
• Deposited Residue Count: 936 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA protection during starvation protein	A, B, C, D, E, F	156	Listeria innocua	Mutation(s): 0  Gene Names: dps, flp, fri, lin0942 EC: 1.16
UniProt
Find proteins for P80725 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)) Explore P80725  Go to UniProtKB:  P80725

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	AA [auth B], AB [auth D], BA [auth B], BB [auth D], CA [auth B], CB [auth D], DA [auth B], DB [auth D], EA [auth B], EB [auth D], FA [auth B], FB [auth D], G [auth A], GA [auth B], GB [auth D], H [auth A], HA [auth B], HB [auth E], I [auth A], IA [auth B], IB [auth E], J [auth A], JA [auth B], JB [auth E], K [auth A], KA [auth B], KB [auth F], L [auth A], LA [auth B], LB [auth F], M [auth A], MA [auth B], MB [auth F], N [auth A], NA [auth C], NB [auth F], O [auth A], OA [auth C], OB [auth F], P [auth A], PA [auth C], PB [auth F], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], VA [auth D], W [auth A], WA [auth D], X [auth B], XA [auth D], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.284 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.33	α = 90
b = 86.33	β = 90
c = 269.298	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-04 
Deposition Author(s): Zeth, K., Okuda, M.

Revision History  

• Version 1.0: 2019-09-04
  Type: Initial release
  
• Version 1.1: 2019-09-11
  Changes: Data collection, Database references, Derived calculations