6HUI

The structure of Dps from Listeria innocua soaked with zinc


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 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

    Roskilde University , Department of Science and Environment , Universitetsvej 1 , 4000 Roskilde , Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA protection during starvation protein
A, B, C, D, E
A, B, C, D, E, F
156Listeria innocuaMutation(s): 0 
Gene Names: dpsflpfrilin0942
EC: 1.16
UniProt
Find proteins for P80725 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262))
Go to UniProtKB:  P80725
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth D]
BA [auth B]
BB [auth D]
CA [auth B]
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 = 86.33α = 90
b = 86.33β = 90
c = 269.298γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-09-11
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references, Derived calculations