8FFD

Crystal structure of manganeese bound Dps protein (PA0962) from Pseudomonas aeruginosa (cubic form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Pseudomonas aeruginosa Dps (PA0962) Functions in H 2 O 2 Mediated Oxidative Stress Defense and Exhibits In Vitro DNA Cleaving Activity.

Rajapaksha, N.Soldano, A.Yao, H.Donnarumma, F.Kashipathy, M.M.Seibold, S.Battaile, K.P.Lovell, S.Rivera, M.

(2023) Int J Mol Sci 24

  • DOI: https://doi.org/10.3390/ijms24054669
  • Primary Citation of Related Structures:  
    8FF9, 8FFA, 8FFB, 8FFC, 8FFD

  • PubMed Abstract: 

    We report the structural, biochemical, and functional characterization of the product of gene PA0962 from Pseudomonas aeruginosa PAO1. The protein, termed Pa Dps, adopts the Dps subunit fold and oligomerizes into a nearly spherical 12-mer quaternary structure at pH 6.0 or in the presence of divalent cations at neutral pH and above. The 12-Mer Pa Dps contains two di-iron centers at the interface of each subunit dimer, coordinated by conserved His, Glu, and Asp residues. In vitro, the di-iron centers catalyze the oxidation of Fe 2+ utilizing H 2 O 2 (not O 2 ) as an oxidant, suggesting Pa Dps functions to aid P. aeruginosa to survive H 2 O 2 -mediated oxidative stress. In agreement, a P. aeruginosa Δ dps mutant is significantly more susceptible to H 2 O 2 than the parent strain. The Pa Dps structure harbors a novel network of Tyr residues at the interface of each subunit dimer between the two di-iron centers, which captures radicals generated during Fe 2+ oxidation at the ferroxidase centers and forms di-tyrosine linkages, thus effectively trapping the radicals within the Dps shell. Surprisingly, incubating Pa Dps and DNA revealed unprecedented DNA cleaving activity that is independent of H 2 O 2 or O 2 but requires divalent cations and 12-mer Pa Dps.


  • Organizational Affiliation

    Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable dna-binding stress protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
156Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: PA0962
UniProt
Find proteins for Q9I4Z7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I4Z7 
Go to UniProtKB:  Q9I4Z7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I4Z7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TLA
Query on TLA

Download Ideal Coordinates CCD File 
CA [auth K],
U [auth D]
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
AA [auth J]
BA [auth K]
DA [auth L]
EA [auth M]
FA [auth N]
AA [auth J],
BA [auth K],
DA [auth L],
EA [auth M],
FA [auth N],
GA [auth O],
HA [auth P],
Q [auth A],
R [auth B],
S [auth C],
T [auth D],
V [auth E],
W [auth F],
X [auth G],
Y [auth H],
Z [auth I]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.914α = 90
b = 223.914β = 90
c = 223.914γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI169344
National Institutes of Health/Office of the DirectorUnited StatesS10OD030394

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 1.1: 2023-03-22
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection