8FFB

Crystal structure of iron bound Dps protein (PA0962) from Pseudomonas aeruginosa (orthorhombic form)

Summary for 8FFB

• Entry DOI: 10.2210/pdb8ffb/pdb
• Descriptor: Probable dna-binding stress protein, FE (II) ION (3 entities in total)
• Functional Keywords: metal binding protein
• Biological source: Pseudomonas aeruginosa PAO1
• Total number of polymer chains: 12
• Total formula weight: 211471.27

Authors

Lovell, S.,Kashipathy, M.M.,Battaile, K.P.,Rivera, M. (deposition date: 2022-12-08, release date: 2023-03-08, Last modification date: 2024-05-22)

Primary citation

Rajapaksha, N.,Soldano, A.,Yao, H.,Donnarumma, F.,Kashipathy, M.M.,Seibold, S.,Battaile, K.P.,Lovell, S.,Rivera, M.
Pseudomonas aeruginosa Dps (PA0962) Functions in H 2 O 2 Mediated Oxidative Stress Defense and Exhibits In Vitro DNA Cleaving Activity.
Int J Mol Sci, 24:-, 2023

PubMed Abstract: We report the structural, biochemical, and functional characterization of the product of gene PA0962 from 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 utilizing HO (not O) as an oxidant, suggesting Pa Dps functions to aid to survive HO-mediated oxidative stress. In agreement, a Δ mutant is significantly more susceptible to HO 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 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 HO or O but requires divalent cations and 12-mer Pa Dps.

PubMed: 36902100
DOI: 10.3390/ijms24054669

Experimental method

X-RAY DIFFRACTION (2.25 Å)