Iron Incorporation into Escherichia coli Dps Gives Rise to a Ferritin-like Microcrystalline Core

Abstract

Escherichia coli Dps belongs to a family of bacterial stress-induced proteins to protect DNA from oxidative damage. It shares with Listeria innocua ferritin several structural features, such as the quaternary assemblage and the presence of an unusual ferroxidase center. Indeed, it was recently recognized to be able to oxidize and incorporate iron. Since ferritins are endowed with the unique capacity to direct iron deposition toward formation of a microcrystalline core, the structure of iron deposited in the E. coli Dps cavity was studied. Polarized single crystal absorption microspectrophotometry of iron-loaded Dps shows that iron ions are oriented. The spectral properties in the high spin 3d 5 configuration point to a crystal form with tetrahedral symmetry where the tetrahedron center is occupied by iron ions and the vertices by oxygen. Crystals of iron-loaded Dps also show that, as in mammalian ferritins, iron does not remain bound to the site after oxidation has taken place. The kinetics of the iron reduction/release process induced by dithionite were measured in the crystal and in solution. The reaction appears to have two phases, with t1 ⁄2 of a few seconds and several minutes at neutral pH values, as in canonical ferritins. This behavior is attributed to a similar composition of the iron core.

Iron-oxo clusters biomineralizing on protein surfaces: Structural analysis of Halobacterium salinarum DpsA in its low- and high-iron states

“…This subsite is equidistant from subsites N22-N24 (3.0 Å) and lacks any interactions with the protein. From this study, it is not yet clear whether the observed NII cluster further increases in size on prolonged iron incubations as larger iron-oxo clusters or even as nanocrystals, which may generally be disordered inside the protein shell and hence not trackable by x-ray crystallography (30).…”

The N-terminal Extensions of Deinococcus radiodurans Dps-1 Mediate DNA Major Groove Interactions as well as Assembly of the Dodecamer

“…Once assembly has occurred, stability of the dodecamer is accomplished through extensive interactions between neighboring four-helix bundles. An N-terminal deletion mutant of L. lactis DpsA (lacking residues [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20], in which the N-terminal metal coordination was also disrupted by site directed mutagenesis, was unable to interact with DNA (16). But this DpsA variant eluted from a gel filtration column at a similar elution volume as native DpsA, suggesting that unlike Dps-1, disruption of the metal center at the N terminus has no effect on the dodecameric assembly of DpsA (16).…”

“…Thus, the presence of iron increases the probability of oxidative damage to cellular components. Dps, initially studied in Escherichia coli, was shown to protect DNA by its ability to chelate ferrous iron and also by its physical association with DNA (2)(3)(4)(5).…”

Identification and biochemical properties of Dps (starvation‐induced DNA binding protein) from cyanobacterium Anabaena sp. PCC 7120

“…Based on sequence analysis, Dps are endowed with conserved ferroxidase domain, implicating that they also belong to ferritin family. Following structural and related researches (12,13) further illuminated that Dps proteins are able to capture up to hundreds of free iron atoms and convert them into available forms, thereby guaranteeing continuous supply of iron to microorganisms.…”