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

Abstract

The crystal structure of the Dps-like (Dps, DNA-protecting protein during starvation) ferritin protein DpsA from the halophile Halobacterium salinarum was determined with low endogenous iron content at 1.6-Å resolution. The mechanism of iron uptake and storage was analyzed in this noncanonical ferritin by three highresolution structures at successively increasing iron contents. In the high-iron state of the DpsA protein, up to 110 iron atoms were localized in the dodecameric protein complex. For ultimate iron storage, the archaeal ferritin shell comprises iron-binding sites for iron translocation, oxidation, and nucleation. Initial iron-protein interactions occur through acidic residues exposed along the outer surface in proximity to the iron entry pore. This narrow pore permits translocation of ions toward the ferroxidase centers via two discrete steps. Iron oxidation proceeds by transient formation of tri-iron ferroxidase centers. Iron storage by biomineralization inside the ferritin shell occurs at two iron nucleation centers. Here, a single iron atom provides a structural seed for iron-oxide cluster formation. The clusters with up to five iron atoms adopt a geometry that is different from natural biominerals like magnetite but resembles iron clusters so far known only from bioinorganic model compounds.ferritin ͉ iron-binding ͉ inorganic cluster formation ͉ x-ray crystal structure

An archaeal antioxidant: Characterization of a Dps-like protein from Sulfolobus solfataricus

“…Dps proteins are widely distributed across the bacterial domain; however, before this study, only one other archaeal Dps had been described (DpsA) (35). Interestingly, our phylogenetic analysis indicates that the DpsA protein from Halobacterium salinarum is more closely related to members of the previously identified Dps subclass than it is to the new, predominantly archaeal, Dps subclass identified in this study.…”

“…These suggestions have recently been corroborated by N-terminal deletion mutants of E. coli Dps that do not bind DNA (38). Multiple sequence alignments identify basic residues in extended N-terminal domains of both the SsDps and in the Dps-like protein from H. salinarum, suggesting their role in DNA association (35,39,40). A short C-terminal extension of the SsDps protein also contains three basic amino acids that may also play a role in DNA binding (Fig.…”

From genomes to function: haloarchaea as model organisms

“…While the favourite child of 'mesohalic' biochemists, ion-exchange chromatography, in many cases cannot be used, all other principles are readily available, and numerous proteins have been isolated and characterized. Crystallization and X-ray diffraction have been used to generate high-resolution structures of soluble proteins, membrane proteins in several functional states, membrane protein complexes and the large subunit of the ribosome (selected recent examples: Zeth et al, 2004;Schobert et al, 2003;Gordeliy et al, 2002;Tu et al, 2005).…”

Nanoscale device architectures derived from biological assemblies: The case of tobacco mosaic virus and (apo)ferritin

“…50,51) In addition, there are ferroxidase centers around the twofold axis. 50,51) Similar to apoferritin, the Dps cavity has been used as a nanoscale chamber for NP formation. 25,52,53) The N-and C-termini, which are both positioned on its outer surface, have been used to introduce additional functionalities for device applications, 54) such as dye-sensitized solar cells.…”