Structure of the DPS-Like Protein from Sulfolobus solfataricus Reveals a Bacterioferritin-Like Dimetal Binding Site within a DPS-Like Dodecameric Assembly^,

Abstract

The superfamily of ferritin-like proteins has recently expanded to include a phylogenetically distinct class of proteins termed DPS-like (DPSL) proteins. Despite their distinct genetic signatures, members of this subclass share considerable similarity to previously recognized DPS proteins. Like DPS, these proteins are expressed in response to oxidative stress, form dodecameric cage-like particles, preferentially utilize H 2 O 2 in the controlled oxidation of Fe 2+ , and possess a short N-terminal extension implicated in stabilizing cellular DNA. Given these extensive similarities, the functional properties responsible for the preservation of the DPSL signature in the genomes of diverse prokaryotes have been unclear. Here, we describe the crystal structure of a DPSL protein from the thermoacidophilic archaeon Sulfolobus solfataricus. Although the overall fold of the polypeptide chain and the oligomeric state of this protein are indistinguishable from those of authentic DPS proteins, several important differences are observed. First, rather than a ferroxidase site at the subunit interface, as is observed in all other DPS proteins, the ferroxidase site in SsDPSL is buried within the four-helix bundle, similar to bacterioferritin. Second, the structure reveals a channel leading from the exterior surface of SsDPSL to the bacterioferritin-like dimetal binding site, possibly allowing divalent cations and/or H 2 O 2 to access the active site. Third, a pair of cysteine residues unique to DPSL proteins is found adjacent to the dimetal binding site juxtaposed between the exterior surface of the protein and the active site channel. The cysteine residues in this thioferritin motif may play a redox active role, possibly serving to recycle iron at the ferroxidase center.Oxidative stress, in which reactive oxygen species (ROS 1 ) react indiscriminately with DNA, proteins and lipids, is a universal phenomenon experienced by organisms in all domains of life. † This work was supported by the National Institutes of Health (DK57776) and the National Aeronautics and Space Administration NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author ManuscriptCumulative damage from ROS is now thought to contribute to numerous disease states and a multitude of reports in the primary literature describe the role of oxidative stress in human diseases. Thus, understanding molecular responses to oxidative stress is of significant medical importance. Although much work has been done to characterize the management of oxidative stress in eukaryotes and bacteria, the oxidative stress response in archaea is poorly understood. However, elucidation of the protective mechanisms utilized in archaea is certain to provide insight into the diversity of molecular responses to oxidative stress across all domains of life.Numerous mechanisms have evolved to minimize and repair the damaging effects of ROS. These include enzymes such as superoxide dismutase and superoxide reductase, which convert the superoxide ion into molecular oxygen (O 2 ) and/...

Characterization of the Bacteroides fragilis bfr Gene Product Identifies a Bacterial DPS-Like Protein and Suggests Evolutionary Links in the Ferritin Superfamily

“…Archaeal DPSL proteins are further distinguished by a pair of conserved cysteine residues, apparently unique to the DPSL proteins, that are juxtaposed to the bacterioferritin-like dimetal binding site. This cysteine pair and the bacterioferritin-like ferrioxidase center, all housed within a dodecameric oligomer, are hallmarks of the archaeal DPSL proteins and can be observed in the primary sequence as the thioferritin motif (28). Together, these features differentiate DPSL as a new member of the ferritin superfamily.…”

“…For these reasons, the roles of ferritin (ftnA) and DPS in the B. fragilis oxidative stress response have been investigated in detail (33,(49)(50)(51)(52)61). However, in addition to ferritin and DPS, B.fragilis has a bacterioferritin-related gene, bfr, and a recent expression microarray study shows that expression of the bfr gene is significantly induced by exposure to air, suggesting that it might also help protect against ROS (61).Further interest in B. fragilis bfr and its gene product stems from a study suggesting that it might actually be more closely related to the archaeal DPS-like (DPSL) proteins and that the bfr gene product is a member of the newly identified miniferritin that is structurally distinct from both the larger ferritin and bacterioferritin 24-mers and dodecameric DPS (18,28). Like DPS, the archaeal DPSL proteins are expressed in response to oxidative stress, adopt the overall fold of the DPS subunit, and form dodecameric (12-mer) cage-like particles (28,40,47,67).…”

“…Further interest in B. fragilis bfr and its gene product stems from a study suggesting that it might actually be more closely related to the archaeal DPS-like (DPSL) proteins and that the bfr gene product is a member of the newly identified miniferritin that is structurally distinct from both the larger ferritin and bacterioferritin 24-mers and dodecameric DPS (18,28). Like DPS, the archaeal DPSL proteins are expressed in response to oxidative stress, adopt the overall fold of the DPS subunit, and form dodecameric (12-mer) cage-like particles (28,40,47,67).…”

“…Like DPS, the archaeal DPSL proteins are expressed in response to oxidative stress, adopt the overall fold of the DPS subunit, and form dodecameric (12-mer) cage-like particles (28,40,47,67). However, unlike DPS, where the ferroxidase site is located at the subunit interface, DPSL proteins contain a di-iron carboxylate binding site buried within the four-helix bundle of each subunit, much like ferritin and bacterioferritin.…”

SEp22, Salmonella Dps, a Key Molecule Bearing Both Pathogenicity and Resistance to Environmental Stresses in Salmonella

“…Intensive structural research, especially using with X-ray crystallography, has revealed a highly conserved structural fold of proteins within the Dps protein family isolated from different organisms. 12,16,17,[19][20][21][22][23][24][25] However, most of these studies mainly showed structural features common to other ferritins characterized in bacteria, including the paradigmatic ferritin (FtnA) and the hemecontaining bacterioferritin (Bfr), which are composed of at least 12 subunits folded into four-helix bundles and assembled into spherical protein shells as Dps is. 13,26) E. coli Dps has a very compact and stable structure with protrusion of the highly flexible and lysine-rich N-terminus (Fig.…”