1N1Q

Crystal structure of a Dps protein from Bacillus brevis

Summary for 1N1Q

• Entry DOI: 10.2210/pdb1n1q/pdb
• Descriptor: DPS Protein, MU-OXO-DIIRON (3 entities in total)
• Functional Keywords: four-helix bundle, unknown function
• Biological source: Brevibacillus brevis
• Cellular location: Cytoplasm, nucleoid : P83695
• Total number of polymer chains: 4
• Total formula weight: 65884.02

Authors

Ren, B.,Tibbelin, G.,Kajino, T.,Asami, O.,Ladenstein, R. (deposition date: 2002-10-19, release date: 2003-05-27, Last modification date: 2024-02-14)

Primary citation

Ren, B.,Tibbelin, G.,Kajino, T.,Asami, O.,Ladenstein, R.
The Multi-layered Structure of Dps with a Novel Di-nuclear Ferroxidase Center
J.Mol.Biol., 329:467-477, 2003

PubMed Abstract: The crystallization of cellular components represents a unique survival strategy for bacterial cells under stressed conditions. A highly ordered, layered structure is often formed in such a process, which may involve one or more than one type of bio-macromolecules. The main advantage of biocrystallization has been attributed to the fact that it is a physical process and thus is independent of energy consumption. Dps is a protein that crystallizes to form a multi-layered structure in starved cells in order to protect DNA against oxidative damage and other detrimental factors. The multi-layered crystal structure of a Dps protein from Bacillus brevis has been revealed for the first time at atomic resolution in the absence of DNA. Inspection of the structure provides the first direct evidence for the existence of a di-nuclear ferroxidase center, which possesses unique features among all the di-iron proteins identified so far. It constitutes the structural basis for the ferroxidase activity of Dps in the crystalline state as well as in solution. This finding proves that the enzymatic process of detoxification of metal ions, which may cause severe oxidative damage to DNA, is the other important aspect of the defense mechanism performed by Dps. In the multi-layered structure, Dps dodecamers are organized in a highly ordered manner. They adopt the classic form of hexagonal packing in each layer of the structure. Such arrangement results in reinforced structural features that would facilitate the attraction and absorption of metal ions from the environment. The highly ordered layered structure may provide an ideal basis for the accommodation of DNA between the layers so that it can be isolated and protected from harmful factors under stress conditions.

PubMed: 12767829
DOI: 10.1016/S0022-2836(03)00466-2

Experimental method

X-RAY DIFFRACTION (2.2 Å)