2D5K

Crystal structure of Dps from Staphylococcus aureus

Summary for 2D5K

• Entry DOI: 10.2210/pdb2d5k/pdb
• Related: 1DPS 1JI5 1JIG 1N1Q 1QGH 1UMN
• Descriptor: Dps family protein, GLYCEROL (3 entities in total)
• Functional Keywords: four helix bundle, metal binding protein
• Biological source: Staphylococcus aureus subsp. aureus
• Total number of polymer chains: 4
• Total formula weight: 71575.24

Authors

Tanaka, Y.,Yao, M.,Watanabe, N.,Tanaka, I. (deposition date: 2005-11-02, release date: 2006-10-17, Last modification date: 2023-10-25)

Primary citation

Ushijima, Y.,Ohniwa, R.L.,Maruyama, A.,Saito, S.,Tanaka, Y.,Morikawa, K.
Nucleoid compaction by MrgA(Asp56Ala/Glu60Ala) does not contribute to staphylococcal cell survival against oxidative stress and phagocytic killing by macrophages
FEMS Microbiol. Lett., 360:144-151, 2014

PubMed Abstract: Staphylococcus aureus MrgA (encoded by mrgA) belongs to the Dps family of proteins, which play important roles in coping with various stresses. The staphylococcal mrgA gene is specifically expressed under oxidative stress conditions and is one of the most highly induced genes during phagocytic killing by macrophages. We previously reported that mrgA is essential for oxidative stress resistance, and can cause nucleoid compaction. However, whether nucleoid compaction by itself would contribute to oxidative stress resistance was hard to determine, because Dps family proteins generally have ferroxidase activity to prevent hydroxyl radical formation via the Fenton reaction. In this study, we resolved the crystal structure of MrgA and conducted mutation analysis of Asp56 and Glu60, which are located at the expected ferroxidase centre. In the strain expressing Asp56Ala/Glu60Ala MrgA (termed MrgA*), MrgA* retained dodecamer formation and nucleoid compaction ability. By contrast, the ferroxidase activity of MrgA* decreased by about half. Viability of the mrgA* strain was as low as the mrgA null mutant in oxidative stress and phagocytic killing assays. These results suggest that nucleoid compaction by itself is insufficient for oxidative stress resistance, and Asp56 and Glu60 constitute essential molecular sites in MrgA for oxidative stress resistance and survival against phagocytic killing.

PubMed: 25227518
DOI: 10.1111/1574-6968.12598

Experimental method

X-RAY DIFFRACTION (1.85 Å)