2V15

Terbium binding in Streptococcus suis Dpr protein

Summary for 2V15

• Entry DOI: 10.2210/pdb2v15/pdb
• Related: 1UMN 2BW1 2CF7 2UX1
• Descriptor: DNA PROTECTION DURING STARVATION PROTEIN, CHLORIDE ION, TERBIUM(III) ION, ... (6 entities in total)
• Functional Keywords: oxidoreductase, iron, dps-family, ferroxidase, iron-binding, peroxide resistance, iron storage, metal-binding, ferritin-like
• Biological source: STREPTOCOCCUS SUIS
• Total number of polymer chains: 12
• Total formula weight: 227067.33

Authors

Havukainen, H.,Papageorgiou, A.C.,Kauko, A. (deposition date: 2007-05-22, release date: 2008-06-10, Last modification date: 2023-12-13)

Primary citation

Havukainen, H.,Haataja, S.,Kauko, A.,Pulliainen, A.T.,Salminen, A.,Haikarainen, T.,Finne, J.,Papageorgiou, A.C.
Structural basis of the zinc- and terbium-mediated inhibition of ferroxidase activity in Dps ferritin-like proteins.
Protein Sci., 17:1513-1521, 2008

PubMed Abstract: Streptococcus suis Dpr is an iron-binding protein involved in oxidative stress resistance. It belongs to the bacterial Dps protein family whose members form dodecameric assemblies. Previous studies have shown that zinc and terbium inhibit iron incorporation in Listeria innocua Dps protein. In order to gain structural insights into the inhibitory effect of zinc and terbium, the crystal structures of Streptococcus suis Dpr complexes with these ions were determined at 1.8 A and 2.1 A, respectively. Both ions were found to bind at the ferroxidase center and in the same location as iron. In addition, a novel zinc-binding site formed by His40 and His44 was identified. Both His residues were found to be present within all known Streptococcus suis Dpr variants and in Streptococcus pneumoniae, Streptococcus gordonii, and Streptococcus sanguinis Dpr proteins. Amino acid sequence alignment of Dpr with other Dps family members revealed that His44 is highly conserved, in contrast to His40. The inhibitory effect of zinc and terbium on iron oxidation in Dpr was studied in vitro, and it was found that both ions at concentrations >0.2 mM almost completely abolish iron binding. These results provide a structural basis for the inhibitory effect of zinc and terbium in the Dps family of proteins, and suggest a potential role of the Dps proteins in zinc detoxification mechanisms involving the second zinc-binding site.

PubMed: 18552126
DOI: 10.1110/ps.036236.108

Experimental method

X-RAY DIFFRACTION (2.1 Å)