5WW4

Crystal structure of the second DNA-Binding protein under starvation from Mycobacterium smegmatis soaked with iron in the ratio of 48 iron atoms per dodecamer

Summary for 5WW4

• Entry DOI: 10.2210/pdb5ww4/pdb
• Related: 5WW3 5WW5 5WW6 5WW7 5WW8 5WW9
• Descriptor: Putative starvation-induced DNA protecting protein/Ferritin and Dps, FE (III) ION, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: ferritin-like fold, dna binding, ferroxidation, oxidoreductase, dna binding protein
• Biological source: Mycobacterium smegmatis str. MC2 155
• Total number of polymer chains: 4
• Total formula weight: 71985.73

Authors

Williams, S.M.,Chatterji, D. (deposition date: 2016-12-31, release date: 2017-08-09, Last modification date: 2024-03-20)

Primary citation

Williams, S.M.,Chatterji, D.
Flexible aspartates propel iron to the ferroxidation sites along pathways stabilized by a conserved arginine in Dps proteins from Mycobacterium smegmatis
Metallomics, 9:685-698, 2017

PubMed Abstract: DNA-binding proteins under starvation (Dps) are dodecameric nano-compartments for iron oxidation and storage in bacterial cells. These proteins have roughly spherical structures with a hollow interior where iron is stored. Through mutational analysis of a conserved arginine residue in the second Dps protein from Mycobacterium smegmatis, we have identified residues which stabilize the interfaces between the iron entry and ferroxidation sites. Also, we have used X-ray crystallography to determine the structures of co-crystals of iron and Dps in varying proportions and compare the changes in these ligand-bound forms with respect to the apo-protein. The iron-loaded proteins of low, medium and high iron-bound forms were found to exhibit aspartate residues with alternate conformations, some of which could be directly linked to the sites of ferroxidation and iron entry. We conclude that the increased flexibility of aspartates in the presence of iron facilitates its movement from the entry site to the ferroxidaton site, and the two active sites are stabilized by the interactions of a conserved arginine residue R73.

PubMed: 28418062
DOI: 10.1039/c7mt00008a

Experimental method

X-RAY DIFFRACTION (2.05 Å)