1UVH

X-ray structure of Dps from Mycobacterium smegmatis

1UVH の概要

• エントリーDOI: 10.2210/pdb1uvh/pdb
• 分子名称: STARVATION-INDUCED DNA PROTECTING PROTEIN, FE (III) ION (3 entities in total)
• 機能のキーワード: dna protection from oxidative damage, dna binding protein
• 由来する生物種: MYCOBACTERIUM SMEGMATIS
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 81418.62

構造登録者

Ilari, A.,Ceci, P.,Falvo, E.,Chiancone, E. (登録日: 2004-01-20, 公開日: 2005-02-09, 最終更新日: 2023-12-13)

主引用文献

Ceci, P.,Ilari, A.,Falvo, E.,Giangiacomo, L.,Chiancone, E.
Reassessment of Protein Stability, DNA Binding, and Protection of Mycobacterium Smegmatis Dps.
J.Biol.Chem., 280:34776-, 2005

PubMed Abstract: The structure and function of Mycobacterium smegmatis Dps (DNA-binding proteins from starved cells) and of the protein studied by Gupta and Chatterji, in which the C terminus that is used for binding DNA contains a histidine tag, have been characterized in parallel. The native dodecamer dissociated reversibly into dimers above pH 7.5 and below pH 6.0, with apparent pK(a) values of approximately 7.65 and 4.75; at pH approximately 4.0, dimers formed monomers. Based on structural analysis, the two dissociation steps have been attributed to breakage of the salt bridges between Glu(157) and Arg(99) located at the 3-fold symmetry axes and to protonation of Asp(66) hydrogen-bonded to Lys(36) across the dimer interface, respectively. The C-terminal tag did not affect subunit dissociation, but altered DNA binding dramatically. At neutral pH, protonation of the histidine tag promoted DNA condensation, whereas in the native C terminus, compensation of negative and positive charges led to DNA binding without condensation. This different mode of interaction with DNA has important functional consequences as indicated by the failure of the native protein to protect DNA from DNase-mediated cleavage and by the efficiency of the tagged protein in doing so as a result of DNA sequestration in the condensates. Chemical protection of DNA from oxidative damage is realized by Dps proteins in a multistep iron oxidation/uptake/mineralization process. Dimers have a decreased protection efficiency due to disruption of the dodecamer internal cavity, where iron is deposited and mineralized after oxidation at the ferroxidase center.

PubMed: 16030020
DOI: 10.1074/JBC.M502343200

実験手法

X-RAY DIFFRACTION (2.8 Å)