6IZ2

Crystal structure of DinB/YfiT protein DR0053 from D. radiodurans R1

Summary for 6IZ2

• Entry DOI: 10.2210/pdb6iz2/pdb
• Descriptor: DinB/YfiT family protein, ACETATE ION, ZINC ION, ... (4 entities in total)
• Functional Keywords: damage response, four helix bundle, unknown function
• Biological source: Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
• Total number of polymer chains: 2
• Total formula weight: 40074.44

Authors

Kim, M.-K.,Zhang, J.,Zhao, L. (deposition date: 2018-12-18, release date: 2019-05-15, Last modification date: 2024-03-27)

Primary citation

Zhang, J.,Zhao, L.,Seo, H.S.,Jung, J.H.,Choi, J.I.,Kim, M.K.,Lim, S.
Crystal structure of the highly radiation-inducible DinB/YfiT superfamily protein DR0053 from Deinococcus radiodurans R1.
Biochem.Biophys.Res.Commun., 513:354-359, 2019

PubMed Abstract: Deinococcus radiodurans is an extremophilic bacterium well-known for its extraordinary resistance to ionizing radiation and other DNA damage- and oxidative stress-generating agents. In addition to its efficient DNA damage repair and oxidative stress resistance mechanisms, protein family expansions and stress-induced genes/proteins are also regarded as important components that add to the robustness of this bacterium. D. radiodurans encodes specific expansions of 13 DinB/YfiT homologs, which is a relatively large number when compared to those found in Gram-positive bacteria. In this study, we investigated the expression profiles of 13 dinB genes after γ-irradiation, mitomycin C and HO treatment. dr0053 had the highest expression levels after DNA-damage inducing γ-irradiation and MMC treatment, increasing ∼200-fold and ∼16-fold, respectively. We also determined the crystal structure of DR0053 at 2.07 Å resolution. DR0053 adopted a typical four-helix bundle structure that is characteristic of DinB/YfiT proteins. A putative metal binding site was occupied by zinc even though the highly conserved His triad of DinB/YfiT proteins was replaced by Glu-Asn-His.

PubMed: 30961930
DOI: 10.1016/j.bbrc.2019.03.209

Experimental method

X-RAY DIFFRACTION (2.069 Å)