Crystal structure of the highly radiation-inducible DinB/YfiT superfamily protein DR0053 from Deinococcus radiodurans R1

Jing Zhang; Lei Zhao; Ho Seong Seo; Jong-Hyun Jung; Jong-Il Choi; Min-Kyu Kim; Sangyong Lim

doi:10.1016/j.bbrc.2019.03.209

Crystal structure of the highly radiation-inducible DinB/YfiT superfamily protein DR0053 from Deinococcus radiodurans R1

Biochem Biophys Res Commun. 2019 May 28;513(2):354-359. doi: 10.1016/j.bbrc.2019.03.209. Epub 2019 Apr 5.

Authors

Jing Zhang¹, Lei Zhao¹, Ho Seong Seo², Jong-Hyun Jung², Jong-Il Choi³, Min-Kyu Kim⁴, Sangyong Lim⁵

Affiliations

¹ Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Biotechnology and Bioengineering, Interdisciplinary Program for Bioenergy and Biomaterials, Chonnam National University, Gwangju, 61186, Republic of Korea.
² Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea.
³ Department of Biotechnology and Bioengineering, Interdisciplinary Program for Bioenergy and Biomaterials, Chonnam National University, Gwangju, 61186, Republic of Korea.
⁴ Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea. Electronic address: mkkim@kaeri.re.kr.
⁵ Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea. Electronic address: saylim@kaeri.re.kr.

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

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 H₂O₂ 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.

Keywords: D. radiodurans; DR0053 crystal structure; Damage-inducible protein; DinB/YfiT superfamily; Radiation-resistance.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alkylating Agents / pharmacology
Bacterial Proteins / chemistry*
Bacterial Proteins / genetics
Crystallography, X-Ray
Deinococcus / chemistry*
Deinococcus / drug effects
Deinococcus / genetics
Deinococcus / radiation effects
Gamma Rays
Gene Expression Regulation, Bacterial / drug effects
Gene Expression Regulation, Bacterial / radiation effects
Mitomycin / pharmacology
Models, Molecular
Protein Conformation

Substances

Alkylating Agents
Bacterial Proteins
Mitomycin