Biochemical and Structural Analyses Shed Light on the Mechanisms of RadD DNA Binding and Its ATPase from Escherichia coli

doi:10.3390/ijms24010741

	Biochemical and Structural Analyses Shed Light on the Mechanisms of RadD DNA Binding and Its ATPase from Escherichia coli
	Tian, Li-Fei 1; Kuang, Xiaolin 1; Ding, Ke 1,2; Gao, Hongwei 1,2; Tang, Qun 1; Yan, Xiao-Xue 1; Xu, Wenqing1,3
	2023
发表期刊	INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
EISSN	1422-0067
卷号	24 期号:1
发表状态	已发表
DOI	10.3390/ijms24010741
摘要	DNA double-strand breaks (DSBs) are the most perilous and harmful type of DNA damage and can cause tumorigenesis or cell death if left repaired with an error or unrepaired. RadD, a member of the SF2 family, is a recently discovered DNA repair protein involved in the repair of DSBs after radiation or chemical damage. However, the function of RadD in DNA repair remains unclear. Here, we determined the crystal structures of RadD/ATP gamma S and RadD/ATP complexes and revealed the novel mechanism of RadD binding to DNA and ATP hydrolysis with biochemical data. In the RadD catalytic center, the Gly34 and Gly36 on the P-loop are key residues for ATP binding besides the conserved amino acids Lys37 and Arg343 in the SF2 family. If any of them mutate, then RadD loses ATPase activity. Asp117 polarizes the attacking water molecule, which then starts a nucleophilic reaction toward gamma-phosphate, forming the transition state. Lys68 acts as a pocket switch to regulate substrate entry and product release. We revealed that the C-terminal peptide of single-stranded DNA-binding protein (SSB) binds the RadD C-terminal domain (CTD) and promotes the RadD ATPase activity. Our mutagenesis studies confirmed that the residues Arg428 on the zinc finger domain (ZFD) and Lys488 on the CTD of RadD are the key sites for binding branched DNA. Using the Coot software combined with molecular docking, we propose a RadD-binding DNA model for the DNA damage repair process.
关键词	DNA repair ATPase helicase superfamily 2 SSB protein DNA binding crystal structure
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收录类别	SCI ; SCOPUS
语种	英语
资助项目	National Natural Science Foundation of China[XDB37030302] ; [32171218]
WOS研究方向	Biochemistry & Molecular Biology ; Chemistry
WOS类目	Biochemistry & Molecular Biology ; Chemistry, Multidisciplinary
WOS记录号	WOS:000910247200001
出版者	MDPI
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/272813
专题	生命科学与技术学院_PI研究组_许文青组
通讯作者	Yan, Xiao-Xue; Xu, Wenqing
作者单位	1.Chinese Acad Sci, Inst Biophys, CAS Ctr Excellence Biomacromol, Natl Lab Biomacromol, Beijing 100101, Peoples R China 2.Univ Chinese Acad Sci, Coll Life Sci, Beijing 100049, Peoples R China 3.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai 201210, Peoples R China
通讯作者单位	生命科学与技术学院
推荐引用方式 GB/T 7714	Tian, Li-Fei,Kuang, Xiaolin,Ding, Ke,et al. Biochemical and Structural Analyses Shed Light on the Mechanisms of RadD DNA Binding and Its ATPase from Escherichia coli[J]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,2023,24(1).
APA	Tian, Li-Fei.,Kuang, Xiaolin.,Ding, Ke.,Gao, Hongwei.,Tang, Qun.,...&Xu, Wenqing.(2023).Biochemical and Structural Analyses Shed Light on the Mechanisms of RadD DNA Binding and Its ATPase from Escherichia coli.INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,24(1).
MLA	Tian, Li-Fei,et al."Biochemical and Structural Analyses Shed Light on the Mechanisms of RadD DNA Binding and Its ATPase from Escherichia coli".INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 24.1(2023).