Crystal structure of the RNA 2′,3′-cyclic phosphodiesterase from<i>Deinococcus radiodurans</i>

Han, Wanchun; Cheng, Jiahui; Zhou, Changjiang; Hua, Yuejin; Zhao, Ye

doi:10.1107/s2053230x17004964

Cited by 1 publication

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“…to high-dose IR or toxic concentrations of mitomycin C. Along the same lines, Han et al (35) recently reported that another putative Deinococcus RNA end-processing enzyme, DR_2239, plays an important role in resistance to nucleic acid damage. The DR_2239 gene, which is strongly transcriptionally upregulated during recovery from IR (25,26), encodes a member of the 2H phosphoesterase enzyme superfamily (36). Disruption of the DR_2239 gene renders Deinococcus 5-fold more sensitive to 10 kGy of IR exposure but 2,000-fold more sensitive to treatment with 40 g/ml mitomycin C vis à vis the wild-type strain (35).…”

Section: Discussionmentioning

confidence: 99%

Deinococcus radiodurans HD-Pnk, a Nucleic Acid End-Healing Enzyme, Abets Resistance to Killing by Ionizing Radiation and Mitomycin C

Schmier

Shuman

2018

J Bacteriol

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5'- and 3'-end healing are key steps in nucleic acid break repair in which 5'-OH and 3'-PO or 2',3'-cyclic-PO ends are converted to 5'-PO and 3'-OH termini suitable for sealing by polynucleotide ligases. Here, we characterize HD-Pnk as a bifunctional end-healing enzyme composed of N-terminal HD (histidine-aspartate) phosphoesterase and C-terminal P-loop polynucleotide kinase (Pnk) domains. HD-Pnk phosphorylates 5'-OH DNA in the presence of ATP and magnesium. HD-Pnk has 3'-phosphatase and 2',3'-cyclic-phosphodiesterase activity in the presence of transition metals, optimally cobalt or copper, and catalyzes copper-dependent hydrolysis of-nitrophenylphosphate. HD-Pnk is encoded by the LIG-PARG-HD-Pnk three-gene operon, which includes polynucleotide ligase and poly(ADP-ribose) glycohydrolase genes. We show that whereas HD-Pnk is inessential for growth, its absence sensitizes by 80-fold bacteria to killing by 9 kGy of ionizing radiation (IR). HD-Pnk protein is depleted during early stages of post-IR recovery and then replenished at 15 h, after reassembly of the genome from shattered fragments. ΔHD-Pnk mutant cells are competent for genome reassembly, as gauged by pulsed-field gel electrophoresis. Our findings suggest a role for HD-Pnk in repairing residual single-strand gaps or nicks in the reassembled genome. HD-Pnk-Ala mutations that ablate kinase or phosphoesterase activity sensitize to killing by mitomycin C. End healing is a process whereby nucleic acid breaks with "dirty" 3'-PO or 2',3'-cyclic-PO and 5'-OH ends are converted to 3'-OH and 5'-PO termini that are amenable to downstream repair reactions. is resistant to massive doses of ionizing radiation (IR) that generate hundreds of dirty DNA double-strand breaks and thousands of single-strand breaks. This study highlights HD-Pnk as a bifunctional 3'- and 5'-end-healing enzyme that helps protect against killing by IR. HD-Pnk appears to act late in the process of post-IR recovery, subsequent to genome reassembly from shattered fragments. HD-Pnk also contributes to resistance to killing by mitomycin C. These findings are significant in that they establish a role for end-healing enzymes in bacterial DNA damage repair.

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