The structure of DdrB from Deinococcus: a new fold for single-stranded DNA binding proteins.

Nucleic Acids Research
Seiji N Sugiman-Marangos, Murray S Junop

Abstract

Deinococcus spp. are renowned for their amazing ability to recover rapidly from severe genomic fragmentation as a result of exposure to extreme levels of ionizing radiation or desiccation. Despite having been originally characterized over 50 years ago, the mechanism underlying this remarkable repair process is still poorly understood. Here, we report the 2.8 A structure of DdrB, a single-stranded DNA (ssDNA) binding protein unique to Deinococcus spp. that is crucial for recovery following DNA damage. DdrB forms a pentameric ring capable of binding single-stranded but not double-stranded DNA. Unexpectedly, the crystal structure reveals that DdrB comprises a novel fold that is structurally and topologically distinct from all other single-stranded binding (SSB) proteins characterized to date. The need for a unique ssDNA binding function in response to severe damage, suggests a distinct role for DdrB which may encompass not only standard SSB protein function in protection of ssDNA, but also more specialized roles in protein recruitment or DNA architecture maintenance. Possible mechanisms of DdrB action in damage recovery are discussed.

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Citations

Nov 23, 2011·Proceedings of the National Academy of Sciences of the United States of America·Sonia PaytubiMalcolm F White
Oct 13, 2011·Molecular & Cellular Proteomics : MCP·Bhakti Basu, Shree Kumar Apte
Nov 30, 2012·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Seiji Sugiman-Marangos, Murray Junop
Mar 5, 2011·Microbiology and Molecular Biology Reviews : MMBR·Dea Slade, Miroslav Radman
Aug 28, 2014·BioMed Research International·Yen-Hua Huang, Cheng-Yang Huang
Apr 5, 2016·Proceedings of the National Academy of Sciences of the United States of America·Seiji N Sugiman-MarangosMurray S Junop
Jun 5, 2015·Extremophiles : Life Under Extreme Conditions·Alexandra- Cristina MunteanuAdrian Andries
Nov 3, 2020·Computational and Structural Biotechnology Journal·Zijing ChenYe Zhao
Jul 25, 2021·International Journal of Molecular Sciences·Katerina ZakharovaCharles E Bell

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Methods Mentioned

BETA
X-ray
electrophoretic mobility shift assay
electrophoresis
gel-filtration

Software Mentioned

iCOPS
3D
HKL2000
PSIpred
AreaIMol
Refine
DALI
Phenix
BLAST
Coot

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