Literature DB >> 22102252

Purification, crystallization and preliminary X-ray analysis of the DndE protein from Salmonella enterica serovar Cerro 87, which is involved in DNA phosphorothioation.

Fukun Chen1, Kui Lin, Zhenyi Zhang, Leyi Chen, Xiaoshan Shi, Chunyang Cao, Zhijun Wang, Jingdan Liang, Zixin Deng, Geng Wu.   

Abstract

The phenomenon of DNA phosphorothioation (DNA sulfur modification) is widespread among prokaryotes and may serve as a mechanism to restrict gene transfer among bacteria. DndE is one of five essential proteins that are required for the DNA phosphorothioation process. However, its exact biochemical role in sulfur modification of DNA remains unclear. In this study, the DndE protein homologue from Salmonella enterica serovar Cerro 87 was overexpressed, purified and crystallized. The crystals of the DndE protein diffracted to 2.7 Å resolution and belonged to space group P3(1)21. These results will facilitate detailed structural analysis of DndE and further elucidation of its biochemical function.
© 2011 International Union of Crystallography. All rights reserved.

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Year:  2011        PMID： 22102252      PMCID： PMC3212471          DOI： 10.1107/S1744309111036694

Source DB:  PubMed          Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun        ISSN： 1744-3091


  10 in total

1.  DNA phosphorothioation is widespread and quantized in bacterial genomes.

Authors:  Lianrong Wang; Shi Chen; Kevin L Vergin; Stephen J Giovannoni; Simon W Chan; Michael S DeMott; Koli Taghizadeh; Otto X Cordero; Michael Cutler; Sonia Timberlake; Eric J Alm; Martin F Polz; Jarone Pinhassi; Zixin Deng; Peter C Dedon
Journal:  Proc Natl Acad Sci U S A       Date:  2011-02-01       Impact factor: 11.205

2.  Functional analysis of spfD gene involved in DNA phosphorothioation in Pseudomonas fluorescens Pf0-1.

Authors:  Fen Yao; Tiegang Xu; Xiufen Zhou; Zixin Deng; Delin You
Journal:  FEBS Lett       Date:  2009-01-24       Impact factor: 4.124

3.  A novel DNA modification by sulphur.

Authors:  Xiufen Zhou; Xinyi He; Jingdan Liang; Aiying Li; Tiegang Xu; Tobias Kieser; John D Helmann; Zixin Deng
Journal:  Mol Microbiol       Date:  2005-09       Impact factor: 3.501

4.  A novel host-specific restriction system associated with DNA backbone S-modification in Salmonella.

Authors:  Tiegang Xu; Fen Yao; Xiufen Zhou; Zixin Deng; Delin You
Journal:  Nucleic Acids Res       Date:  2010-07-12       Impact factor: 16.971

5.  A novel DNA modification by sulfur: DndA is a NifS-like cysteine desulfurase capable of assembling DndC as an iron-sulfur cluster protein in Streptomyces lividans.

Authors:  Delin You; Lianrong Wang; Fen Yao; Xiufen Zhou; Zixin Deng
Journal:  Biochemistry       Date:  2007-05-01       Impact factor: 3.162

6.  Site-specific degradation of Streptomyces lividans DNA during electrophoresis in buffers contaminated with ferrous iron.

Authors:  X Zhou; Z Deng; J L Firmin; D A Hopwood; T Kieser
Journal:  Nucleic Acids Res       Date:  1988-05-25       Impact factor: 16.971

7.  Cleavage of phosphorothioated DNA and methylated DNA by the type IV restriction endonuclease ScoMcrA.

Authors:  Guang Liu; Hong-Yu Ou; Tao Wang; Li Li; Huarong Tan; Xiufen Zhou; Kumar Rajakumar; Zixin Deng; Xinyi He
Journal:  PLoS Genet       Date:  2010-12-23       Impact factor: 5.917

8.  DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites.

Authors:  Jingdan Liang; Zhijun Wang; Xinyi He; Jialiang Li; Xiufen Zhou; Zixin Deng
Journal:  Nucleic Acids Res       Date:  2007-04-16       Impact factor: 16.971

9.  dndDB: a database focused on phosphorothioation of the DNA backbone.

Authors:  Hong-Yu Ou; Xinyi He; Yucheng Shao; Cui Tai; Kumar Rajakumar; Zixin Deng
Journal:  PLoS One       Date:  2009-04-09       Impact factor: 3.240

10.  DNA phosphorothioation in Streptomyces lividans: mutational analysis of the dnd locus.

Authors:  Tiegang Xu; Jingdan Liang; Shi Chen; Lianrong Wang; Xinyi He; Delin You; Zhijun Wang; Aiying Li; Zhongli Xu; Xiufen Zhou; Zixin Deng
Journal:  BMC Microbiol       Date:  2009-02-20       Impact factor: 3.605
  10 in total
  4 in total

1.  Pathological phenotypes and in vivo DNA cleavage by unrestrained activity of a phosphorothioate-based restriction system in Salmonella.

Authors:  Bo Cao; Qiuxiang Cheng; Chen Gu; Fen Yao; Michael S DeMott; Xiaoqing Zheng; Zixin Deng; Peter C Dedon; Delin You
Journal:  Mol Microbiol       Date:  2014-07-23       Impact factor: 3.501

2.  Crystal structure of the cysteine desulfurase DndA from Streptomyces lividans which is involved in DNA phosphorothioation.

Authors:  Fukun Chen; Zhenyi Zhang; Kui Lin; Tianle Qian; Yan Zhang; Delin You; Xinyi He; Zhijun Wang; Jingdan Liang; Zixin Deng; Geng Wu
Journal:  PLoS One       Date:  2012-05-03       Impact factor: 3.240

Review 3.  DNA phosphorothioate modification-a new multi-functional epigenetic system in bacteria.

Authors:  Lianrong Wang; Susu Jiang; Zixin Deng; Peter C Dedon; Shi Chen
Journal:  FEMS Microbiol Rev       Date:  2019-03-01       Impact factor: 16.408

4.  Development of Methods Derived from Iodine-Induced Specific Cleavage for Identification and Quantitation of DNA Phosphorothioate Modifications.

Authors:  Sucheng Zhu; Tao Zheng; Lingxin Kong; Jinli Li; Bo Cao; Michael S DeMott; Yihua Sun; Ying Chen; Zixin Deng; Peter C Dedon; Delin You
Journal:  Biomolecules       Date:  2020-10-28
  4 in total

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