scholarly journals How Mg2+ stimulates DNA repair in prokaryotic (6-4) photolyases

2018 ◽  
Author(s):  
Hongju Ma ◽  
Daniel Holub ◽  
Natacha Gillet ◽  
Gero Kaeser ◽  
Katharina Thoulass ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Dna Repair ◽  
Amino Acid ◽  
Dna Binding ◽  
Freshwater Environment ◽  
Dna Lesion ◽  
Dna Binding Site ◽  
Positively Charged ◽  
Overlapping Region ◽  
Charge Stabilization

AbstractProkaryotic (6-4) photolyases branch at the base of the evolution of cryptochromes and photolyases. In the Agrobacterium (6-4) photolyase PhrB, the repair of DNA with UV-induced (6-4) pyrimidin dimers is stimulated by Mg2+. We show that Mg2+ is required for efficient lesion binding and for charge stabilization after electron transfer from the FADH- chromophore to the DNA lesion. Two highly conserved Asp residues close to the DNA binding site are essential for the Mg2+ effect. Simulations showed that two Mg2+ bind to the region around these residues. DNA repair by eukaryotic (6-4) photolyases is not increased by Mg2+. Here, the structurally overlapping region contains no Asp but positively charged Lys or Arg. During evolution, charge stabilization and DNA binding by Mg2+ was therefore replaced by a positive amino acid. We argue that this transition has evolved in a freshwater environment. Prokaryotic (6-4) photolyases usually contain an FeS cluster. DNA repair of a cyanobacterial member of this group which is missing the FeS cluster was also found to be stimulated by Mg2+.

scholarly journals Structure and DNA binding of alkylation response protein AidB

2008 ◽  
Vol 105 (40) ◽  
pp. 15299-15304 ◽  
Author(s):  
Timothy Bowles ◽  
Audrey H. Metz ◽  
Jami O'Quin ◽  
Zdzislaw Wawrzak ◽  
Brandt F. Eichman
Keyword(s):  
Dna Repair ◽  
Dna Binding ◽  
Mutational Analysis ◽  
Alkylating Agents ◽  
Alkylation Damage ◽  
Superficial Resemblance ◽  
Dna Binding Site ◽  
Dna Alkylators ◽  
Mutagenic Effects ◽  
Fad Binding

Exposure of Escherichia coli to alkylating agents activates expression of AidB in addition to DNA repair proteins Ada, AlkA, and AlkB. AidB was recently shown to possess a flavin adenine dinucleotide (FAD) cofactor and to bind to dsDNA, implicating it as a flavin-dependent DNA repair enzyme. However, the molecular mechanism by which AidB acts to reduce the mutagenic effects of specific DNA alkylators is unknown. We present a 1.7-Å crystal structure of AidB, which bears superficial resemblance to the acyl-CoA dehydrogenase superfamily of flavoproteins. The structure reveals a unique quaternary organization and a distinctive FAD active site that provides a rationale for AidB's limited dehydrogenase activity. A highly electropositive C-terminal domain not present in structural homologs was identified by mutational analysis as the DNA binding site. Structural analysis of the DNA and FAD binding sites provides evidence against AidB-catalyzed DNA repair and supports a model in which AidB acts to prevent alkylation damage by protecting DNA and destroying alkylating agents that have yet to reach their DNA target.

scholarly journals Identifying amino acid residues that contribute to the cellular-DNA binding site on retroviral integrase

Virology ◽  
2009 ◽  
Vol 389 (1-2) ◽  
pp. 141-148 ◽  
Author(s):  
Matthew G. Nowak ◽  
Malgorzata Sudol ◽  
Noelle E. Lee ◽  
Wesley M. Konsavage ◽  
Michael Katzman
Keyword(s):  
Amino Acid ◽  
Dna Binding ◽  
Binding Site ◽  
Amino Acid Residues ◽  
Dna Binding Site ◽  
Cellular Dna ◽  
Retroviral Integrase

scholarly journals Motifs of the C-terminal Domain of MCM9 Direct Localization to Sites of Mitomycin-C Damage for RAD51 Recruitment

2020 ◽  
Author(s):  
David R. McKinzey ◽  
Shivasankari Gomathinayagam ◽  
Wezley C. Griffin ◽  
Kathleen N. Klinzing ◽  
Elizabeth P. Jeffries ◽  
...  
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Amino Acid ◽  
Mitomycin C ◽  
Nuclear Localization ◽  
Nuclear Import ◽  
Impaired Ability ◽  
Direct Localization ◽  
Functional Components ◽  
Positively Charged

AbstractThe MCM8/9 complex is implicated in aiding fork progression and facilitating homologous recombination (HR) in response to several DNA damage agents. MCM9 itself is an outlier within the MCM family containing a long C-terminal extension (CTE) comprising 42% of the total length, but with no known functional components and high predicted disorder. In this report, we identify and characterize two unique motifs within the primarily unstructured CTE that are required for localization of MCM8/9 to sites of mitomycin C (MMC) induced DNA damage. First, an unconventional ‘bipartite-like’ nuclear localization (NLS) motif consisting of two positively charged amino acid stretches separated by a long intervening sequence is required for the nuclear import of both MCM8 and MCM9. Second, a variant of the BRC motif (BRCv), similar to that found in other HR helicases, is necessary for localization to sites of MMC damage. The MCM9-BRCv directly interacts with and recruits RAD51 downstream to MMC-induced damage to aid in DNA repair. Patient lymphocytes devoid of functional MCM9 and discrete MCM9 knockout cells have a significantly impaired ability to form RAD51 foci after MMC treatment. Therefore, the disordered CTE in MCM9 is functionally important in promoting MCM8/9 activity and in recruiting downstream interactors; thus, requiring full length MCM9 for proper DNA repair.

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