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Structure of Escherichia coli AlkA in complex with undamaged DNA.

Bowman BR, Lee S, Wang S, Verdine GL
J Biol Chem 285 35783-91 (2010)
Related entries: 3oh6, 3oh9

Cited: 17 times
EuropePMC logo PMID: 20843803

Abstract

Because DNA damage is so rare, DNA glycosylases interact for the most part with undamaged DNA. Whereas the structural basis for recognition of DNA lesions by glycosylases has been studied extensively, less is known about the nature of the interaction between these proteins and undamaged DNA. Here we report the crystal structures of the DNA glycosylase AlkA in complex with undamaged DNA. The structures revealed a recognition mode in which the DNA is nearly straight, with no amino acid side chains inserted into the duplex, and the target base pair is fully intrahelical. A comparison of the present structures with that of AlkA recognizing an extrahelical lesion revealed conformational changes in both the DNA and protein as the glycosylase transitions from the interrogation of undamaged DNA to catalysis of nucleobase excision. Modeling studies with the cytotoxic lesion 3-methyladenine and accompanying biochemical experiments suggested that AlkA actively interrogates the minor groove of the DNA while probing for the presence of lesions.

Reviews - 3ogd mentioned but not cited (1)

  1. Recent advances in the structural mechanisms of DNA glycosylases. Brooks SC, Adhikary S, Rubinson EH, Eichman BF. Biochim Biophys Acta 1834 247-271 (2013)

Articles - 3ogd mentioned but not cited (2)

  1. Structure of Escherichia coli AlkA in complex with undamaged DNA. Bowman BR, Lee S, Wang S, Verdine GL. J Biol Chem 285 35783-35791 (2010)
  2. Modelling and Recognition of Protein Contact Networks by Multiple Kernel Learning and Dissimilarity Representations. Martino A, De Santis E, Giuliani A, Rizzi A. Entropy (Basel) 22 E794 (2020)


Reviews citing this publication (1)

  1. Computational investigations on target-site searching and recognition mechanisms by thymine DNA glycosylase during DNA repair process. Wang L, Song K, Yu J, Da LT. Acta Biochim Biophys Sin (Shanghai) 54 796-806 (2022)

Articles citing this publication (13)

  1. Duplex interrogation by a direct DNA repair protein in search of base damage. Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ, Dinner AR, Yang CG, He C. Nat Struct Mol Biol 19 671-676 (2012)
  2. Active destabilization of base pairs by a DNA glycosylase wedge initiates damage recognition. Kuznetsov NA, Bergonzo C, Campbell AJ, Li H, Mechetin GV, de los Santos C, Grollman AP, Fedorova OS, Zharkov DO, Simmerling C. Nucleic Acids Res 43 272-281 (2015)
  3. Enforced presentation of an extrahelical guanine to the lesion recognition pocket of human 8-oxoguanine glycosylase, hOGG1. Crenshaw CM, Nam K, Oo K, Kutchukian PS, Bowman BR, Karplus M, Verdine GL. J Biol Chem 287 24916-24928 (2012)
  4. Conformational Dynamics of DNA Repair by Escherichia coli Endonuclease III. Kuznetsov NA, Kladova OA, Kuznetsova AA, Ishchenko AA, Saparbaev MK, Zharkov DO, Fedorova OS. J Biol Chem 290 14338-14349 (2015)
  5. Lesion search and recognition by thymine DNA glycosylase revealed by single molecule imaging. Buechner CN, Maiti A, Drohat AC, Tessmer I. Nucleic Acids Res 43 2716-2729 (2015)
  6. Base-flipping dynamics from an intrahelical to an extrahelical state exerted by thymine DNA glycosylase during DNA repair process. Da LT, Yu J. Nucleic Acids Res 46 5410-5425 (2018)
  7. Searching for DNA lesions: structural evidence for lower- and higher-affinity DNA binding conformations of human alkyladenine DNA glycosylase. Setser JW, Lingaraju GM, Davis CA, Samson LD, Drennan CL. Biochemistry 51 382-390 (2012)
  8. Structural Basis for the Lesion-scanning Mechanism of the MutY DNA Glycosylase. Wang L, Chakravarthy S, Verdine GL. J Biol Chem 292 5007-5017 (2017)
  9. Analysis of substrate specificity of Schizosaccharomyces pombe Mag1 alkylpurine DNA glycosylase. Adhikary S, Eichman BF. EMBO Rep 12 1286-1292 (2011)
  10. The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase. Shigdel UK, Ovchinnikov V, Lee SJ, Shih JA, Karplus M, Nam K, Verdine GL. Nat Commun 11 4437 (2020)
  11. Kinetic mechanism for the excision of hypoxanthine by Escherichia coli AlkA and evidence for binding to DNA ends. Zhao B, O'Brien PJ. Biochemistry 50 4350-4359 (2011)
  12. Finding optimal interaction interface alignments between biological complexes. Cui X, Naveed H, Gao X. Bioinformatics 31 i133-41 (2015)
  13. Non-productive DNA damage binding by DNA glycosylase-like protein Mag2 from Schizosaccharomyces pombe. Adhikary S, Cato MC, McGary KL, Rokas A, Eichman BF. DNA Repair (Amst) 12 196-204 (2013)


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