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DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion.

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Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG, Roberts RJ, Cheng X
OpenAccess logo Nucleic Acids Res 34 939-48 (2006)
Related entries: 2fkc, 2fkh, 2flc

Cited: 37 times
EuropePMC logo PMID: 16473850

Abstract

HinP1I recognizes and cleaves the palindromic tetranucleotide sequence G downward arrowCGC in DNA. We report three structures of HinP1I-DNA complexes: in the presence of Ca(2+) (pre-reactive complex), in the absence of metal ion (binary complex) and in the presence of Mg(2+) (post-reactive complex). HinP1I forms a back-to-back dimer with two active sites and two DNA duplexes bound on the outer surfaces of the dimer facing away from each other. The 10 bp DNA duplexes undergo protein-induced distortions exhibiting features of A-, B- and Z-conformations: bending on one side (by intercalation of a phenylalanine side chain into the major groove), base flipping on the other side of the recognition site (by expanding the step rise distance of the local base pair to Z-form) and a local A-form conformation between the two central C:G base pairs of the recognition site (by binding of the N-terminal helix in the minor groove). In the pre- and post-reactive complexes, two metals (Ca(2+) or Mg(2+)) are found in the active site. The enzyme appears to cleave DNA sequentially, hydrolyzing first one DNA strand, as seen in the post-reactive complex in the crystalline state, and then the other, as supported by the observation that, in solution, a nicked DNA intermediate accumulates before linearization.

Articles - 2fl3 mentioned but not cited (6)

  1. A protein-DNA docking benchmark. van Dijk M, Bonvin AM. Nucleic Acids Res 36 e88 (2008)
  2. DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion. Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG, Roberts RJ, Cheng X. Nucleic Acids Res 34 939-948 (2006)
  3. Assessment of the optimization of affinity and specificity at protein-DNA interfaces. Ashworth J, Baker D. Nucleic Acids Res 37 e73 (2009)
  4. Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructure. Suma A, Stopar A, Nicholson AW, Castronovo M, Carnevale V. Nucleic Acids Res 48 4672-4680 (2020)
  5. Structural changes in DNA-binding proteins on complexation. Poddar S, Chakravarty D, Chakrabarti P. Nucleic Acids Res 46 3298-3308 (2018)
  6. CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations. Marchetto A, Si Chaib Z, Rossi CA, Ribeiro R, Pantano S, Rossetti G, Giorgetti A. Molecules 25 E5934 (2020)


Reviews citing this publication (2)

  1. CRISPR-mediated adaptive immune systems in bacteria and archaea. Sorek R, Lawrence CM, Wiedenheft B. Annu Rev Biochem 82 237-266 (2013)
  2. Type II restriction endonucleases--a historical perspective and more. Pingoud A, Wilson GG, Wende W. Nucleic Acids Res 42 7489-7527 (2014)

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