Role of protein-induced bending in the specificity of DNA recognition: crystal structure of EcoRV endonuclease complexed with d(AAAGAT) + d(ATCTT)

Journal of Molecular Biology
N C Horton, J J Perona

Abstract

The crystal structure of EcoRV endonuclease has been determined at 2. 1 A resolution complexed to two five-base-pair DNA duplexes each containing the cognate recognition half-site. The highly localized 50 degrees bend into the major groove seen at the center TA-step of the continuous GATATC site is preserved in this discontinuous DNA complex lacking the scissile phosphates. Thus, this crystal structure provides evidence that covalent constraints associated with a continuous target site are not essential to enzyme-induced DNA bending, even when these constraints are removed directly at the locus of the bend. The scissile phosphates are also absent in the crystal structure of EcoRV bound to the non-specific site TCGCGA, which shows a straight B-like conformation. We conclude that DNA bending by EcoRV is governed only by the sequence and is not influenced by the continuity of the phosphodiester backbone. Together with other data showing that cleavable non-cognate sites are bent, these results indicate that EcoRV bends non-cognate sites differing by one or two base-pairs from GATATC, but does not bend non-specific sites that are less similar. Structural and thermodynamic considerations suggest that the sequence-dependent energy cos...Continue Reading

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Citations

Sep 15, 2001·Nucleic Acids Research·A Pingoud, A Jeltsch
May 15, 2008·Nucleic Acids Research·Daniel SvozilBohdan Schneider
Sep 24, 2010·Nucleic Acids Research·Malgorzata FirczukMatthias Bochtler
Apr 23, 2013·Nucleic Acids Research·Nick Kamps-HughesEric A Johnson
May 10, 2000·Proceedings of the National Academy of Sciences of the United States of America·N C Horton, J J Perona
Mar 31, 1999·Proceedings of the National Academy of Sciences of the United States of America·L I PietrasantaH Hansma
Dec 18, 2013·Nucleic Acids Research·Bohdan SchneiderAlexandre G de Brevern
Nov 2, 1999·Journal of Molecular Biology·D J Fitzgerald, J N Anderson
Feb 17, 2001·Journal of Molecular Recognition : JMR·A P Demchenko
Sep 23, 2010·Chemistry : a European Journal·Joanne I YehCatalina Achim
Dec 25, 2007·Journal of Fluorescence·J P Neves SilvaM E C D Real Oliveira
Apr 2, 2020·Nucleic Acids Research·Ken-Ichi MiyazonoMasaru Tanokura
Jul 13, 2000·Journal of Molecular Biology·X J LuW K Olson
Mar 20, 2001·Journal of Molecular Biology·L E EnglerL Jen-Jacobson
Jun 11, 2002·Journal of Molecular Biology·James C Samuelson, Shuang-yong Xu
Nov 15, 2002·Methods : a Companion to Methods in Enzymology·John J Perona
Apr 21, 2007·Journal of Molecular Biology·Monika SokolowskaMatthias Bochtler
Sep 11, 2002·Biochemistry·Eleanore SeibertRoman Osman

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