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Testing water-mediated DNA recognition by the Hin recombinase.

Chiu TK, Sohn C, Dickerson RE, Johnson RC
EMBO J 21 801-14 (2002)
Related entries: 1ijw, 1jj8, 1jko, 1jkp, 1jkq, 1jkr

Cited: 21 times
EuropePMC logo PMID: 11847127

Abstract

The Hin recombinase specifically recognizes its DNA-binding site by means of both major and minor groove interactions. A previous X-ray structure, together with new structures of the Hin DNA-binding domain bound to a recombination half-site that were solved as part of the present study, have revealed that two ordered water molecules are present within the major groove interface. In this report, we test the importance of these waters directly by X-ray crystal structure analysis of complexes with four mutant DNA sequences. These structures, combined with their Hin-binding properties, provide strong support for the critical importance of one of the intermediate waters. A lesser but demonstrable role is ascribed to the second water molecule. The mutant structures also illustrate the prominent roles of thymine methyls both in stabilizing intermediate waters and in interfering with water or amino acid side chain interactions with DNA.

Articles - 1jj6 mentioned but not cited (3)

  1. Probing the role of interfacial waters in protein-DNA recognition using a hybrid implicit/explicit solvation model. Li S, Bradley P. Proteins 81 1318-1329 (2013)
  2. research-article Computational design of sequence-specific DNA-binding proteins. Glasscock CJ, Pecoraro R, McHugh R, Doyle LA, Chen W, Boivin O, Lonnquist B, Na E, Politanska Y, Haddox HK, Cox D, Norn C, Coventry B, Goreshnik I, Vafeados D, Lee GR, Gordan R, Stoddard BL, DiMaio F, Baker D. bioRxiv 2023.09.20.558720 (2023)
  3. Exploring protein structural dissimilarity to facilitate structure classification. Jain P, Hirst JD. BMC Struct Biol 9 60 (2009)


Reviews citing this publication (1)

  1. The role of water in protein-DNA recognition. Jayaram B, Jain T. Annu Rev Biophys Biomol Struct 33 343-361 (2004)

Articles citing this publication (17)

  1. The shape of the DNA minor groove directs binding by the DNA-bending protein Fis. Stella S, Cascio D, Johnson RC. Genes Dev 24 814-826 (2010)
  2. Synthesis of programmable integrases. Gordley RM, Gersbach CA, Barbas CF. Proc Natl Acad Sci U S A 106 5053-5058 (2009)
  3. Regulation of directionality in bacteriophage lambda site-specific recombination: structure of the Xis protein. Sam MD, Papagiannis CV, Connolly KM, Corselli L, Iwahara J, Lee J, Phillips M, Wojciak JM, Johnson RC, Clubb RT. J Mol Biol 324 791-805 (2002)
  4. Energetics of the protein-DNA-water interaction. Spyrakis F, Cozzini P, Bertoli C, Marabotti A, Kellogg GE, Mozzarelli A. BMC Struct Biol 7 4 (2007)
  5. Architecture of the hin synaptic complex during recombination: the recombinase subunits translocate with the DNA strands. Dhar G, Sanders ER, Johnson RC. Cell 119 33-45 (2004)
  6. Sequence-specific minor groove binding by bis-benzimidazoles: water molecules in ligand recognition. Bailly C, Chessari G, Carrasco C, Joubert A, Mann J, Wilson WD, Neidle S. Nucleic Acids Res 31 1514-1524 (2003)
  7. Stepwise dissection of the Hin-catalyzed recombination reaction from synapsis to resolution. Sanders ER, Johnson RC. J Mol Biol 340 753-766 (2004)
  8. Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environment. Yamane T, Okamura H, Ikeguchi M, Nishimura Y, Kidera A. Proteins 71 1970-1983 (2008)
  9. Exploiting a reduced set of weighted average features to improve prediction of DNA-binding residues from 3D structures. Xiong Y, Xia J, Zhang W, Liu J. PLoS One 6 e28440 (2011)
  10. The Hin recombinase assembles a tetrameric protein swivel that exchanges DNA strands. Dhar G, McLean MM, Heiss JK, Johnson RC. Nucleic Acids Res 37 4743-4756 (2009)
  11. Site-specific DNA Inversion by Serine Recombinases. Johnson RC. Microbiol Spectr 3 1-36 (2015)
  12. Multiple interfaces between a serine recombinase and an enhancer control site-specific DNA inversion. McLean MM, Chang Y, Dhar G, Heiss JK, Johnson RC. Elife 2 e01211 (2013)
  13. Structural and dynamic basis of a supercoiling-responsive DNA element. Bae SH, Yun SH, Sun D, Lim HM, Choi BS. Nucleic Acids Res 34 254-261 (2006)
  14. Cooperative DNA binding by proteins through DNA shape complementarity. Hancock SP, Cascio D, Johnson RC. Nucleic Acids Res 47 8874-8887 (2019)
  15. Finding optimal interaction interface alignments between biological complexes. Cui X, Naveed H, Gao X. Bioinformatics 31 i133-41 (2015)
  16. Intrasubunit and intersubunit interactions controlling assembly of active synaptic complexes during Hin-catalyzed DNA recombination. Heiss JK, Sanders ER, Johnson RC. J Mol Biol 411 744-764 (2011)
  17. Controlling tetramer formation, subunit rotation and DNA ligation during Hin-catalyzed DNA inversion. Chang Y, Johnson RC. Nucleic Acids Res 43 6459-6472 (2015)


Related citations provided by authors (2)

  1. How Hin Recombinase, FIS and Cations Bind DNA. Chapter 4. Water-Mediated Sequence-Specific Recognition by Hin Recombinase. Chiu TK Thesis 145-241 (2001)
  2. Hin Recombinase Bound to DNA: The Origin of Specificity in Major and Minor Groove Interactions. Feng JA, Johnson RC, Dickerson RE Science 263 348-355 (1994)

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