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NMR structure of the Tn916 integrase-DNA complex.

Wojciak JM, Connolly KM, Clubb RT
Nat Struct Biol 6 366-73 (1999)
Cited: 37 times
EuropePMC logo PMID: 10201406

Abstract

The integrase protein catalyzes the excision and integration of the Tn916 conjugative transposon, a promiscuous genetic element that spreads antibiotic resistance in pathogenic bacteria. The solution structure of the N-terminal domain of the Tn916 integrase protein bound to its DNA-binding site within the transposon arm has been determined. The structure reveals an interesting mode of DNA recognition, in which the face of a three-stranded antiparallel beta-sheet is positioned within the major groove. A comparison to the structure of the homing endonuclease I-Ppol-DNA complex suggests that the three-stranded sheet may represent a new DNA-binding motif whose residue composition and position within the major groove are varied to alter specificity. The structure also provides insights into the mechanism of conjugative transposition. The DNA in the complex is bent approximately 35 degrees and may, together with potential interactions between bound integrase proteins at directly repeated sites, significantly bend the arms of the transposon.

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  1. Molecular Modeling the Proteins from the exo-xis Region of Lambda and Shigatoxigenic Bacteriophages. Donaldson LW. Antibiotics (Basel) 10 1282 (2021)

Articles - 1b69 mentioned but not cited (1)

  1. THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves. Sabogal A, Lyubimov AY, Corn JE, Berger JM, Rio DC. Nat Struct Mol Biol 17 117-123 (2010)


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  1. Structures and evolutionary origins of plant-specific transcription factor DNA-binding domains. Yamasaki K, Kigawa T, Inoue M, Watanabe S, Tateno M, Seki M, Shinozaki K, Yokoyama S. Plant Physiol Biochem 46 394-401 (2008)
  2. The λ Integrase Site-specific Recombination Pathway. Landy A. Microbiol Spectr 3 MDNA3-0051-2014 (2015)
  3. Nuclear magnetic resonance analysis of protein-DNA interactions. Campagne S, Gervais V, Milon A. J R Soc Interface 8 1065-1078 (2011)

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  2. A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors. Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Nunokawa E, Ishizuka Y, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S. J Mol Biol 337 49-63 (2004)
  3. The solution structure of the domain from MeCP2 that binds to methylated DNA. Wakefield RI, Smith BO, Nan X, Free A, Soteriou A, Uhrin D, Bird AP, Barlow PN. J Mol Biol 291 1055-1065 (1999)
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  5. Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1. Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Tomo Y, Hayami N, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S. Plant Cell 16 3448-3459 (2004)
  6. Structural basis for sequence-specific DNA recognition by an Arabidopsis WRKY transcription factor. Yamasaki K, Kigawa T, Watanabe S, Inoue M, Yamasaki T, Seki M, Shinozaki K, Yokoyama S. J Biol Chem 287 7683-7691 (2012)
  7. Structure of the GCM domain-DNA complex: a DNA-binding domain with a novel fold and mode of target site recognition. Cohen SX, Moulin M, Hashemolhosseini S, Kilian K, Wegner M, Müller CW. EMBO J 22 1835-1845 (2003)
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  9. Arm-site binding by lambda -integrase: solution structure and functional characterization of its amino-terminal domain. Wojciak JM, Sarkar D, Landy A, Clubb RT. Proc Natl Acad Sci U S A 99 3434-3439 (2002)
  10. Solution structure of the major DNA-binding domain of Arabidopsis thaliana ethylene-insensitive3-like3. Yamasaki K, Kigawa T, Inoue M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Tomo Y, Terada T, Shirouzu M, Tanaka A, Seki M, Shinozaki K, Yokoyama S. J Mol Biol 348 253-264 (2005)
  11. Structural determinants of specific DNA-recognition by the THAP zinc finger. Campagne S, Saurel O, Gervais V, Milon A. Nucleic Acids Res 38 3466-3476 (2010)
  12. The crystal structure of porcine reproductive and respiratory syndrome virus nonstructural protein Nsp1beta reveals a novel metal-dependent nuclease. Xue F, Sun Y, Yan L, Zhao C, Chen J, Bartlam M, Li X, Lou Z, Rao Z. J Virol 84 6461-6471 (2010)
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  15. Interactions between integrase and excisionase in the phage lambda excisive nucleoprotein complex. Cho EH, Gumport RI, Gardner JF. J Bacteriol 184 5200-5203 (2002)
  16. Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver. Peng Y, Sun L, Jia Z, Li L, Alexov E. Bioinformatics 34 779-786 (2018)
  17. Structure-specific binding of MeCP2 to four-way junction DNA through its methyl CpG-binding domain. Galvão TC, Thomas JO. Nucleic Acids Res 33 6603-6609 (2005)
  18. Arm sequences contribute to the architecture and catalytic function of a lambda integrase-Holliday junction complex. Radman-Livaja M, Shaw C, Azaro M, Biswas T, Ellenberger T, Landy A. Mol Cell 11 783-794 (2003)
  19. Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes. Smyshlyaev G, Bateman A, Barabas O. Mol Syst Biol 17 e9880 (2021)
  20. The structure of the excisionase (Xis) protein from conjugative transposon Tn916 provides insights into the regulation of heterobivalent tyrosine recombinases. Abbani M, Iwahara M, Clubb RT. J Mol Biol 347 11-25 (2005)
  21. NMR structure of the amino-terminal domain of the lambda integrase protein in complex with DNA: immobilization of a flexible tail facilitates beta-sheet recognition of the major groove. Fadeev EA, Sam MD, Clubb RT. J Mol Biol 388 682-690 (2009)
  22. Xis protein binding to the left arm stimulates excision of conjugative transposon Tn916. Connolly KM, Iwahara M, Clubb RT. J Bacteriol 184 2088-2099 (2002)
  23. Interactions of the integrase protein of the conjugative transposon Tn916 with its specific DNA binding sites. Jia Y, Churchward G. J Bacteriol 181 6114-6123 (1999)
  24. Major groove recognition by three-stranded beta-sheets: affinity determinants and conserved structural features. Connolly KM, Ilangovan U, Wojciak JM, Iwahara M, Clubb RT. J Mol Biol 300 841-856 (2000)
  25. New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements. Mageeney CM, Lau BY, Wagner JM, Hudson CM, Schoeniger JS, Krishnakumar R, Williams KP. Nucleic Acids Res 48 4052-4065 (2020)
  26. Specific binding of integrase to the origin of transfer (oriT) of the conjugative transposon Tn916. Hinerfeld D, Churchward G. J Bacteriol 183 2947-2951 (2001)
  27. Interaction of related Tn916-like transposons: analysis of excision events promoted by Tn916 and Tn5386 integrases. Rice LB, Carias LL, Hutton-Thomas R, Rudin S. J Bacteriol 189 3909-3917 (2007)
  28. Extending the applicability of the O-ring theory to protein-DNA complexes. Ramos RM, Fernandes LF, Moreira IS. Comput Biol Chem 44 31-39 (2013)
  29. Structures of the arm-type binding domains of HPI and HAI7 integrases. Szwagierczak A, Antonenka U, Popowicz GM, Sitar T, Holak TA, Rakin A. J Biol Chem 284 31664-31671 (2009)
  30. Molecular dynamics study of DNA binding by INT-DBD under a polarized force field. Yao XX, Ji CG, Xie DQ, Zhang JZ. J Comput Chem 34 1136-1142 (2013)
  31. Prediction of hot spots in protein-DNA binding interfaces based on discrete wavelet transform and wavelet packet transform. Sun Y, Wu H, Xu Z, Yue Z, Li K. BMC Bioinformatics 24 129 (2023)
  32. Preparation and optimization of protein-DNA complexes suitable for detailed NMR studies. Sam MD, Clubb RT. Methods Mol Biol 831 219-232 (2012)


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