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Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate.

Van Roey P, Waddling CA, Fox KM, Belfort M, Derbyshire V
EMBO J 20 3631-7 (2001)
Cited: 56 times
EuropePMC logo PMID: 11447104

Abstract

I-TevI is a site-specific, sequence-tolerant intron endonuclease. The crystal structure of the DNA-binding domain of I-TevI complexed with the 20 bp primary binding region of its DNA target reveals an unusually extended structure composed of three subdomains: a Zn finger, an elongated segment containing a minor groove-binding alpha-helix, and a helix-turn-helix. The protein wraps around the DNA, mostly following the minor groove, contacting the phosphate backbone along the full length of the duplex. Surprisingly, while the minor groove-binding helix and the helix-turn- helix subdomain make hydrophobic contacts, the few base-specific hydrogen bonds occur in segments that lack secondary structure and flank the intron insertion site. The multiple base-specific interactions over a long segment of the substrate are consistent with the observed high site specificity in spite of sequence tolerance, while the modular composition of the domain is pertinent to the evolution of homing endonucleases.

Reviews - 1i3j mentioned but not cited (1)

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  18. Activity, specificity and structure of I-Bth0305I: a representative of a new homing endonuclease family. Taylor GK, Heiter DF, Pietrokovski S, Stoddard BL. Nucleic Acids Res 39 9705-9719 (2011)
  19. Thermodynamics of DNA target site recognition by homing endonucleases. Eastberg JH, McConnell Smith A, Zhao L, Ashworth J, Shen BW, Stoddard BL. Nucleic Acids Res 35 7209-7221 (2007)
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  30. Mycobacterium tuberculosis RecA intein, a LAGLIDADG homing endonuclease, displays Mn(2+) and DNA-dependent ATPase activity. Guhan N, Muniyappa K. Nucleic Acids Res 31 4184-4191 (2003)
  31. Perpetuating the homing endonuclease life cycle: identification of mutations that modulate and change I-TevI cleavage preference. Roy AC, Wilson GG, Edgell DR. Nucleic Acids Res 44 7350-7359 (2016)
  32. Glucocorticoid receptor-like Zn(Cys)4 motifs in BslI restriction endonuclease. Vanamee ES, Hsieh Pc, Zhu Z, Yates D, Garman E, Xu Sy, Aggarwal AK. J Mol Biol 334 595-603 (2003)
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