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Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism.

Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton NC
J Biol Chem 281 23852-69 (2006)
Related entries: 2gie, 2gig, 2gii, 2gij

Cited: 19 times
EuropePMC logo PMID: 16675462

Abstract

The functional and structural consequences of a mutation of the DNA intercalating residue of HincII, Q138F, are presented. Modeling has suggested that the DNA intercalation by Gln-138 results in DNA distortions potentially used by HincII in indirect readout of its cognate DNA, GTYRAC (Y = C or T, R = A or G) (Horton, N. C., Dorner, L. F., and Perona, J. J. (2002) Nat. Struct. Biol. 9, 42-47). Kinetic data presented here indicate that the mutation of glutamine 138 to phenylalanine (Q138F) results in a change in sequence specificity at the center two base pairs of the cognate recognition site. We show that the preference of HincII for cutting, but not binding, the three cognate sites differing in the center two base pairs has been altered by the mutation Q138F. Five new crystal structures are presented including Q138F HincII bound to GTTAAC and GTCGAC both with and without Ca2+ as well as the structure of wild type HincII bound to GTTAAC. The Q138F HincII/DNA structures show conformational changes in the protein, bound DNA, and at the protein-DNA interface, consistent with the formation of adaptive complexes. Analysis of these structures and the effect of Ca2+ binding on the protein-DNA interface illuminates the origin of the altered specificity by the mutation Q138F in the HincII enzyme.

Articles - 2gih mentioned but not cited (2)

  1. DNA distortion and specificity in a sequence-specific endonuclease. Babic AC, Little EJ, Manohar VM, Bitinaite J, Horton NC. J Mol Biol 383 186-204 (2008)
  2. DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target. Shen BW, Heiter DF, Lunnen KD, Wilson GG, Stoddard BL. Nucleic Acids Res 45 1516-1528 (2017)


Reviews citing this publication (1)

  1. Restriction endonucleases: natural and directed evolution. Gupta R, Capalash N, Sharma P. Appl Microbiol Biotechnol 94 583-599 (2012)

Articles citing this publication (16)

  1. Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses. Orlowski J, Bujnicki JM. Nucleic Acids Res 36 3552-3569 (2008)
  2. Dxo1 is a new type of eukaryotic enzyme with both decapping and 5'-3' exoribonuclease activity. Chang JH, Jiao X, Chiba K, Oh C, Martin CE, Kiledjian M, Tong L. Nat Struct Mol Biol 19 1011-1017 (2012)
  3. Monomeric restriction endonuclease BcnI in the apo form and in an asymmetric complex with target DNA. Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler M. J Mol Biol 369 722-734 (2007)
  4. Early interrogation and recognition of DNA sequence by indirect readout. Little EJ, Babic AC, Horton NC. Structure 16 1828-1837 (2008)
  5. The crystal structure of D212 from sulfolobus spindle-shaped virus ragged hills reveals a new member of the PD-(D/E)XK nuclease superfamily. Menon SK, Eilers BJ, Young MJ, Lawrence CM. J Virol 84 5890-5897 (2010)
  6. Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity. Lambert AR, Hallinan JP, Shen BW, Chik JK, Bolduc JM, Kulshina N, Robins LI, Kaiser BK, Jarjour J, Havens K, Scharenberg AM, Stoddard BL. Structure 24 862-873 (2016)
  7. Activation of DNA cleavage by oligomerization of DNA-bound SgrAI. Park CK, Stiteler AP, Shah S, Ghare MI, Bitinaite J, Horton NC. Biochemistry 49 8818-8830 (2010)
  8. Massively parallel characterization of restriction endonucleases. Kamps-Hughes N, Quimby A, Zhu Z, Johnson EA. Nucleic Acids Res 41 e119 (2013)
  9. Structural analysis of activated SgrAI-DNA oligomers using ion mobility mass spectrometry. Ma X, Shah S, Zhou M, Park CK, Wysocki VH, Horton NC. Biochemistry 52 4373-4381 (2013)
  10. DNA intercalation without flipping in the specific ThaI-DNA complex. Firczuk M, Wojciechowski M, Czapinska H, Bochtler M. Nucleic Acids Res 39 744-754 (2011)
  11. Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases. McMurrough TA, Brown CM, Zhang K, Hausner G, Junop MS, Gloor GB, Edgell DR. Nucleic Acids Res 46 11990-12007 (2018)
  12. Probing the run-on oligomer of activated SgrAI bound to DNA. Shah S, Sanchez J, Stewart A, Piperakis MM, Cosstick R, Nichols C, Park CK, Ma X, Wysocki V, Bitinaite J, Horton NC. PLoS One 10 e0124783 (2015)
  13. Structural and functional analyses of PolyProline-II helices in globular proteins. Kumar P, Bansal M. J Struct Biol 196 414-425 (2016)
  14. Escherichia coli DNA adenine methyltransferase: the structural basis of processive catalysis and indirect read-out. Coffin SR, Reich NO. J Biol Chem 284 18390-18400 (2009)
  15. Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease. Manakova E, Grazulis S, Zaremba M, Tamulaitiene G, Golovenko D, Siksnys V. Nucleic Acids Res 40 6741-6751 (2012)
  16. Alteration of sequence specificity of the type IIS restriction endonuclease BtsI. Guan S, Blanchard A, Zhang P, Zhu Z. PLoS One 5 e11787 (2010)


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