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The structure of SgrAI bound to DNA; recognition of an 8 base pair target.

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Dunten PW, Little EJ, Gregory MT, Manohar VM, Dalton M, Hough D, Bitinaite J, Horton NC
OpenAccess logo Nucleic Acids Res 36 5405-16 (2008)
Related entries: 3dpg, 3dvo

Cited: 24 times
EuropePMC logo PMID: 18701646

Abstract

The three-dimensional X-ray crystal structure of the 'rare cutting' type II restriction endonuclease SgrAI bound to cognate DNA is presented. SgrAI forms a dimer bound to one duplex of DNA. Two Ca(2+) bind in the enzyme active site, with one ion at the interface between the protein and DNA, and the second bound distal from the DNA. These sites are differentially occupied by Mn(2+), with strong binding at the protein-DNA interface, but only partial occupancy of the distal site. The DNA remains uncleaved in the structures from crystals grown in the presence of either divalent cation. The structure of the dimer of SgrAI is similar to those of Cfr10I, Bse634I and NgoMIV, however no tetrameric structure of SgrAI is observed. DNA contacts to the central CCGG base pairs of the SgrAI canonical target sequence (CR|CCGGYG, | marks the site of cleavage) are found to be very similar to those in the NgoMIV/DNA structure (target sequence G|CCGGC). Specificity at the degenerate YR base pairs of the SgrAI sequence may occur via indirect readout using DNA distortion. Recognition of the outer GC base pairs occurs through a single contact to the G from an arginine side chain located in a region unique to SgrAI.

Articles - 3dw9 mentioned but not cited (4)

  1. The structure of SgrAI bound to DNA; recognition of an 8 base pair target. Dunten PW, Little EJ, Gregory MT, Manohar VM, Dalton M, Hough D, Bitinaite J, Horton NC. Nucleic Acids Res. 36 5405-5416 (2008)
  2. Structure and Mechanism of a Cyclic Trinucleotide-Activated Bacterial Endonuclease Mediating Bacteriophage Immunity. Lau RK, Ye Q, Birkholz EA, Berg KR, Patel L, Mathews IT, Watrous JD, Ego K, Whiteley AT, Lowey B, Mekalanos JJ, Kranzusch PJ, Jain M, Pogliano J, Corbett KD. Mol Cell 77 723-733.e6 (2020)
  3. 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)
  4. Functional significance of protein assemblies predicted by the crystal structure of the restriction endonuclease BsaWI. Tamulaitis G, Rutkauskas M, Zaremba M, Grazulis S, Tamulaitiene G, Siksnys V. Nucleic Acids Res. 43 8100-8110 (2015)


Reviews citing this publication (1)

  1. Structures, functions, and mechanisms of filament forming enzymes: a renaissance of enzyme filamentation. Park CK, Horton NC. Biophys Rev 11 927-994 (2019)

Articles citing this publication (19)

  1. On the divalent metal ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family. Pingoud V, Wende W, Friedhoff P, Reuter M, Alves J, Jeltsch A, Mones L, Fuxreiter M, Pingoud A. J. Mol. Biol. 393 140-160 (2009)
  2. Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII. Golovenko D, Manakova E, Tamulaitiene G, Grazulis S, Siksnys V. Nucleic Acids Res. 37 6613-6624 (2009)
  3. DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme. Zaremba M, Owsicka A, Tamulaitis G, Sasnauskas G, Shlyakhtenko LS, Lushnikov AY, Lyubchenko YL, Laurens N, van den Broek B, Wuite GJ, Siksnys V. Nucleic Acids Res. 38 7142-7154 (2010)
  4. Cofactor requirement of HpyAV restriction endonuclease. Chan SH, Opitz L, Higgins L, O'loane D, Xu SY. PLoS ONE 5 e9071 (2010)
  5. 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)
  6. Allosteric regulation of DNA cleavage and sequence-specificity through run-on oligomerization. Lyumkis D, Talley H, Stewart A, Shah S, Park CK, Tama F, Potter CS, Carragher B, Horton NC. Structure 21 1848-1858 (2013)
  7. Domain swapping in allosteric modulation of DNA specificity. Park CK, Joshi HK, Agrawal A, Ghare MI, Little EJ, Dunten PW, Bitinaite J, Horton NC. PLoS Biol. 8 e1000554 (2010)
  8. 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)
  9. An Mrr-family nuclease motif in the single polypeptide restriction-modification enzyme LlaGI. Smith RM, Josephsen J, Szczelkun MD. Nucleic Acids Res. 37 7231-7238 (2009)
  10. 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)
  11. The run-on oligomer filament enzyme mechanism of SgrAI: Part 1. Assembly kinetics of the run-on oligomer filament. Park CK, Sanchez JL, Barahona C, Basantes LE, Sanchez J, Hernandez C, Horton NC. J. Biol. Chem. 293 14585-14598 (2018)
  12. The run-on oligomer filament enzyme mechanism of SgrAI: Part 2. Kinetic modeling of the full DNA cleavage pathway. Park CK, Sanchez JL, Barahona C, Basantes LE, Sanchez J, Hernandez C, Horton NC. J. Biol. Chem. 293 14599-14615 (2018)
  13. Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA. Tamulaitiene G, Jovaisaite V, Tamulaitis G, Songailiene I, Manakova E, Zaremba M, Grazulis S, Xu SY, Siksnys V. Nucleic Acids Res. 45 3547-3558 (2017)
  14. The architecture of restriction enzymes. Dryden DT. Structure 21 1720-1721 (2013)
  15. Mechanism of Filamentation-Induced Allosteric Activation of the SgrAI Endonuclease. Polley S, Lyumkis D, Horton NC. Structure 27 1497-1507.e3 (2019)
  16. The Need for Speed: Run-On Oligomer Filament Formation Provides Maximum Speed with Maximum Sequestration of Activity. Barahona CJ, Basantes LE, Tompkins KJ, Heitman DM, Chukwu BI, Sanchez J, Sanchez JL, Ghadirian N, Park CK, Horton NC. J. Virol. 93 (2019)
  17. Unique mechanism of target recognition by PfoI restriction endonuclease of the CCGG-family. Tamulaitiene G, Manakova E, Jovaisaite V, Tamulaitis G, Grazulis S, Bochtler M, Siksnys V. Nucleic Acids Res. 47 997-1010 (2019)
  18. Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI. Shen BW, Doyle L, Bradley P, Heiter DF, Lunnen KD, Wilson GG, Stoddard BL. Nucleic Acids Res. 47 450-467 (2019)
  19. The role of filamentation in activation and DNA sequence specificity of the sequence-specific endonuclease SgrAI. Lyumkis D, Horton NC. Biochem Soc Trans 50 1703-1714 (2022)


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