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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)



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