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Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.

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Golovenko D, Manakova E, Tamulaitiene G, Grazulis S, Siksnys V
OpenAccess logo Nucleic Acids Res 37 6613-24 (2009)
Related entries: 1na6, 3hqg

Cited: 23 times
EuropePMC logo PMID: 19729506

Abstract

EcoRII restriction endonuclease is specific for the 5'-CCWGG sequence (W stands for A or T); however, it shows no activity on a single recognition site. To activate cleavage it requires binding of an additional target site as an allosteric effector. EcoRII dimer consists of three structural units: a central catalytic core, made from two copies of the C-terminal domain (EcoRII-C), and two N-terminal effector DNA binding domains (EcoRII-N). Here, we report DNA-bound EcoRII-N and EcoRII-C structures, which show that EcoRII combines two radically different structural mechanisms to interact with the effector and substrate DNA. The catalytic EcoRII-C dimer flips out the central T:A base pair and makes symmetric interactions with the CC:GG half-sites. The EcoRII-N effector domain monomer binds to the target site asymmetrically in a single defined orientation which is determined by specific hydrogen bonding and van der Waals interactions with the central T:A pair in the major groove. The EcoRII-N mode of the target site recognition is shared by the large class of higher plant transcription factors of the B3 superfamily.

Articles - 3hqf mentioned but not cited (6)

  1. 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)
  2. The Arabidopsis B3 domain protein VERNALIZATION1 (VRN1) is involved in processes essential for development, with structural and mutational studies revealing its DNA-binding surface. King GJ, Chanson AH, McCallum EJ, Ohme-Takagi M, Byriel K, Hill JM, Martin JL, Mylne JS. J Biol Chem 288 3198-3207 (2013)
  3. Structural insight into the specificity of the B3 DNA-binding domains provided by the co-crystal structure of the C-terminal fragment of BfiI restriction enzyme. Golovenko D, Manakova E, Zakrys L, Zaremba M, Sasnauskas G, Gražulis S, Siksnys V. Nucleic Acids Res 42 4113-4122 (2014)
  4. Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII. Tamulaitiene G, Silanskas A, Grazulis S, Zaremba M, Siksnys V. Nucleic Acids Res 42 14022-14030 (2014)
  5. UbaLAI is a monomeric Type IIE restriction enzyme. Sasnauskas G, Tamulaitiene G, Tamulaitis G, Calyševa J, Laime M, Rimšeliene R, Lubys A, Siksnys V. Nucleic Acids Res 45 9583-9594 (2017)
  6. The crystal structure of the Helicobacter pylori LlaJI.R1 N-terminal domain provides a model for site-specific DNA binding. Hosford CJ, Chappie JS. J Biol Chem 293 11758-11771 (2018)


Reviews citing this publication (2)

  1. Type II restriction endonucleases--a historical perspective and more. Pingoud A, Wilson GG, Wende W. Nucleic Acids Res 42 7489-7527 (2014)
  2. Mechanisms and clinical importance of bacteriophage resistance. Egido JE, Costa AR, Aparicio-Maldonado C, Haas PJ, Brouns SJJ. FEMS Microbiol Rev 46 fuab048 (2022)

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