PMID: 19729506 , Related PDB ids: 3HQF, 3HQG

Authors:

Golovenko D, Manakova E, Tamulaitiene G, Grazulis S, Siksnys V

Title:

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

Journal:

Nucleic Acids Res. 2009 Oct;37(19):6613-24. Epub 2009 Sep 3.

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.