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Nucleic Acids Research Advance Access first published online on September 3, 2009
This version published online on October 6, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp699
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

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

Dmitrij Golovenko, Elena Manakova, Giedre Tamulaitiene, Saulius Grazulis and Virginijus Siksnys*

Institute of Biotechnology, Graiciuno 8, LT-02241 Vilnius, Lithuania

*To whom correspondence should be addressed. Tel: +370 5 2602108; Fax: +370 5 2602116; Email: siksnys{at}ibt.lt

Received June 12, 2009. Revised August 5, 2009. Accepted August 6, 2009.

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.


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