First time at Proteopedia? Click on the green links: they change the 3D image. Click and drag the molecules. Proteopedia is a 3D, interactive encyclopedia of proteins, RNA, DNA and other molecules. With a free user account, you can edit pages in Proteopedia. Visit the Main Page to learn more.
|3hqg, resolution 2.60Å ()|
|Gene:||ECORII, ecoRIIR (Escherichia coli)|
Crystal structure of restriction endonuclease EcoRII catalytic C-terminal domain in complex with cognate DNA
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.
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. 2009 Oct;37(19):6613-24. Epub 2009 Sep 3. PMID:19729506
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
About this Structure
- Golovenko D, Manakova E, Tamulaitiene G, Grazulis S, Siksnys V. Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII. Nucleic Acids Res. 2009 Oct;37(19):6613-24. Epub 2009 Sep 3. PMID:19729506 doi:10.1093/nar/gkp699
- Zhou XE, Wang Y, Reuter M, Mucke M, Kruger DH, Meehan EJ, Chen L. Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold. J Mol Biol. 2004 Jan 2;335(1):307-19. PMID:14659759