3HQF

Crystal structure of restriction endonuclease EcoRII N-terminal effector-binding domain in complex with cognate DNA

Summary for 3HQF

• Entry DOI: 10.2210/pdb3hqf/pdb
• Related: 1na6 3HQG
• Descriptor: Restriction endonuclease, 5'-D(*GP*CP*CP*CP*TP*GP*GP*CP*G)-3', 5'-D(*CP*GP*CP*CP*AP*GP*GP*GP*C)-3', ... (4 entities in total)
• Functional Keywords: restriction endonuclease, ecorii, dna-binding pseudobarrel fold, protein-dna complex, dna recognition, endonuclease, hydrolase-dna complex, hydrolase/dna
• Biological source: Escherichia coli
• Total number of polymer chains: 3
• Total formula weight: 25383.82

Authors

Golovenko, D.,Manakova, E.,Grazulis, S.,Tamulaitiene, G.,Siksnys, V. (deposition date: 2009-06-06, release date: 2009-09-22, Last modification date: 2023-09-06)

Primary citation

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., 37:6613-6624, 2009

PubMed 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.

PubMed: 19729506
DOI: 10.1093/nar/gkp699

Experimental method

X-RAY DIFFRACTION (2.51 Å)