3hqg

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3hqg, resolution 2.60Å ()
Ligands:
Gene: ECORII, ecoRIIR (Escherichia coli)
Activity: Type II site-specific deoxyribonuclease, with EC number 3.1.21.4
Related: 1na6, 3hqf
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



Contents

Crystal structure of restriction endonuclease EcoRII catalytic C-terminal domain in complex with cognate DNA

Publication Abstract from PubMed

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

3hqg is a 3 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA.

See Also

Reference

  • 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

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