3HQG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.

(2009) Nucleic Acids Res. 37: 6613-6624

  • DOI: 10.1093/nar/gkp699
  • Primary Citation of Related Structures:  3HQF

  • 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 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.


    Related Citations: 
    • Crystal structure of type iie restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold
      Zhou, X.E.,Wang, Y.,Reuter, M.,Mucke, M.,Kruger, D.H.,Meehan, E.J.,Chen, L.
      (2004) J.Mol.Biol. 335: 307


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Type-2 restriction enzyme EcoRII
A
222Escherichia coliGene Names: ecoRIIR
EC: 3.1.21.4
Find proteins for P14633 (Escherichia coli)
Go to UniProtKB:  P14633
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*CP*GP*AP*CP*CP*AP*GP*GP*CP*TP*A)-3'B12N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*TP*AP*GP*CP*CP*TP*GP*GP*TP*CP*GP*A)-3'C12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.054α = 90.00
b = 57.971β = 90.00
c = 61.010γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
AMoREphasing
MOSFLMdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance