Biological Assembly 1  

 3D View: Structure

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 90.91 kDa 
• Atom Count: 6281 
• Residue Count: 760 
• Unique protein chains: 1

1NA6

Crystal structure of restriction endonuclease EcoRII mutant R88A

• DOI: 10.2210/pdb1NA6/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-11-26 Released: 2003-12-16 
• Deposition Author(s): Zhou, X.E., Wang, Y., Reuter, M., Mucke, M., Kruger, D.H., Meehan, E.J., Chen, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.284 
• R-Value Work: 0.230 
• R-Value Observed: 0.236 

Literature

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: 307-319

• PubMed: 14659759 
• DOI: 10.1016/j.jmb.2003.10.030
• Structures With Same Primary Citation


• PubMed Abstract: 
  

EcoRII is a type IIE restriction endonuclease that interacts with two copies of the DNA recognition sequence 5'CCWGG, one being the actual target of cleavage, the other serving as the allosteric effector. The mode of enzyme activation by effector binding is unknown. To investigate the molecular basis of activation and cleavage mechanisms by EcoRII, the crystal structure of EcoRII mutant R88A has been solved at 2.1A resolution. The EcoRII monomer has two domains linked through a hinge loop. The N-terminal effector-binding domain has a novel DNA recognition fold with a prominent cleft. The C-terminal catalytic domain has a restriction endonuclease-like fold. Structure-based sequence alignment identified the putative catalytic site of EcoRII that is spatially blocked by the N-terminal domain. The structure together with the earlier characterized EcoRII enzyme activity enhancement in the absence of its N-terminal domain reveal an autoinhibition/activation mechanism of enzyme activity mediated by a novel effector-binding fold. This is the first case of autoinhibition, a mechanism described for many transcription factors and signal transducing proteins, of a restriction endonuclease.

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Organizational Affiliation: 

Laboratory for Structural Biology, Department of Chemistry, Graduate Programs of Biotechnology, Chemistry and Materials Science, University of Alabama in Huntsville, Huntsville, AL 35899, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Restriction endonuclease EcoRII	A, B	404	Escherichia coli	Mutation(s): 1  Gene Names: EcoRII, ecoRIIR EC: 3.1.21.4
Find proteins for P14633 (Escherichia coli) Go to UniProtKB:  P14633

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.284 
• R-Value Work: 0.230 
• R-Value Observed: 0.236 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.746	α = 90
b = 92.36	β = 108.08
c = 88.308	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
ISIRAS	model building
CNS	refinement
HKL-2000	data reduction
ISIRAS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-11-26 
• Released Date: 2003-12-16 
Deposition Author(s): Zhou, X.E., Wang, Y., Reuter, M., Mucke, M., Kruger, D.H., Meehan, E.J., Chen, L.

Revision History 

• Version 1.0: 2003-12-16
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance