Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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: 18.95 kDa 
• Atom Count: 1325 
• Residue Count: 154 
• Unique protein chains: 1

4IA8

Crystal Structure of a Y37A mutant of the Restriction-Modification Controller Protein C.Esp1396I

• DOI: 10.2210/pdb4IA8/pdb

• Classification: TRANSCRIPTION
• Organism(s): Enterobacter sp. RFL1396
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-12-06 Released: 2013-12-11 
• Deposition Author(s): Martin, R.N.A., McGeehan, J.E., Kneale, G.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.220 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Literature

Structural and Mutagenic Analysis of the RM Controller Protein C.Esp1396I.

Martin, R.N., McGeehan, J.E., Kneale, G.

(2014) PLoS One 9: e98365-e98365

• PubMed: 24887147 
• DOI: 10.1371/journal.pone.0098365
• Primary Citation of Related Structures:  
  4I6R, 4I6T, 4I6U, 4IA8, 4IVZ, 4F8D, 4FBI, 4FN3


• PubMed Abstract: 
  

Bacterial restriction-modification (RM) systems are comprised of two complementary enzymatic activities that prevent the establishment of foreign DNA in a bacterial cell: DNA methylation and DNA restriction. These two activities are tightly regulated to prevent over-methylation or auto-restriction. Many Type II RM systems employ a controller (C) protein as a transcriptional regulator for the endonuclease gene (and in some cases, the methyltransferase gene also). All high-resolution structures of C-protein/DNA-protein complexes solved to date relate to C.Esp1396I, from which the interactions of specific amino acid residues with DNA bases and/or the phosphate backbone could be observed. Here we present both structural and DNA binding data for a series of mutations to the key DNA binding residues of C.Esp1396I. Our results indicate that mutations to the backbone binding residues (Y37, S52) had a lesser affect on DNA binding affinity than mutations to those residues that bind directly to the bases (T36, R46), and the contributions of each side chain to the binding energies are compared. High-resolution X-ray crystal structures of the mutant and native proteins showed that the fold of the proteins was unaffected by the mutations, but also revealed variation in the flexible loop conformations associated with DNA sequence recognition. Since the tyrosine residue Y37 contributes to DNA bending in the native complex, we have solved the structure of the Y37F mutant protein/DNA complex by X-ray crystallography to allow us to directly compare the structure of the DNA in the mutant and native complexes.

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Related Citations: 

• Structure of the restriction-modification controller protein C.Esp1396I.
  Ball, N., Streeter, S.D., Kneale, G.G., McGeehan, J.E.
  (2009) Acta Crystallogr D Biol Crystallogr 65: 900

• Recognition of dual symmetry by the controller protein C.Esp1396I based on the structure of the transcriptional activation complex.
  McGeehan, J.E., Ball, N.J., Streeter, S.D., Thresh, S.J., Kneale, G.G.
  (2012) Nucleic Acids Res 40: 4158

• The structural basis of differential DNA sequence recognition by restriction-modification controller proteins.
  Ball, N.J., McGeehan, J.E., Streeter, S.D., Thresh, S.J., Kneale, G.G.
  (2012) Nucleic Acids Res 40: 10532

• Structure of the restriction-modification controller protein C.Esp1396I.
  Ball, N., Streeter, S.D., Kneale, G.G., McGeehan, J.E.
  (2009) Acta Crystallogr D Biol Crystallogr 65: 900

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Organizational Affiliation: 

Biophysics Laboratories, School of Biological Sciences, Institute of Biomedical and Biomolecular Science, University of Portsmouth, Portsmouth, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulatory protein	A, B	82	Enterobacter sp. RFL1396	Mutation(s): 1  Gene Names: esp1396IC
Find proteins for Q8GGH0 (Enterobacter sp. RFL1396) Explore Q8GGH0  Go to UniProtKB:  Q8GGH0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.220 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.26	α = 104.44
b = 34.28	β = 108.92
c = 41.12	γ = 97.42

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
GDA	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-12-06 
• Released Date: 2013-12-11 
Deposition Author(s): Martin, R.N.A., McGeehan, J.E., Kneale, G.G.

Revision History 

• Version 1.0: 2013-12-11
  Type: Initial release
  
• Version 1.1: 2014-06-18
  Changes: Database references