4I6U

Crystal Structure of a Y37F mutant of the Restriction-Modification Controller Protein C.Esp1396I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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 ...

    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.


    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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Regulatory proteinABCDEF82Enterobacter sp. RFL1396Mutation(s): 1 
Gene Names: esp1396IC
Find proteins for Q8GGH0 (Enterobacter sp. RFL1396)
Explore Q8GGH0 
Go to UniProtKB:  Q8GGH0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, F
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A, C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.61α = 90
b = 81.85β = 90
c = 135.08γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
GDAdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2014-06-18
    Changes: Database references