5LBM

The asymmetric tetrameric structure of the formaldehyde sensing transcriptional repressor FrmR from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb5LBM/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli O157:H7
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2016-06-16 Released: 2016-12-21 
• Deposition Author(s): Bisson, C., Baker, P.J., Green, J., Chivers, P.T.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.266 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 

Literature

The mechanism of a formaldehyde-sensing transcriptional regulator.

Denby, K.J., Iwig, J., Bisson, C., Westwood, J., Rolfe, M.D., Sedelnikova, S.E., Higgins, K., Maroney, M.J., Baker, P.J., Chivers, P.T., Green, J.

(2016) Sci Rep 6: 38879-38879

• PubMed: 27934966 
• DOI: https://doi.org/10.1038/srep38879
• Primary Citation of Related Structures:  
  5LBM


• PubMed Abstract: 
  

  Most organisms are exposed to the genotoxic chemical formaldehyde, either from endogenous or environmental sources. Therefore, biology has evolved systems to perceive and detoxify formaldehyde. The frmRA(B) operon that is present in many bacteria represents one such system. The FrmR protein is a transcriptional repressor that is specifically inactivated in the presence of formaldehyde, permitting expression of the formaldehyde detoxification machinery (FrmA and FrmB, when the latter is present). The X-ray structure of the formaldehyde-treated Escherichia coli FrmR (EcFrmR) protein reveals the formation of methylene bridges that link adjacent Pro2 and Cys35 residues in the EcFrmR tetramer. Methylene bridge formation has profound effects on the pattern of surface charge of EcFrmR and combined with biochemical/biophysical data suggests a mechanistic model for formaldehyde-sensing and derepression of frmRA(B) expression in numerous bacterial species.

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Organizational Affiliation: 

Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.77 kDa 
• Atom Count: 2,746 
• Modelled Residue Count: 346 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional repressor FrmR	A, B, C, D	91	Escherichia coli O157:H7	Mutation(s): 0  Gene Names: frmR, Z0457, ECs0412
UniProt
Find proteins for Q8X5J3 (Escherichia coli O157:H7) Explore Q8X5J3  Go to UniProtKB:  Q8X5J3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FOR	E [auth A], F [auth B]	FORMYL GROUP C H2 O WSFSSNUMVMOOMR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.266 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.069	α = 90
b = 82.069	β = 90
c = 55.251	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
xia2	data reduction
Aimless	data scaling
PHASER	phasing
BUCCANEER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Bisson, C., Baker, P.J., Green, J., Chivers, P.T.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/L008114/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/J014443/1

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Author supporting evidence