2OXL

Structure and Function of the E. coli Protein YmgB: a Protein Critical for Biofilm Formation and Acid Resistance


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and Function of the Escherichia coli Protein YmgB: A Protein Critical for Biofilm Formation and Acid-resistance.

Lee, J.Page, R.Garcia-Contreras, R.Palermino, J.M.Zhang, X.S.Doshi, O.Wood, T.K.Peti, W.

(2007) J.Mol.Biol. 373: 11-26

  • DOI: 10.1016/j.jmb.2007.07.037

  • PubMed Abstract: 
  • The Escherichia coli gene cluster ymgABC was identified in transcriptome studies to have a role in biofilm development and stability. In this study, we showed that YmgB represses biofilm formation in rich medium containing glucose, decreases cellular ...

    The Escherichia coli gene cluster ymgABC was identified in transcriptome studies to have a role in biofilm development and stability. In this study, we showed that YmgB represses biofilm formation in rich medium containing glucose, decreases cellular motility, and protects the cell from acid indicating that YmgB has a major role in acid-resistance in E. coli. Our data show that these phenotypes are potentially mediated through interactions with the important cell signal indole. In addition, gel mobility-shift assays suggest that YmgB may be a non-specific DNA-binding protein. Using nickel-enrichment DNA microarrays, we showed that YmgB binds, either directly or indirectly, via a probable ligand, genes important for biofilm formation. To advance our understanding of the function of YmgB, we used X-ray crystallography to solve the structure of the protein to 1.8 A resolution. YmgB is a biological dimer that is structurally homologous to the E. coli gene regulatory protein Hha, despite having only 5% sequence identity. This supports our DNA microarray data showing that YmgB is a gene regulatory protein. Therefore, this protein, which clearly has a critical role in acid-resistance in E. coli, has been renamed as AriR for regulator of acid resistance influenced by indole.


    Organizational Affiliation

    Artie McFerrin Department of Chemical Engineering, Texas A & M University, College Station, TX 77843-3122, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypothetical protein ymgB
A, B
64Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ariR (ymgB)
Find proteins for P75993 (Escherichia coli (strain K12))
Go to UniProtKB:  P75993
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BOG
Query on BOG

Download SDF File 
Download CCD File 
A, B
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.215 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 69.919α = 90.00
b = 69.945β = 90.00
c = 55.021γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
HKL-2000data scaling
ADSCdata collection
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
RESOLVEphasing
SOLVEphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-10-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-10-18
    Type: Refinement description