3UB9

Periplasmic portion of the Helicobacter pylori chemoreceptor TlpB with hydroxyurea bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.133 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and proposed mechanism for the pH-sensing Helicobacter pylori chemoreceptor TlpB.

Goers Sweeney, E.Henderson, J.N.Goers, J.Wreden, C.Hicks, K.G.Foster, J.K.Parthasarathy, R.Remington, S.J.Guillemin, K.

(2012) Structure 20: 1177-1188

  • DOI: 10.1016/j.str.2012.04.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • pH sensing is crucial for survival of most organisms, yet the molecular basis of such sensing is poorly understood. Here, we present an atomic resolution structure of the periplasmic portion of the acid-sensing chemoreceptor, TlpB, from the gastric p ...

    pH sensing is crucial for survival of most organisms, yet the molecular basis of such sensing is poorly understood. Here, we present an atomic resolution structure of the periplasmic portion of the acid-sensing chemoreceptor, TlpB, from the gastric pathogen Helicobacter pylori. The structure reveals a universal signaling fold, a PAS domain, with a molecule of urea bound with high affinity. Through biophysical, biochemical, and in vivo mutagenesis studies, we show that urea and the urea-binding site residues play critical roles in the ability of H. pylori to sense acid. Our signaling model predicts that protonation events at Asp114, affected by changes in pH, dictate the stability of TlpB through urea binding.


    Organizational Affiliation

    Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
chemoreceptor TlpB
A, B
181Helicobacter pylori (strain P12)Mutation(s): 0 
Gene Names: tlpB
Find proteins for B6JPK4 (Helicobacter pylori (strain P12))
Go to UniProtKB:  B6JPK4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NHY
Query on NHY

Download SDF File 
Download CCD File 
A, B
N-HYDROXYUREA
1-HYDROXYUREA
C H4 N2 O2
VSNHCAURESNICA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.133 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 79.611α = 90.00
b = 81.539β = 90.00
c = 94.554γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2013-01-09
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description