3UB8

Periplasmic portion of the Helicobacter pylori chemoreceptor TlpB with formamide bound

• PDB DOI: https://doi.org/10.2210/pdb3UB8/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Helicobacter pylori SS1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-10-23 Released: 2012-06-27 
• Deposition Author(s): Henderson, J.N., Sweeney, E.G., Goers, J., Wreden, C., Hicks, K.G., Parthasarathy, R., Guillemin, K.J., Remington, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 0.165 
• R-Value Work: 0.139 
• R-Value Observed: 0.140 

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

• PubMed: 22705207 
• DOI: https://doi.org/10.1016/j.str.2012.04.021
• Primary Citation of Related Structures:  
  3UB6, 3UB7, 3UB8, 3UB9, 4EXO


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.11 kDa 
• Atom Count: 3,009 
• Modelled Residue Count: 315 
• Deposited Residue Count: 362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
chemoreceptor TlpB	A, B	181	Helicobacter pylori SS1	Mutation(s): 0
UniProt
Find proteins for B6JPK4 (Helicobacter pylori (strain P12)) Explore B6JPK4  Go to UniProtKB:  B6JPK4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth A], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ARF	C [auth A], E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], L [auth B], M [auth B]	FORMAMIDE C H3 N O ZHNUHDYFZUAESO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 0.165 
• R-Value Work: 0.139 
• R-Value Observed: 0.140 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.61	α = 90
b = 81.713	β = 90
c = 94.538	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-27 
Deposition Author(s): Henderson, J.N., Sweeney, E.G., Goers, J., Wreden, C., Hicks, K.G., Parthasarathy, R., Guillemin, K.J., Remington, S.J.

Revision History  

• Version 1.0: 2012-06-27
  Type: Initial release
  
• Version 1.1: 2013-01-09
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations