4EXO

Revised, rerefined crystal structure of PDB entry 2QHK, methyl accepting chemotaxis protein

• PDB DOI: https://doi.org/10.2210/pdb4EXO/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Vibrio parahaemolyticus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-04-30 Released: 2012-05-30 
• Deposition Author(s): Sweeney, E.G., Henderson, J.N., Goers, J., Wreden, C., Hicks, K.G., Foster, J.K., Parthasarathy, R., Remington, S.J., Guillemin, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.206 
• R-Value Work: 0.156 
• R-Value Observed: 0.159 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2QHK

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: 16.74 kDa 
• Atom Count: 1,410 
• Modelled Residue Count: 146 
• Deposited Residue Count: 146 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyl-accepting chemotaxis protein	A	146	Vibrio parahaemolyticus	Mutation(s): 0  Gene Names: GI:28896957, VP0183
UniProt
Find proteins for Q87T87 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87T87  Go to UniProtKB:  Q87T87

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PYR	B [auth A]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.206 
• R-Value Work: 0.156 
• R-Value Observed: 0.159 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.268	α = 90
b = 112.268	β = 90
c = 62.731	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-30 
Deposition Author(s): Sweeney, E.G., Henderson, J.N., Goers, J., Wreden, C., Hicks, K.G., Foster, J.K., Parthasarathy, R., Remington, S.J., Guillemin, K.

Revision History  

• Version 1.0: 2012-05-30
  Type: Initial release
  
• Version 1.1: 2012-08-29
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection