3I9Y | pdb_00003i9y

Crystal structure of the V. parahaemolyticus histidine kinase sensor TorS sensor domain

• PDB DOI: https://doi.org/10.2210/pdb3I9Y/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio parahaemolyticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-13 Released: 2009-10-06 
• Deposition Author(s): Moore, J.O., Hendrickson, W.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 
  0.261 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.225 (DCC) 

Literature

Structural analysis of sensor domains from the TMAO-responsive histidine kinase receptor TorS

Moore, J.O., Hendrickson, W.A.

(2009) Structure 17: 1195-1204

• PubMed: 19748340 
• DOI: https://doi.org/10.1016/j.str.2009.07.015
• Primary Citation Related Structures: 
  3I9W, 3I9Y


• PubMed Abstract: 
  

  Histidine kinase receptors respond to diverse signals and mediate signal transduction across the plasma membrane in all prokaryotes and certain eukaryotes. Each receptor is part of a two-component system that regulates a particular cellular process. Organisms that use trimethylamine-N-oxide (TMAO) as a terminal electron acceptor typically control their anaerobic respiration through the TMAO reductase (Tor) pathway, which the TorS histidine kinase activates when sensing TMAO in the environment. We have determined crystal structures for the periplasmic sensor domains of TorS receptors from Escherichia coli and Vibrio parahaemolyticus. TorS sensor domains have a novel fold consisting of a membrane-proximal right-handed four-helical bundle and a membrane-distal left-handed four-helical bundle, but conformational dispositions differ significantly in the two structures. Isolated TorS sensor domains dimerize in solution; and from comparisons with dimeric NarX and Tar sensors, we postulate that signaling through TorS dimers involves a piston-type displacement between helices.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 31.57 kDa 
• Atom Count: 1,926 
• Modeled Residue Count: 229 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensor protein	A	276	Vibrio parahaemolyticus	Mutation(s): 0  Gene Names: torS, VPA0675 EC: 2.7.13.3
UniProt
Find proteins for Q87ID1 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87ID1  Go to UniProtKB:  Q87ID1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free:  0.261 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.225 (DCC) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.88	α = 90
b = 149.88	β = 90
c = 42.712	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Moore, J.O., Hendrickson, W.A.

Revision History  

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references