2YFB

X-ray structure of McpS ligand binding domain in complex with succinate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Evidence for Chemoreceptors with Bimodular Ligand-Binding Regions Harboring Two Signal-Binding Sites.

Pineda-Molina, E.Reyes-Darias, J.Lacal, J.Ramos, J.L.Garcia-Ruiz, J.M.Gavira, J.A.Krell, T.

(2012) Proc.Natl.Acad.Sci.USA 109: 18926

  • DOI: 10.1073/pnas.1201400109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chemoreceptor-based signaling is a central mechanism in bacterial signal transduction. Receptors are classified according to the size of their ligand-binding region. The well-studied cluster I proteins have a 100- to 150-residue ligand-binding region ...

    Chemoreceptor-based signaling is a central mechanism in bacterial signal transduction. Receptors are classified according to the size of their ligand-binding region. The well-studied cluster I proteins have a 100- to 150-residue ligand-binding region that contains a single site for chemoattractant recognition. Cluster II receptors, which contain a 220- to 300-residue ligand-binding region and which are almost as abundant as cluster I receptors, remain largely uncharacterized. Here, we report high-resolution structures of the ligand-binding region of the cluster II McpS chemotaxis receptor (McpS-LBR) of Pseudomonas putida KT2440 in complex with different chemoattractants. The structure of McpS-LBR represents a small-molecule binding domain composed of two modules, each able to bind different signal molecules. Malate and succinate were found to bind to the membrane-proximal module, whereas acetate binds to the membrane-distal module. A structural alignment of the two modules revealed that the ligand-binding sites could be superimposed and that amino acids involved in ligand recognition are conserved in both binding sites. Ligand binding to both modules was shown to trigger chemotactic responses. Further analysis showed that McpS-like receptors were found in different classes of proteobacteria, indicating that this mode of response to different carbon sources may be universally distributed. The physiological relevance of the McpS architecture may lie in its capacity to respond with high sensitivity to the preferred carbon sources malate and succinate and, at the same time, mediate lower sensitivity responses to the less preferred but very abundant carbon source acetate.


    Related Citations: 
    • Crystallization and Crystallographic Analysis of the Ligand-Binding Domain of the Pseudomonas Putida Chemoreceptor Mcps in Complex with Malate and Succinate.
      Gavira, J.A.,Lacal, J.,Ramos, J.L.,Garcia-Ruiz, J.M.,Krell, T.,Pineda-Molina, E.
      (2012) Acta Crystallogr.,Sect.F 68: 428


    Organizational Affiliation

    Laboratoiro de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Granada, 18100 Armilla-Granada, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METHYL-ACCEPTING CHEMOTAXIS TRANSDUCER
A, B
258Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)Mutation(s): 0 
Gene Names: mcpS
Find proteins for Q88E10 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440))
Go to UniProtKB:  Q88E10
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A, B
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 226.067α = 90.00
b = 46.039β = 95.92
c = 50.823γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2012-05-30
    Type: Other
  • Version 1.2: 2013-07-10
    Type: Database references