2YFA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 U S A 109: 18926

  • DOI: 10.1073/pnas.1201400109
  • Primary Citation of Related Structures:  
    2YFA, 2YFB

  • 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 that contains a single site for chemoattractant recognition ...

    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 Struct Biol Cryst Commun 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
METHYL-ACCEPTING CHEMOTAXIS TRANSDUCERA, B258Pseudomonas putida KT2440Mutation(s): 0 
Gene Names: mcpSPP_4658
UniProt
Find proteins for Q88E10 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440))
Explore Q88E10 
Go to UniProtKB:  Q88E10
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88E10
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
LMR PDBBind:  2YFA Kd: 8500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 226.35α = 90
b = 45.85β = 95.81
c = 51.18γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references