9KUP | pdb_00009kup

Crystal structure of MCP2201LBD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.185 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Insights into Chemoreceptor MCP2201-Sensing D-Malate.

Cui, R.Li, J.Hong, Y.Guo, L.Wang, Y.H.Bai, Y.F.Li, D.F.

(2025) Int J Mol Sci 26

  • DOI: https://doi.org/10.3390/ijms26104902
  • Primary Citation of Related Structures:  
    9KUP

  • PubMed Abstract: 

    Bacterial chemoreceptors sense extracellular stimuli and drive bacteria toward a beneficial environment or away from harm. Their ligand-binding domains (LBDs) are highly diverse in terms of sequence and structure, and their ligands cover various chemical molecules that could serve as nitrogen, carbon, and energy sources. The mechanism of how this diverse range of LBDs senses different ligands is essential to signal transduction. Previously, we reported that the chemoreceptor MCP2201 from Comamonas testosteroni CNB-1 sensed citrate and L-malate, altered the ligand-free monomer-dimer equilibrium of LBD to citrate-bound monomer (with limited monomer) and L-malate-bound dimer, and triggered positive and negative chemotactic responses. Here, we present our findings, showing that D-malate binds to MCP2201, induces LBD dimerization, and triggers the chemorepellent response exactly as L-malate did. A single site mutation, T105A, can alter the D-malate-bound LBD dimer into a monomer-dimer equilibrium and switch the negative chemotactic response to D-malate to a positive one. Differences in attractant-bound LBD oligomerization, such as citrate-bound wildtype LBD monomer and D-malate-bound T105A dimer, indicated that LBD oligomerization is a consequence of signal transduction instead of a trigger. Our study expands our knowledge of chemoreceptor-sensing ligands and provides insight into the evolution of bacterial chemoreceptors.


  • Organizational Affiliation
    • State Key Laboratory of Microbial Diversity and Innovative Utilization, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methyl-accepting chemotaxis sensory transducer
A, B
179Comamonas thiooxydansMutation(s): 0 
Gene Names: CtCNB1_2201
UniProt
Find proteins for A0ABF7PFR0 (Comamonas thiooxydans)
Explore A0ABF7PFR0 
Go to UniProtKB:  A0ABF7PFR0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ABF7PFR0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.185 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.8α = 90
b = 59.8β = 90
c = 158.201γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China111111

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release