6IOU

The ligand binding domain of Mlp24 with serine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Calcium Ions Modulate Amino Acid Sensing of the Chemoreceptor Mlp24 ofVibrio cholerae.

Takahashi, Y.Nishiyama, S.I.Sumita, K.Kawagishi, I.Imada, K.

(2019) J Bacteriol 201

  • DOI: https://doi.org/10.1128/JB.00779-18
  • Primary Citation of Related Structures:  
    6IOP, 6IOQ, 6IOR, 6IOS, 6IOT, 6IOU

  • PubMed Abstract: 

    Bacteria sense environmental chemicals using chemosensor proteins, most of which are present in the cytoplasmic membrane. Canonical chemoreceptors bind their specific ligands in their periplasmic domain, and the ligand binding creates a molecular stimulus that is transmitted into the cytoplasm, leading to various cellular responses, such as chemotaxis and specific gene expression. Vibrio cholerae , the causative agent of cholera, contains about 44 putative sensor proteins, which are homologous to methyl-accepting chemotaxis proteins involved in chemotaxis. Two of them, Mlp24 and Mlp37, have been identified as chemoreceptors that mediate chemotactic responses to various amino acids. Although most of the residues of Mlp37 involved in ligand binding are conserved in Mlp24, these chemoreceptors bind the same ligands with different affinities. Moreover, they have distinct cellular roles. Here we determined a series of ligand complex structures of the periplasmic domains of Mlp24 (Mlp24p). The structures revealed that Ca 2+ binds to the loop that forms the upper wall of the ligand-binding pocket. Ca 2+ does not bind to the corresponding loop of Mlp37, implying that the structural difference of the loop may cause the ligand affinity difference. Isothermal titration calorimetry (ITC) measurements indicated that Ca 2+ changes the ligand binding affinity of Mlp24p. Furthermore, Ca 2+ affected chemotactic behaviors to various amino acids mediated by Mlp24. Thus, Ca 2+ is suggested to serve as a cosignal for the primary signal mediated by Mlp24p, and V. cholerae fine-tunes its chemotactic behavior depending on the Ca 2+ concentration by modulating the ligand sensitivity of Mlp24. IMPORTANCE Mlp24 and Mlp37 are homologous chemoreceptors of Vibrio cholerae that bind various amino acids. Although most of the residues involved in ligand interaction are conserved, these chemoreceptors show different affinities for the same ligand and play different cellular roles. A series of ligand complex structures of the periplasmic region of Mlp24 (Mlp24p) and following ITC analysis revealed that Ca 2+ binds to the loop of Mlp24p and modulates the ligand binding affinity of Mlp24p. Moreover, Ca 2+ changes the chemotactic behaviors mediated by Mlp24. We propose that Ca 2+ acts as a cosignal that modulates the affinity of Mlp24 for the primary signal, thereby changing the chemotactic behavior of V. cholerae .


  • Organizational Affiliation

    Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methyl-accepting chemotaxis protein
A, B
256Vibrio choleraeMutation(s): 0 
Gene Names: mcpB_4ERS013206_02812
UniProt
Find proteins for Q9KQ43 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KQ43 
Go to UniProtKB:  Q9KQ43
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KQ43
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.67α = 90
b = 62.32β = 105.55
c = 73.17γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan15H02386
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan23115008
Japan Society for the Promotion of ScienceJapan17J02169
Japan Society for the Promotion of ScienceJapan17KT0026

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Derived calculations