8BMV

Ligand binding domain of the P. Putida receptor McpH in complex with Uric acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Ubiquitous purine sensor modulates diverse signal transduction pathways in bacteria.

Monteagudo-Cascales, E.Gumerov, V.M.Fernandez, M.Matilla, M.A.Gavira, J.A.Zhulin, I.B.Krell, T.

(2024) Nat Commun 15: 5867-5867

  • DOI: https://doi.org/10.1038/s41467-024-50275-3
  • Primary Citation of Related Structures:  
    8BMV

  • PubMed Abstract: 

    Purines and their derivatives control intracellular energy homeostasis and nucleotide synthesis, and act as signaling molecules. Here, we combine structural and sequence information to define a purine-binding motif that is present in sensor domains of thousands of bacterial receptors that modulate motility, gene expression, metabolism, and second-messenger turnover. Microcalorimetric titrations of selected sensor domains validate their ability to specifically bind purine derivatives, and evolutionary analyses indicate that purine sensors share a common ancestor with amino-acid receptors. Furthermore, we provide experimental evidence of physiological relevance of purine sensing in a second-messenger signaling system that modulates c-di-GMP levels.


  • Organizational Affiliation

    Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008, Granada, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methyl-accepting chemotaxis protein McpH
A, B
276Pseudomonas putida KT2440Mutation(s): 0 
Gene Names: mcpHPP_0320
UniProt
Find proteins for Q88R14 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440))
Explore Q88R14 
Go to UniProtKB:  Q88R14
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88R14
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.581α = 90
b = 124.322β = 99.33
c = 57.201γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PHENIXrefinement
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2020-112612GB-I00
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2020-116261GB- I00

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release