9B9X | pdb_00009b9x

Crystal structure of the ligand binding domain of the Halomonas titanicae chemoreceptor Htc10 in complex with hypoxanthine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.63 Å
  • R-Value Free: 
    0.294 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.242 (Depositor) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

The chemoreceptor controlling the Wsp-like transduction pathway in Halomonas titanicae KHS3 binds and responds to purine derivatives.

Ramos Ricciuti, F.E.Soldano, A.Herrera Seitz, M.K.Gasperotti, A.F.Boyko, A.Jung, K.Bellinzoni, M.Lisa, M.N.Studdert, C.A.

(2025) FEBS J 292: 1034-1051

  • DOI: https://doi.org/10.1111/febs.17320
  • Primary Citation Related Structures: 
    9B9S, 9B9X, 9BA3

  • PubMed Abstract: 

    The chemosensory pathway HtChe2 from the marine bacterium Halomonas titanicae KHS3 controls the activity of a diguanylate cyclase. Constitutive activation of this pathway results in colony morphology alterations and an increased ability to form biofilm. Such characteristics resemble the behavior of the Wsp pathway of Pseudomonas. In this work, we investigate the specificity of Htc10, the only chemoreceptor coded within the HtChe2 gene cluster. The purine derivatives guanine and hypoxanthine were identified as ligands of the recombinantly produced Htc10 ligand-binding domain, with dissociation constants in the micromolar range, and its structure was solved by X-ray protein crystallography. The sensor domain of Htc10 adopts a double Cache folding, with ligands bound to the membrane-distal pocket. A high-resolution structure of the occupied guanine-binding pocket allowed the identification of residues involved in ligand recognition. Such residues were validated by site-directed mutagenesis and isothermal titration calorimetry analyses of the protein variants. Moreover, heterologous expression of Htc10 in a Pseudomonas putida mutant lacking the native Wsp chemoreceptor promoted biofilm formation, a phenotype that was further enhanced by Htc10-specific ligands. To our knowledge, this is the first description of binding specificity of a chemoreceptor that controls the activity of an associated diguanylate cyclase, opening the way for dynamic studies of the signaling behavior of this kind of sensory complex.


  • Organizational Affiliation
    • Instituto de Agrobiotecnología del Litoral (IAL, CONICET-UNL), Santa Fe, Argentina.

Macromolecule Content 

  • Total Structure Weight: 32.75 kDa 
  • Atom Count: 1,707 
  • Modeled Residue Count: 214 
  • Deposited Residue Count: 288 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chemotaxis protein288Vreelandella titanicaeMutation(s): 0 
Gene Names: RO22_21155
UniProt
Find proteins for L9UCI1 (Vreelandella titanicae BH1)
Explore L9UCI1 
Go to UniProtKB:  L9UCI1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL9UCI1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HPA
(Subject of Investigation/LOI)

Query on HPA



Download:Ideal Coordinates CCD File
B [auth A]HYPOXANTHINE
C5 H4 N4 O
FDGQSTZJBFJUBT-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.63 Å
  • R-Value Free:  0.294 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.242 (Depositor) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.856α = 90
b = 175.856β = 90
c = 88.611γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)ArgentinaPICT2016-1629
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)ArgentinaPICT2020-3814

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Database references
  • Version 1.2: 2025-03-19
    Changes: Database references