8C6E

CRYSTAL STRUCTURE OF ODORANT BINDING PROTEIN 4 FROM ANOPHELES GAMBIAE (AGAMOBP4) AT PH 8.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Influence of pH on indole-dependent heterodimeric interactions between Anopheles gambiae odorant-binding proteins OBP1 and OBP4.

Mam, B.Tsitsanou, K.E.Liggri, P.G.V.Saitta, F.Stamati, E.C.V.Mahita, J.Leonis, G.Drakou, C.E.Papadopoulos, M.Arnaud, P.Offmann, B.Fessas, D.Sowdhamini, R.Zographos, S.E.

(2023) Int J Biol Macromol 245: 125422-125422

  • DOI: https://doi.org/10.1016/j.ijbiomac.2023.125422
  • Primary Citation of Related Structures:  
    8C68, 8C6E

  • PubMed Abstract: 

    Insect Odorant Binding Proteins (OBPs) constitute important components of their olfactory apparatus, as they are essential for odor recognition. OBPs undergo conformational changes upon pH change, altering their interactions with odorants. Moreover, they can form heterodimers with novel binding characteristics. Anopheles gambiae OBP1 and OBP4 were found capable of forming heterodimers possibly involved in the specific perception of the attractant indole. In order to understand how these OBPs interact in the presence of indole and to investigate the likelihood of a pH-dependent heterodimerization mechanism, the crystal structures of OBP4 at pH 4.6 and 8.5 were determined. Structural comparison to each other and with the OBP4-indole complex (3Q8I, pH 6.85) revealed a flexible N-terminus and conformational changes in the α4-loop-α5 region at acidic pH. Fluorescence competition assays showed a weak binding of indole to OBP4 that becomes further impaired at acidic pH. Additional Molecular Dynamic and Differential Scanning Calorimetry studies displayed that the influence of pH on OBP4 stability is significant compared to the modest effect of indole. Furthermore, OBP1-OBP4 heterodimeric models were generated at pH 4.5, 6.5, and 8.5, and compared concerning their interface energy and cross-correlated motions in the absence and presence of indole. The results indicate that the increase in pH may induce the stabilization of OBP4 by increasing its helicity, thereby enabling indole binding at neutral pH that further stabilizes the protein and possibly promotes the creation of a binding site for OBP1. A decrease in interface stability and loss of correlated motions upon transition to acidic pH may provoke the heterodimeric dissociation allowing indole release. Finally, we propose a potential OBP1-OBP4 heterodimer formation/disruption mechanism induced by pH change and indole binding.


  • Organizational Affiliation

    National Centre for Biological Sciences, Bangalore, Karnataka, India; The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, Karnataka, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AGAP010489-PA125Anopheles gambiaeMutation(s): 0 
Gene Names: OBP-41275228AgamOBP4OBP4AgaP_AGAP010489agCG48601
UniProt
Find proteins for Q8T6R7 (Anopheles gambiae)
Explore Q8T6R7 
Go to UniProtKB:  Q8T6R7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8T6R7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.95α = 90
b = 55.58β = 90
c = 56.26γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentGreeceT1EDK-00996
Other governmentGreeceMIS5000432

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2023-07-26
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection
  • Version 1.3: 2024-02-14
    Changes: Refinement description