8Q89 | pdb_00008q89

Crystal structure of Apis mellifera glutathione transferase delta 1 in a covalent dimeric state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.243 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8Q89

This is version 1.3 of the entry. See complete history

Literature

Structure-activity analysis suggests an olfactory function for the unique antennal delta glutathione transferase of Apis mellifera.

Schwartz, M.Boichot, V.Muradova, M.Fournier, P.Senet, P.Nicolai, A.Canon, F.Lirussi, F.Ladeira, R.Maibeche, M.Chertemps, T.Aubert, E.Didierjean, C.Neiers, F.

(2023) FEBS Lett 597: 3038-3048

  • DOI: https://doi.org/10.1002/1873-3468.14770
  • Primary Citation Related Structures: 
    8Q89, 8Q8A, 8Q8B

  • PubMed Abstract: 

    Glutathione transferases (GST) are detoxification enzymes that conjugate glutathione to a wide array of molecules. In the honey bee Apis mellifera, AmGSTD1 is the sole member of the delta class of GSTs, with expression in antennae. Here, we structurally and biochemically characterized AmGSTD1 to elucidate its function. We showed that AmGSTD1 can efficiently catalyse the glutathione conjugation of classical GST substrates. Additionally, AmGSTD1 exhibits binding properties with a range of odorant compounds. AmGSTD1 has a peculiar interface with a structural motif we propose to call 'sulfur sandwich'. This motif consists of a cysteine disulfide bridge sandwiched between the sulfur atoms of two methionine residues and is stabilized by CH…S hydrogen bonds and S…S sigma-hole interactions. Thermal stability studies confirmed that this motif is important for AmGSTD1 stability and, thus, could facilitate its functions in olfaction.


  • Organizational Affiliation
    • CSGA, Flavour Perception: Molecular Mechanisms (Flavours), Université de Bourgogne, INRAE, CNRS, Institut Agro, Dijon, France.

Macromolecule Content 

  • Total Structure Weight: 24.99 kDa 
  • Atom Count: 1,595 
  • Modeled Residue Count: 188 
  • Deposited Residue Count: 215 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutathione S-transferase D1 isoform X1215Apis melliferaMutation(s): 0 
Gene Names: 409490Gst1GstD1
UniProt
Find proteins for A0A7M7GUY7 (Apis mellifera)
Explore A0A7M7GUY7 
Go to UniProtKB:  A0A7M7GUY7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7M7GUY7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.243 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.971α = 90
b = 77.971β = 90
c = 81.455γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)France--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-18
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Database references
  • Version 1.3: 2024-11-06
    Changes: Structure summary