8AKH

Crystal structure of DltE from L. plantarum soaked with LTA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure-function analysis of Lactiplantibacillus plantarum DltE& reveals D-alanylated lipoteichoic acids as direct cues supporting Drosophila juvenile growth.

Nikolopoulos, N.Matos, R.Ravaud, S.Courtin, P.Akherraz, H.Palussiere, S.Gueguen-Chaignon, V.Salomon-Mallet, M.Guillot, A.Guerardel, Y.Chapot-Chartier, M.P.Grangeasse, C.Leulier, F.

(2023) Elife 12

  • DOI: https://doi.org/10.7554/eLife.84669
  • Primary Citation of Related Structures:  
    8AGR, 8AIK, 8AJI, 8AKH

  • PubMed Abstract: 

    Metazoans establish mutually beneficial interactions with their resident microorganisms. However, our understanding of the microbial cues contributing to host physiology remains elusive. Previously, we identified a bacterial machinery encoded by the dlt operon involved in Drosophila melanogaster 's juvenile growth promotion by Lactiplantibacillus plantarum . Here, using crystallography combined with biochemical and cellular approaches, we investigate the physiological role of an uncharacterized protein (DltE) encoded by this operon. We show that lipoteichoic acids (LTAs) but not wall teichoic acids are D-alanylated in Lactiplantibacillus plantarum NC8 cell envelope and demonstrate that DltE is a D-Ala carboxyesterase removing D-Ala from LTA. Using the mutualistic association of L. plantarum NC8 and Drosophila melanogaster as a symbiosis model, we establish that D-alanylated LTAs (D-Ala-LTAs) are direct cues supporting intestinal peptidase expression and juvenile growth in Drosophila . Our results pave the way to probing the contribution of D-Ala-LTAs to host physiology in other symbiotic models.


  • Organizational Affiliation

    Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, Université Claude Bernard Lyon 1, Lyon, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase family protein
A, B
374Lactiplantibacillus plantarumMutation(s): 0 
Gene Names: pbpX2pbpX_4C7M36_02596E3O64_07015E3U93_06380FEE41_04205IV39_GL001648LPJSA22_01868SN35N_2987
EC: 3.4.16.4
UniProt
Find proteins for A0A0P7JVD2 (Lactiplantibacillus plantarum)
Explore A0A0P7JVD2 
Go to UniProtKB:  A0A0P7JVD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0P7JVD2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G3P (Subject of Investigation/LOI)
Query on G3P

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
J [auth B],
K [auth B]
SN-GLYCEROL-3-PHOSPHATE
C3 H9 O6 P
AWUCVROLDVIAJX-GSVOUGTGSA-N
TLA
Query on TLA

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.678α = 90
b = 96.066β = 90
c = 150.828γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique (CNRS)France--
Agence Nationale de la Recherche (ANR)France18-CE15-0011

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description