7R49

Crystal structure of the L. plantarum acyl carrier protein synthase (AcpS)in complex with D-alanyl carrier protein (DltC1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

DltC acts as an interaction hub for AcpS, DltA and DltB in the teichoic acid D-alanylation pathway of Lactiplantibacillus plantarum.

Nikolopoulos, N.Matos, R.C.Courtin, P.Ayala, I.Akherraz, H.Simorre, J.P.Chapot-Chartier, M.P.Leulier, F.Ravaud, S.Grangeasse, C.

(2022) Sci Rep 12: 13133-13133

  • DOI: https://doi.org/10.1038/s41598-022-17434-2
  • Primary Citation of Related Structures:  
    7R27, 7R49

  • PubMed Abstract: 

    Teichoic acids (TA) are crucial for the homeostasis of the bacterial cell wall as well as their developmental behavior and interplay with the environment. TA can be decorated by different modifications, modulating thus their biochemical properties. One major modification consists in the esterification of TA by D-alanine, a process known as D-alanylation. TA D-alanylation is performed by the Dlt pathway, which starts in the cytoplasm and continues extracellularly after D-Ala transportation through the membrane. In this study, we combined structural biology and in vivo approaches to dissect the cytoplasmic steps of this pathway in Lactiplantibacillus plantarum, a bacterial species conferring health benefits to its animal host. After establishing that AcpS, DltB, DltC1 and DltA are required for the promotion of Drosophila juvenile growth under chronic undernutrition, we solved their crystal structure and/or used NMR and molecular modeling to study their interactions. Our work demonstrates that the suite of interactions between these proteins is ordered with a conserved surface of DltC1 docking sequentially AcpS, DltA and eventually DltB. Altogether, we conclude that DltC1 acts as an interaction hub for all the successive cytoplasmic steps of the TA D-alanylation pathway.


  • 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
Holo-[acyl-carrier-protein] synthaseA,
C [auth B],
E [auth C]
121Lactiplantibacillus plantarum subsp. plantarum NC8Mutation(s): 0 
Gene Names: acpSlp_0522
EC: 2.7.8.7
UniProt
Find proteins for Q88Z44 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1))
Explore Q88Z44 
Go to UniProtKB:  Q88Z44
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88Z44
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
D-alanyl carrier protein 1B [auth H],
D [auth E],
F
88Lactiplantibacillus plantarum subsp. plantarum NC8Mutation(s): 0 
Gene Names: dltC1lp_2017
UniProt
Find proteins for Q88VM8 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1))
Explore Q88VM8 
Go to UniProtKB:  Q88VM8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88VM8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PNS (Subject of Investigation/LOI)
Query on PNS

Download Ideal Coordinates CCD File 
G [auth H]4'-PHOSPHOPANTETHEINE
C11 H23 N2 O7 P S
JDMUPRLRUUMCTL-VIFPVBQESA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
H [auth C]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.537α = 90
b = 94.888β = 90
c = 98.709γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)France18-CE15-011-03

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2022-08-10
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description