9XGL | pdb_00009xgl

D-alanyl carrier protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 
    0.255 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural Insights into the Staphylococcus aureus DltC-Mediated D-Alanine Transfer.

Jeon, H.Lee, H.Song, C.Lee, I.G.

(2025) Biomolecules 16

  • DOI: https://doi.org/10.3390/biom16010044
  • Primary Citation Related Structures: 
    9XGL, 9XGM

  • PubMed Abstract: 

    Staphylococcus aureus ( S. aureus ) is a major Gram-positive pathogen, and treatment of S. aureus infections is often challenging due to widespread antibiotic resistance. In Gram-positive bacteria such as S. aureus , D-alanylation of teichoic acids (TA) reduces the net negative charge of the cell envelope and contributes to resistance to diverse antibiotics, particularly cationic antimicrobial peptides. D-alanylation is mediated by the dlt ABCD operon, which encodes four proteins (DltA, DltB, DltC, and DltD), all of which is essential for the multistep transfer of D-alanine to teichoic acids. Here, we present the first crystal structure of the S. aureus D-alanyl carrier protein DltC and analyze its interaction with DltA using AlphaFold3 and all-atom molecular dynamics simulations. We further show that single substitutions of Sa DltA- Sa DltC interface residues abolish Sa DltC mediated enhancement of Sa DltA catalysis. Together, these findings define a catalytically critical S. aureus DltA-DltC interface and provide a structural insight for targeting the D-alanylation pathway as a potential anti- Staphylococcus strategy.


  • Organizational Affiliation
    • College of Pharmacy, Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 36.28 kDa 
  • Atom Count: 2,620 
  • Modeled Residue Count: 312 
  • Deposited Residue Count: 312 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
D-alanyl carrier protein
A, B, C, D
78Staphylococcus aureus subsp. aureus Mu50Mutation(s): 0 
Gene Names: dltCSAV0934
UniProt
Find proteins for P0A018 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore P0A018 
Go to UniProtKB:  P0A018
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A018
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free:  0.255 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.137α = 90
b = 63.968β = 93.95
c = 77.145γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-21
    Type: Initial release
  • Version 1.1: 2026-02-11
    Changes: Database references