4DZ1 | pdb_00004dz1

Crystal structure of DalS, an ATP binding cassette transporter for D-alanine from Salmonella enterica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.203 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4DZ1

This is version 1.3 of the entry. See complete history

Literature

Characterization of DalS, an ATP-binding Cassette Transporter for D-Alanine, and Its Role in Pathogenesis in Salmonella enterica.

Osborne, S.E.Tuinema, B.R.Mok, M.C.Lau, P.S.Bui, N.K.Tomljenovic-Berube, A.M.Vollmer, W.Zhang, K.Junop, M.Coombes, B.K.

(2012) J Biological Chem 287: 15242-15250

  • DOI: https://doi.org/10.1074/jbc.M112.348227
  • Primary Citation Related Structures: 
    4DZ1

  • PubMed Abstract: 

    Expansion into new host niches requires bacterial pathogens to adapt to changes in nutrient availability and to evade an arsenal of host defenses. Horizontal acquisition of Salmonella Pathogenicity Island (SPI)-2 permitted the expansion of Salmonella enterica serovar Typhimurium into the intracellular environment of host cells by allowing it to deliver bacterial effector proteins across the phagosome membrane. This is facilitated by the SsrA-SsrB two-component regulatory system and a type III secretion system encoded within SPI-2. SPI-2 acquisition was followed by evolution of existing regulatory DNA, creating an expanded SsrB regulon involved in intracellular fitness and host infection. Here, we identified an SsrB-regulated operon comprising an ABC transporter in Salmonella. Biochemical and structural studies determined that the periplasmic solute-binding component, STM1633/DalS, transports D-alanine and that DalS is required for intracellular survival of the bacteria and for fitness in an animal host. This work exemplifies the role of nutrient exchange at the host-pathogen interface as a critical determinant of disease outcome.


  • Organizational Affiliation
    • Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario, L8N 3Z5, Canada.

Macromolecule Content 

  • Total Structure Weight: 29.86 kDa 
  • Atom Count: 1,985 
  • Modeled Residue Count: 229 
  • Deposited Residue Count: 259 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DalS D-Alanine transporter259Salmonella entericaMutation(s): 0 
Gene Names: LTSEBAI_2502

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DAL

Query on DAL



Download:Ideal Coordinates CCD File
B [auth A]D-ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-UWTATZPHSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.203 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.076α = 90
b = 81.076β = 90
c = 187.926γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Database references
  • Version 1.2: 2012-05-23
    Changes: Database references
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary