5LRR

The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with glutathione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural basis for glutathione-mediated activation of the virulence regulatory protein PrfA in Listeria.

Hall, M.Grundstrom, C.Begum, A.Lindberg, M.J.Sauer, U.H.Almqvist, F.Johansson, J.Sauer-Eriksson, A.E.

(2016) Proc Natl Acad Sci U S A 113: 14733-14738

  • DOI: https://doi.org/10.1073/pnas.1614028114
  • Primary Citation of Related Structures:  
    5LEJ, 5LEK, 5LRR, 5LRS

  • PubMed Abstract: 

    Infection by the human bacterial pathogen Listeria monocytogenes is mainly controlled by the positive regulatory factor A (PrfA), a member of the Crp/Fnr family of transcriptional activators. Published data suggest that PrfA requires the binding of a cofactor for full activity, and it was recently proposed that glutathione (GSH) could fulfill this function. Here we report the crystal structures of PrfA in complex with GSH and in complex with GSH and its cognate DNA, the hly operator PrfA box motif. These structures reveal the structural basis for a GSH-mediated allosteric mode of activation of PrfA in the cytosol of the host cell. The crystal structure of PrfA WT in complex only with DNA confirms that PrfA WT can adopt a DNA binding-compatible structure without binding the GSH activator molecule. By binding to PrfA in the cytosol of the host cell, GSH induces the correct fold of the HTH motifs, thus priming the PrfA protein for DNA interaction.


  • Organizational Affiliation

    Department of Chemistry, Umeå University, 901 87 Umeå, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Listeriolysin positive regulatory factor A
A, B, C, D, E
A, B, C, D, E, F, G, H
237Listeria monocytogenesMutation(s): 0 
Gene Names: prfAM643_11230
UniProt
Find proteins for P22262 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore P22262 
Go to UniProtKB:  P22262
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22262
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GSH
Query on GSH

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
O [auth C]
P [auth D]
R [auth E]
I [auth A],
L [auth B],
O [auth C],
P [auth D],
R [auth E],
T [auth F],
V [auth G],
W [auth H]
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
PI
Query on PI

Download Ideal Coordinates CCD File 
K [auth A],
M [auth B],
N [auth B]
HYDROGENPHOSPHATE ION
H O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-L
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth A],
Q [auth D],
S [auth E],
U [auth F],
X [auth H]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.265α = 90
b = 184.227β = 90
c = 100.457γ = 90
Software Package:
Software NamePurpose
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
Swedish Research CouncilSweden--
Knut and Alice Wallenberg FoundationSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Database references
  • Version 1.2: 2017-01-11
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description