5F1R

The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with a ring-fused 2-pyridone (C10)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Attenuating Listeria monocytogenes Virulence by Targeting the Regulatory Protein PrfA.

Good, J.A.Andersson, C.Hansen, S.Wall, J.Krishnan, K.S.Begum, A.Grundstrom, C.Niemiec, M.S.Vaitkevicius, K.Chorell, E.Wittung-Stafshede, P.Sauer, U.H.Sauer-Eriksson, A.E.Almqvist, F.Johansson, J.

(2016) Cell Chem Biol 23: 404-414

  • DOI: 10.1016/j.chembiol.2016.02.013
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The transcriptional activator PrfA, a member of the Crp/Fnr family, controls the expression of some key virulence factors necessary for infection by the human bacterial pathogen Listeria monocytogenes. Phenotypic screening identified ring-fused 2-pyr ...

    The transcriptional activator PrfA, a member of the Crp/Fnr family, controls the expression of some key virulence factors necessary for infection by the human bacterial pathogen Listeria monocytogenes. Phenotypic screening identified ring-fused 2-pyridone molecules that at low micromolar concentrations attenuate L. monocytogenes cellular uptake by reducing the expression of virulence genes. These inhibitors bind the transcriptional regulator PrfA and decrease its affinity for the consensus DNA-binding site. Structural characterization of this interaction revealed that one of the ring-fused 2-pyridones, compound 1, binds at two separate sites on the protein: one within a hydrophobic pocket or tunnel, located between the C- and N-terminal domains of PrfA, and the second in the vicinity of the DNA-binding helix-turn-helix motif. At both sites the compound interacts with residues important for PrfA activation and helix-turn-helix formation. Ring-fused 2-pyridones represent a new class of chemical probes for studying virulence in L. monocytogenes.


    Organizational Affiliation

    Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden; Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden; Molecular Infection Medicine, Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden. Electronic address: jorgen.johansson@umu.se.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Listeriolysin regulatory protein
A, B
237Listeria monocytogenes EGD-eMutation(s): 0 
Gene Names: prfAlmo0200
Find proteins for P22262 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Go to UniProtKB:  P22262
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
42O
Query on 42O

Download CCD File 
A, B
(3~{R})-8-cyclopropyl-7-(naphthalen-1-ylmethyl)-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridine-3-carboxylic acid
C22 H19 N O3 S
BMDMKWJIRFLEEY-SFHVURJKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
42OKd:  1000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.34α = 90
b = 80.97β = 112.54
c = 62.34γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden--
Swedish Research CouncilSweden--

Revision History 

  • Version 1.0: 2016-03-16
    Type: Initial release
  • Version 1.1: 2016-03-30
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence