Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 55413.70 
• Atom Count: 3792 
• Residue Count: 474 
• Unique protein chains: 1

5F1R

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

• DOI: 10.2210/pdb5F1R/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
• Expression System: Escherichia coli


• Deposited: 2015-11-30 Released: 2016-03-16 
• Deposition Author(s): Begum, A., Grundstrom, C., Good, J.A.D., Andersson, C., ALmqvist, F., Johansson, J., Sauer, U.H., Sauer-Eriksson, A.E.
• Funding Organization(s): Knut and Alice Wallenberg Foundation; Swedish Research Council 

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Experimental Data Snapshot

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

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

• PubMed: 26991105 
• DOI: 10.1016/j.chembiol.2016.02.013
• Also Cited By: 6EXK, 6EXM, 6EXL, 6EV0, 6EUZ, 6EUU, 6EUT


• 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-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.

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Organizational Affiliation: 

Department of Chemistry, Umeå University, 901 87 Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Listeriolysin regulatory protein	A, B	237	Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)	Mutation(s): 0  Gene Names: prfA
Find proteins for P22262 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Go to UniProtKB:  P22262

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
42O	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
42O	Kd: 1000 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.259 
• R-Value Work: 0.198 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 56.340	α = 90.00
b = 80.970	β = 112.54
c = 62.340	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-11-30 
• Released Date: 2016-03-16 
• Deposition Author(s): Begum, A., Grundstrom, C., Good, J.A.D., Andersson, C., ALmqvist, F., Johansson, J., Sauer, U.H., Sauer-Eriksson, A.E.

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Funding Organization	Location	Grant Number
Knut and Alice Wallenberg Foundation	Sweden	--
Swedish Research Council	Sweden	--

Revision History 

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