6T5I | pdb_00006t5i

The Transcriptional Regulator PrfA from Listeria Monocytogenes in complex with inhibitor of WNT production (IWP)-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.252 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Inhibition of the master regulator of Listeria monocytogenes virulence enables bacterial clearance from spacious replication vacuoles in infected macrophages.

Tran, T.T.Mathmann, C.D.Gatica-Andrades, M.Rollo, R.F.Oelker, M.Ljungberg, J.K.Nguyen, T.T.K.Zamoshnikova, A.Kummari, L.K.Wyer, O.J.K.Irvine, K.M.Melo-Bolivar, J.Gross, A.Brown, D.Mak, J.Y.W.Fairlie, D.P.Hansford, K.A.Cooper, M.A.Giri, R.Schreiber, V.Joseph, S.R.Simpson, F.Barnett, T.C.Johansson, J.Dankers, W.Harris, J.Wells, T.J.Kapetanovic, R.Sweet, M.J.Latomanski, E.A.Newton, H.J.Guerillot, R.J.R.Hachani, A.Stinear, T.P.Ong, S.Y.Chandran, Y.Hartland, E.L.Kobe, B.Stow, J.L.Sauer-Eriksson, A.E.Begun, J.Kling, J.C.Blumenthal, A.

(2022) PLoS Pathog 18: e1010166-e1010166

  • DOI: https://doi.org/10.1371/journal.ppat.1010166
  • Primary Citation Related Structures: 
    6T5I

  • PubMed Abstract: 

    A hallmark of Listeria (L.) monocytogenes pathogenesis is bacterial escape from maturing entry vacuoles, which is required for rapid bacterial replication in the host cell cytoplasm and cell-to-cell spread. The bacterial transcriptional activator PrfA controls expression of key virulence factors that enable exploitation of this intracellular niche. The transcriptional activity of PrfA within infected host cells is controlled by allosteric coactivation. Inhibitory occupation of the coactivator site has been shown to impair PrfA functions, but consequences of PrfA inhibition for L. monocytogenes infection and pathogenesis are unknown. Here we report the crystal structure of PrfA with a small molecule inhibitor occupying the coactivator site at 2.0 Å resolution. Using molecular imaging and infection studies in macrophages, we demonstrate that PrfA inhibition prevents the vacuolar escape of L. monocytogenes and enables extensive bacterial replication inside spacious vacuoles. In contrast to previously described spacious Listeria-containing vacuoles, which have been implicated in supporting chronic infection, PrfA inhibition facilitated progressive clearance of intracellular L. monocytogenes from spacious vacuoles through lysosomal degradation. Thus, inhibitory occupation of the PrfA coactivator site facilitates formation of a transient intravacuolar L. monocytogenes replication niche that licenses macrophages to effectively eliminate intracellular bacteria. Our findings encourage further exploration of PrfA as a potential target for antimicrobials and highlight that intra-vacuolar residence of L. monocytogenes in macrophages is not inevitably tied to bacterial persistence.


  • Organizational Affiliation
    • The University of Queensland Diamantina Institute, Brisbane, Australia.

Macromolecule Content 

  • Total Structure Weight: 56.29 kDa 
  • Atom Count: 3,977 
  • Modeled Residue Count: 464 
  • Deposited Residue Count: 478 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Listeriolysin positive regulatory factor A
A, B
239Listeria monocytogenesMutation(s): 0 
Gene Names: prfAAJN46_04535BWI22_01025
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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9XK
(Subject of Investigation/LOI)

Query on 9XK



Download:Ideal Coordinates CCD File
C [auth A]~{N}-(6-methyl-1,3-benzothiazol-2-yl)-2-[(4-oxidanylidene-3-phenyl-6,7-dihydrothieno[3,2-d]pyrimidin-2-yl)sulfanyl]ethanamide
C22 H18 N4 O2 S3
WRKPZSMRWPJJDH-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
J [auth A],
P [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.252 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.951α = 90
b = 92.667β = 90
c = 101.447γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
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--
National Health and Medical Research Council (Australia)AustraliaGNT1142456

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-27
    Type: Initial release
  • Version 1.1: 2022-01-19
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description