6WPZ | pdb_00006wpz

The structure of Pf4r from a superinfective isolate of the filamentous phage Pf4 of Pseudomonas aeruginosa PA01

PDB DOI: https://doi.org/10.2210/pdb6WPZ/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-04-28 Released: 2021-04-07
Deposition Author(s): Michie, K.A., Norrian, P., Duggin, I.G., McDougald, D., Rice, S.A.
Funding Organization(s): National Research Foundation (NRF, Singapore), Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.231 (Depositor), 0.233 (DCC)
R-Value Work:
0.186 (Depositor), 0.196 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The Repressor C Protein, Pf4r, Controls Superinfection of Pseudomonas aeruginosa PAO1 by the Pf4 Filamentous Phage and Regulates Host Gene Expression.

Ismail, M.H., Michie, K.A., Goh, Y.F., Noorian, P., Kjelleberg, S., Duggin, I.G., McDougald, D., Rice, S.A.

(2021) Viruses 13

PubMed: 34452479 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/v13081614
Primary Citation Related Structures:
6WNM, 6WPZ, 6X6F

PubMed Abstract:
It has been shown that the filamentous phage, Pf4, plays an important role in biofilm development, stress tolerance, genetic variant formation and virulence in Pseudomonas aeruginosa PAO1. These behaviours are linked to the appearance of superinfective phage variants. Here, we have investigated the molecular mechanism of superinfection as well as how the Pf4 phage can control host gene expression to modulate host behaviours. Pf4 exists as a prophage in PAO1 and encodes a homologue of the P2 phage repressor C and was recently named Pf4r. Through a combination of molecular techniques, ChIPseq and transcriptomic analyses, we show a critical site in repressor C (Pf4r) where a mutation in the site, 788799A>G (Ser4Pro), causes Pf4r to lose its function as the immunity factor against reinfection by Pf4. X-ray crystal structure analysis shows that Pf4r forms symmetric homo-dimers homologous to the E.coli bacteriophage P2 RepC protein. A mutation, Pf4r*, associated with the superinfective Pf4r variant, found at the dimer interface, suggests dimer formation may be disrupted, which derepresses phage replication. This is supported by multi-angle light scattering (MALS) analysis, where the Pf4r* protein only forms monomers. The loss of dimerisation also explains the loss of Pf4r's immunity function. Phenotypic assays showed that Pf4r increased LasB activity and was also associated with a slight increase in the percentage of morphotypic variants. ChIPseq and transcriptomic analyses suggest that Pf4r also likely functions as a transcriptional regulator for other host genes. Collectively, these data suggest the mechanism by which filamentous phages play such an important role in P. aeruginosa biofilm development.

Organizational Affiliation

Singapore Centre for Environmental Life Sciences Engineering, Singapore 637551, Singapore.

Macromolecule Content

Total Structure Weight: 21.03 kDa
Atom Count: 1,345
Modeled Residue Count: 166
Deposited Residue Count: 190
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pf4r	A, B	95	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: CGU42_23305

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]