6H48 | pdb_00006h48

A polyamorous repressor: deciphering the evolutionary strategy used by the phage-inducible chromosomal islands to spread in nature.

• PDB DOI: https://doi.org/10.2210/pdb6H48/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-07-20 Released: 2019-08-28 
• Deposition Author(s): Ciges-Tomas, J.R., Alite, C., Bowring, J.Z., Donderis, J., Penades, J.R., Marina, A.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness, Medical Research Council (United Kingdom), Biotechnology and Biological Sciences Research Council, European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.264 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Literature

The structure of a polygamous repressor reveals how phage-inducible chromosomal islands spread in nature.

Rafael Ciges-Tomas, J., Alite, C., Humphrey, S., Donderis, J., Bowring, J., Salvatella, X., Penades, J.R., Marina, A.

(2019) Nat Commun 10: 3676-3676

• PubMed: 31417084 
• DOI: https://doi.org/10.1038/s41467-019-11504-2
• Primary Citation Related Structures: 
  6H48, 6H49, 6H4B, 6H4C


• PubMed Abstract: 
  

  Stl is a master repressor encoded by Staphylococcus aureus pathogenicity islands (SaPIs) that maintains integration of these elements in the bacterial chromosome. After infection or induction of a resident helper phage, SaPIs are de-repressed by specific interactions of phage proteins with Stl. SaPIs have evolved a fascinating mechanism to ensure their promiscuous transfer by targeting structurally unrelated proteins performing identically conserved functions for the phage. Here we decipher the molecular mechanism of this elegant strategy by determining the structure of SaPIbov1 Stl alone and in complex with two structurally unrelated dUTPases from different S. aureus phages. Remarkably, SaPIbov1 Stl has evolved different domains implicated in DNA and partner recognition specificity. This work presents the solved structure of a SaPI repressor protein and the discovery of a modular repressor that acquires multispecificity through domain recruiting. Our results establish the mechanism that allows widespread dissemination of SaPIs in nature.

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Organizational Affiliation: 
• Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, 46010, Spain.
Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK.
ICREA and Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, 08010, Spain.
Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK. [e-mail].
Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, 46010, Spain. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 11.58 kDa 
• Atom Count: 684 
• Modeled Residue Count: 77 
• Deposited Residue Count: 96 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orf20	A	96	Staphylococcus aureus	Mutation(s): 0
UniProt
Find proteins for Q9F0J8 (Staphylococcus aureus) Explore Q9F0J8  Go to UniProtKB:  Q9F0J8

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.264 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.357	α = 90
b = 77.357	β = 90
c = 37.318	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
SOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-08-28 
Deposition Author(s): Ciges-Tomas, J.R., Alite, C., Bowring, J.Z., Donderis, J., Penades, J.R., Marina, A.

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Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BIO2016-78571-P
Spanish Ministry of Economy and Competitiveness	Spain	FPU13/02880
Spanish Ministry of Economy and Competitiveness	Spain	BES-2014-068617
Medical Research Council (United Kingdom)	United Kingdom	MR/M003876/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/N002873/1
European Research Council	United Kingdom	ERC-ADG-2014 670932

Revision History  

• Version 1.0: 2019-08-28
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Database references, Structure summary