6H4C

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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

  • DOI: 10.1038/s41467-019-11504-2
  • Primary Citation of 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 ...

    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.


    Organizational Affiliation

    Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Valencia, 46010, Spain. amarina@ibv.csic.es.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
dUTPaseA, C, E, G191Staphylococcus virus 11Mutation(s): 0 
UniProt
Find proteins for Q8SDV3 (Staphylococcus phage phi 11)
Explore Q8SDV3 
Go to UniProtKB:  Q8SDV3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8SDV3
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Orf20B, D, F, H157Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for Q9F0J8 (Staphylococcus aureus)
Explore Q9F0J8 
Go to UniProtKB:  Q9F0J8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F0J8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
L [auth C],
M [auth C],
N [auth C],
P [auth D],
Q [auth E],
L [auth C],
M [auth C],
N [auth C],
P [auth D],
Q [auth E],
R [auth E],
U [auth H]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
J [auth A],
K [auth B],
O [auth C],
S [auth E],
V [auth H]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A],
T [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.49α = 90
b = 144.49β = 90
c = 149.42γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBIO2016-78571-P
Spanish Ministry of Economy and CompetitivenessSpainFPU13/02880
Spanish Ministry of Economy and CompetitivenessSpainBES-2014-068617
Medical Research Council (United Kingdom)United KingdomMR/M003876/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/N002873/1
European Research CouncilUnited KingdomERC-ADG/2014 670932

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-28
    Type: Initial release