6W1F

Crystal structure of Streptococcus thermophilus SHP pheromone receptor Rgg3 bound to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report



Literature

Structure-function studies of Rgg binding to pheromones and target promoters reveal a model of transcription factor interplay.

Capodagli, G.C.Tylor, K.M.Kaelber, J.T.Petrou, V.I.Federle, M.J.Neiditch, M.B.

(2020) Proc Natl Acad Sci U S A 117: 24494-24502

  • DOI: 10.1073/pnas.2008427117
  • Primary Citation of Related Structures:  
    6W1A, 6W1E, 6W1F, 7JI0

  • PubMed Abstract: 
  • Regulator gene of glucosyltransferase (Rgg) family proteins, such as Rgg2 and Rgg3, have emerged as primary quorum-sensing regulated transcription factors in Streptococcus species, controlling virulence, antimicrobial resistance, and biofilm ...

    Regulator gene of glucosyltransferase (Rgg) family proteins, such as Rgg2 and Rgg3, have emerged as primary quorum-sensing regulated transcription factors in Streptococcus species, controlling virulence, antimicrobial resistance, and biofilm formation. Rgg2 and Rgg3 function is regulated by their interaction with oligopeptide quorum-sensing signals called short hydrophobic peptides (SHPs). The molecular basis of Rgg-SHP and Rgg-target DNA promoter specificity was unknown. To close this gap, we determined the cryoelectron microscopy (cryo-EM) structure of Streptococcus thermophilus Rgg3 bound to its quorum-sensing signal, SHP3, and the X-ray crystal structure of Rgg3 alone. Comparison of these structures with that of an Rgg in complex with cyclosporin A (CsA), an inhibitor of SHP-induced Rgg activity, reveals the molecular basis of CsA function. Furthermore, to determine how Rgg proteins recognize DNA promoters, we determined X-ray crystal structures of both Streptococcus dysgalactiae Rgg2 and S. thermophilus Rgg3 in complex with their target DNA promoters. The physiological importance of observed Rgg-DNA interactions was dissected using in vivo genetic experiments and in vitro biochemical assays. Based on these structure-function studies, we present a revised unifying model of Rgg regulatory interplay. In contrast to existing models, where Rgg2 proteins are transcriptional activators and Rgg3 proteins are transcriptional repressors, we propose that both are capable of transcriptional activation. However, when Rgg proteins with different activation requirements compete for the same DNA promoters, those with more stringent activation requirements function as repressors by blocking promoter access of SHP-bound conformationally active Rgg proteins. While a similar gene expression regulatory scenario has not been previously described, in all likelihood it is not unique to streptococci.


    Organizational Affiliation

    Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, NJ 07103; vasileios.petrou@rutgers.edu mfederle@uic.edu matthew.neiditch@rutgers.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Positive transcriptional regulator MutR familyAB284Streptococcus thermophilus LMG 18311Mutation(s): 0 
Gene Names: stu1044
Find proteins for Q5M4D0 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311))
Explore Q5M4D0 
Go to UniProtKB:  Q5M4D0
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (30-MER)E30Streptococcus thermophilus CNRZ1066
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (30-MER)F30Streptococcus thermophilus CNRZ1066
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.222 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.79α = 90
b = 90.79β = 90
c = 245.1γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01AI125452

Revision History 

  • Version 1.0: 2020-10-21
    Type: Initial release