3Q5F

Crystal structure of the Salmonella transcriptional regulator SlyA in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structures of SlyA Protein, a Master Virulence Regulator of Salmonella, in Free and DNA-bound States.

Dolan, K.T.Duguid, E.M.He, C.

(2011) J.Biol.Chem. 286: 22178-22185

  • DOI: 10.1074/jbc.M111.245258
  • Primary Citation of Related Structures:  3QPT

  • PubMed Abstract: 
  • SlyA is a master virulence regulator that controls the transcription of numerous genes in Salmonella enterica. We present here crystal structures of SlyA by itself and bound to a high-affinity DNA operator sequence in the slyA gene. SlyA interacts wi ...

    SlyA is a master virulence regulator that controls the transcription of numerous genes in Salmonella enterica. We present here crystal structures of SlyA by itself and bound to a high-affinity DNA operator sequence in the slyA gene. SlyA interacts with DNA through direct recognition of a guanine base by Arg-65, as well as interactions between conserved Arg-86 and the minor groove and a large network of non-base-specific contacts with the sugar phosphate backbone. Our structures, together with an unpublished structure of SlyA bound to the small molecule effector salicylate (Protein Data Bank code 3DEU), reveal that, unlike many other MarR family proteins, SlyA dissociates from DNA without large conformational changes when bound to this effector. We propose that SlyA and other MarR global regulators rely more on indirect readout of DNA sequence to exert control over many genes, in contrast to proteins (such as OhrR) that recognize a single operator.


    Organizational Affiliation

    Departments of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcriptional regulator slyA
A, B
147Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Gene Names: slyA
Find proteins for P40676 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P40676
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*TP*AP*AP*CP*TP*TP*AP*GP*CP*AP*AP*GP*CP*TP*AP*AP*TP*TP*AP*TP*A)-3')C23N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*AP*TP*AP*AP*TP*TP*AP*GP*CP*TP*TP*GP*CP*TP*AP*AP*GP*TP*TP*AP*T)-3')D23N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.213 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.566α = 90.00
b = 59.566β = 90.00
c = 291.177γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
RESOLVEphasing
SOLVEphasing
SCALEPACKdata scaling
DENZOdata reduction
PDB_EXTRACTdata extraction
JBluIce-EPICSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description