3QPT | pdb_00003qpt

Crystal structure of the Salmonella transcriptional regulator SlyA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.271 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.236 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.237 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 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 Biological Chem 286: 22178-22185

  • DOI: https://doi.org/10.1074/jbc.M111.245258
  • Primary Citation Related Structures: 
    3Q5F, 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 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 Our structures, together with an unpublished structure of SlyA bound to the small molecule effector salicylate (Protein Data Bank code 3DEU), reveal that, unlike many other MarR family proteins, SlyA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.

Macromolecule Content 

  • Total Structure Weight: 16.9 kDa 
  • Atom Count: 1,091 
  • Modeled Residue Count: 132 
  • Deposited Residue Count: 147 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcriptional regulator slyA147Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: slyASTM1444
UniProt
Find proteins for P40676 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P40676 
Go to UniProtKB:  P40676
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40676
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.271 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.237 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.686α = 90
b = 50.686β = 90
c = 173.584γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary