3Q5F

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

• PDB DOI:  https://doi.org/10.2210/pdb3Q5F/pdb
• NAKB: 3Q5F

• Classification: TRANSCRIPTION/DNA
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-12-28 Released: 2011-05-04 
• Deposition Author(s): Dolan, K.T., Duguid, E.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 0.266 
• R-Value Work: 0.213 
• R-Value Observed: 0.219 

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

• PubMed: 21550983 
• DOI: https://doi.org/10.1074/jbc.M111.245258
• Primary Citation of 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 Our structures, together with an unpublished structure of SlyA bound to the small molecule effector salicylate (Protein Data Bank code 3DEU), reveal that, unlike many other MarR family proteins, SlyA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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 47.64 kDa 
• Atom Count: 3,186 
• Modelled Residue Count: 327 
• Deposited Residue Count: 340 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator slyA	A, B	147	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: slyA, STM1444
UniProt
Find proteins for P40676 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P40676  Go to UniProtKB:  P40676

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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')	C	23	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
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')	D	23	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 0.266 
• R-Value Work: 0.213 
• R-Value Observed: 0.219 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.566	α = 90
b = 59.566	β = 90
c = 291.177	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
JBluIce-EPICS	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-04 
Deposition Author(s): Dolan, K.T., Duguid, E.M.

Revision History  

• 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