7FDF | pdb_00007fdf

The E145S mutant of the regulatory domain of YeiE, a sulfite sensing LysR-type transcriptional regulator from Cronobacter sakazakii (sulfate-bound form)

• PDB DOI: https://doi.org/10.2210/pdb7FDF/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Cronobacter sakazakii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-07-16 Released: 2022-03-23 
• Deposition Author(s): Hong, S., Ha, N.-C.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.221 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of YeiE from Cronobacter sakazakii and the role of sulfite tolerance in gram-negative bacteria.

Hong, S., Kim, J., Cho, E., Na, S., Yoo, Y.J., Cho, Y.H., Ryu, S., Ha, N.C.

(2022) Proc Natl Acad Sci U S A 119: e2118002119-e2118002119

• PubMed: 35271389 
• DOI: https://doi.org/10.1073/pnas.2118002119
• Primary Citation Related Structures: 
  7ERP, 7ERQ, 7FDF


• PubMed Abstract: 
  

  SignificanceYeiE has been identified as a master virulence factor of Cronobacter sakazakii . In this study, we determined the crystal structures of the regulatory domain of YeiE in complex with its physiological ligand sulfite ion (SO ₃ ^2- ). The structure provides the basis for the molecular mechanisms for sulfite sensing and the ligand-dependent conformational changes of the regulatory domain. The genes under the control of YeiE in response to sulfite were investigated to reveal the functional roles of YeiE in the sulfite tolerance of the bacteria. We propose the molecular mechanism underlying the ability of gram-negative pathogens to defend against the innate immune response involving sulfite, thus providing a strategy to control the pathogenesis of bacteria.

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Organizational Affiliation: 
• Department of Agricultural Biotechnology, Department of Food and Animal Biotechnology, Seoul National University, Seoul 08826, Republic of Korea.
Center for Food and Bioconvergence, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Gyeonggi-do 13488, Republic of Korea.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 23.32 kDa 
• Atom Count: 1,628 
• Modeled Residue Count: 197 
• Deposited Residue Count: 208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LysR family transcriptional regulator	A	208	Cronobacter sakazakii	Mutation(s): 1  Gene Names: FZH93_18715, FZI36_01190, FZI41_05255, HZZ03_13430
UniProt
Find proteins for H9BVC9 (Cronobacter sakazakii) Explore H9BVC9  Go to UniProtKB:  H9BVC9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.221 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.146	α = 90
b = 60.146	β = 90
c = 213.523	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-23 
Deposition Author(s): Hong, S., Ha, N.-C.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2022-03-23
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description