4QWQ | pdb_00004qwq

Crystal structure of the DNA-binding domain of the response regulator SaeR from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb4QWQ/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-17 Released: 2015-08-19 
• Deposition Author(s): Fan, X., Zhu, Y., Zhang, X., Teng, M., Li, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.281 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Structure of the DNA-binding domain of the response regulator SaeR from Staphylococcus aureus.

Fan, X., Zhang, X., Zhu, Y., Niu, L., Teng, M., Sun, B., Li, X.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1768-1776

• PubMed: 26249357 
• DOI: https://doi.org/10.1107/S1399004715010287
• Primary Citation Related Structures: 
  4QWQ


• PubMed Abstract: 
  

  The SaeR/S two-component regulatory system is essential for controlling the expression of many virulence factors in Staphylococcus aureus. SaeR, a member of the OmpR/PhoB family, is a response regulator with an N-terminal regulatory domain and a C-terminal DNA-binding domain. In order to elucidate how SaeR binds to the promoter regions of target genes, the crystal structure of the DNA-binding domain of SaeR (SaeR(DBD)) was solved at 2.5 Å resolution. The structure reveals that SaeR(DBD) exists as a monomer and has the canonical winged helix-turn-helix module. EMSA experiments suggested that full-length SaeR can bind to the P1 promoter and that the binding affinity is higher than that of its C-terminal DNA-binding domain. Five key residues on the winged helix-turn-helix module were verified to be important for binding to the P1 promoter in vitro and for the physiological function of SaeR in vivo.

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Organizational Affiliation: 
• Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.49 kDa 
• Atom Count: 1,585 
• Modeled Residue Count: 196 
• Deposited Residue Count: 220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Response regulator SaeR	A [auth B], B [auth A]	110	Staphylococcus aureus	Mutation(s): 0  Gene Names: saeR, CH52_02235, X998_0755
UniProt
Find proteins for Q2G2G2 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G2G2  Go to UniProtKB:  Q2G2G2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.281 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.974	α = 90
b = 62.648	β = 90
c = 116.262	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-19 
Deposition Author(s): Fan, X., Zhu, Y., Zhang, X., Teng, M., Li, X.

Revision History  

• Version 1.0: 2015-08-19
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references