5Y9Q | pdb_00005y9q

Crystal structure of the CcpE regulatory domain at 1.95 Angstrom from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb5Y9Q/pdb

• Classification: TRANSCRIPTION
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-08-27 Released: 2017-09-06 
• Deposition Author(s): Chen, J., Wang, L., Shang, F., Xu, Y.
• Funding Organization(s): National Natural Science Foundation of China, the Fundamental Research Funds for the Central Universities

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Structural and Biochemical Analysis of the Citrate-Responsive Mechanism of the Regulatory Domain of Catabolite Control Protein E from Staphylococcus aureus

Chen, J., Shang, F., Wang, L., Zou, L., Bu, T., Jin, L., Dong, Y., Ha, N.C., Quan, C., Nam, K.H., Xu, Y.

(2018) Biochemistry 57: 6054-6060

• PubMed: 30252448 
• DOI: https://doi.org/10.1021/acs.biochem.8b00671
• Primary Citation Related Structures: 
  5Y9Q, 5ZZO


• PubMed Abstract: 
  

  Catabolite control protein E (CcpE) is a LysR-type transcriptional regulator that positively regulates the transcription of the first two enzymes of the TCA cycle, namely, citZ and citB, by sensing accumulated intracellular citrate. CcpE comprises an N-terminal DNA-binding domain and a C-terminal regulatory domain (RD) and senses citrate with conserved arginine residues in the RD. Although the crystal structure of the apo SaCcpE-RD has been reported, the citrate-responsive and DNA-binding mechanisms by which CcpE regulates TCA activity remain unclear. Here, we report the crystal structure of the apo and citrate-bound SaCcpE-RDs. The SaCcpE-RD exhibits conformational changes between the two subdomains via hinge motion of the central β4 and β10 strands. The citrate molecule is located in a positively charged cavity between the two subdomains and interacts with the highly conserved Ser98, Leu100, Arg145, and Arg256 residues. Compared with that of the apo SaCcpE-RD, the distance between the two subdomains of the citrate-bound SaCcpE-RD is more than ∼3 Å due to the binding of the citrate molecule, and this form exhibits a closed structure. The SaCcpE-RD exhibits various citrate-binding-independent conformational changes at the contacting interface. The SaCcpE-RD prefers the dimeric state in solution, whereas the SaCcpE-FL prefers the tetrameric state. Our results provide insight into the molecular function of SaCcpE.

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Organizational Affiliation: 
• Department of Bioengineering, College of Life Science , Dalian Minzu University , Dalian 116600 , Liaoning , China.
Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University) , Ministry of Education , China.
School of Life Science and Biotechnology , Dalian University of Technology , No. 2 Linggong Road , Dalian 116024 , Liaoning , China.
Department of Agricultural Biotechnology, College of Agriculture and Life Sciences , Seoul National University , Gwanak-gu, Seoul 08826 , Republic of Korea.
Division of Biotechnology, College of Life Sciences and Biotechnology , Korea University , Seoul 02841 , Republic of Korea.
Institute of Life Science and Natural Resources , Korea University , Seoul 02841 , 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)

Macromolecule Content 

• Total Structure Weight: 45.52 kDa 
• Atom Count: 3,556 
• Modeled Residue Count: 392 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon catabolite responsive regulator	A, B	198	Staphylococcus aureus	Mutation(s): 0  Gene Names: oxyR, BMF23_07630, ERS073071_00913, ERS073583_00871

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.667	α = 90
b = 111.667	β = 90
c = 123.12	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
HKL-2000	data processing
PHENIX	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-09-06 
Deposition Author(s): Chen, J., Wang, L., Shang, F., Xu, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31200556
the Fundamental Research Funds for the Central Universities	China	DC201502020203

Revision History  

• Version 1.0: 2017-09-06
  Type: Initial release
  
• Version 1.1: 2018-12-12
  Changes: Data collection, Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references