Biological Assembly 1  

 3D View: Structure | Electron Density

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: 47.02 kDa 
• Atom Count: 3888 
• Residue Count: 357 
• Unique protein chains: 1

2ZCM

Crystal structure of IcaR, a repressor of the TetR family

• DOI: 10.2210/pdb2ZCM/pdb

• Classification: TRANSCRIPTION
• Organism(s): Staphylococcus epidermidis RP62A
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-11-10 Released: 2008-02-05 
• Deposition Author(s): Jeng, W.Y., Ko, T.P., Liu, C.I., Guo, R.T., Shr, H.L., Wang, A.H.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.223 
• R-Value Work: 0.190 

Literature

Crystal structure of IcaR, a repressor of the TetR family implicated in biofilm formation in Staphylococcus epidermidis

Jeng, W.Y., Ko, T.P., Liu, C.I., Guo, R.T., Liu, C.L., Shr, H.L., Wang, A.H.J.

(2008) Nucleic Acids Res 36: 1567-1577

• PubMed: 18208836 
• DOI: 10.1093/nar/gkm1176
• Primary Citation of Related Structures:  
  2ZCM, 2ZCN


• PubMed Abstract: 
  

Expression of the gene cluster icaADBC is necessary for biofilm production in Staphylococcus epidermidis. The ica operon is negatively controlled by the repressor IcaR. Here, the crystal structure of IcaR was determined and the refined structure revealed a homodimer comprising entirely alpha-helices, typical of the tetracycline repressor protein family for gene regulations. The N-terminal domain contains a conserved helix-turn-helix DNA-binding motif with some conformational variations, indicating flexibility in this region. The C-terminal domain shows a complementary surface charge distribution about the dyad axis, ideal for efficient and specific dimer formation. The results of the electrophoretic mobility shift assay and isothermal titration calorimetry suggested that a 28 bp core segment of the ica operator is implicated in the cooperative binding of two IcaR dimers on opposite sides of the duplex DNA. Computer modeling based on the known DNA-complex structure of QacR and site-specific mutagenesis experiments showed that direct protein-DNA interactions are mostly conserved, but with slight variations for recognizing the different sequences. By interfering with the binding of IcaR to DNA, aminoglycoside gentamicin and other antibiotics may activate the icaADBC genes and elicit biofilm production in S. epidermidis, and likely S. aureus, as a defense mechanism.

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Organizational Affiliation: 

Institute of Biological Chemistry, Taipei, Taiwan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Biofilm operon icaABCD HTH-type negative transcriptional regulator icaR	A, B	192	Staphylococcus epidermidis RP62A	Mutation(s): 4  Gene Names: icaR, SERP2292
Find proteins for Q5HKQ1 (Staphylococcus epidermidis (strain ATCC 35984 / RP62A)) Explore Q5HKQ1  Go to UniProtKB:  Q5HKQ1

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A,B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.223 
• R-Value Work: 0.190 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.78	α = 90
b = 50.7	β = 97.09
c = 63.34	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-11-10 
• Released Date: 2008-02-05 
Deposition Author(s): Jeng, W.Y., Ko, T.P., Liu, C.I., Guo, R.T., Shr, H.L., Wang, A.H.J.

Revision History 

• Version 1.0: 2008-02-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance