3KP2

Staphylococcus epidermidis TcaR in complex with penicillin G

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.233 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural study of TcaR and its complexes with multiple antibiotics from Staphylococcus epidermidis.

Chang, Y.M., Jeng, W.Y., Ko, T.P., Yeh, Y.J., Chen, C.K., Wang, A.H.

(2010) Proc Natl Acad Sci U S A 107: 8617-8622

  • DOI: 10.1073/pnas.0913302107
  • Primary Citation of Related Structures:  
    3KP2, 3KP3, 3KP4, 3KP5, 3KP6, 3KP7

  • PubMed Abstract: 

    • TcaR and IcaR are a weak and a strong negative regulator of transcription of the ica locus, respectively, and their presence prevents the poly-N-acetylglucosamine production and biofilm formation in Staphylococcus epidermidis. Although TcaR was shown to interact with the ica promoter, the precise binding region and the mechanism of interaction remained unclear ...

    TcaR and IcaR are a weak and a strong negative regulator of transcription of the ica locus, respectively, and their presence prevents the poly-N-acetylglucosamine production and biofilm formation in Staphylococcus epidermidis. Although TcaR was shown to interact with the ica promoter, the precise binding region and the mechanism of interaction remained unclear. Here we present the 3D structure of TcaR in its apo form and in complex with salicylate as well as several aminoglycoside and beta-lactam antibiotics. A comparison of the native and complex TcaR structures indicates that the mechanism of regulation involves a large conformational change in the DNA-binding lobe. Here, we deduced the consensus binding sequence of two [ approximately TTNNAA] hexamers embedded in a 16 bp sequence for a TcaR dimer. Six TcaR dimers bind specifically to three approximately 33 bp segments close to the IcaR binding region with varying affinities, and their repressor activity is directly interfered by salicylate and different classes of natural antimicrobial compounds. We also found in this study that the antimicrobial compounds we tested were shown not only to inhibit TcaR-DNA interaction but also to further induce biofilm formation in S. epidermidis in our in vivo assay. The results support a general mechanism for antibiotics in regulating TcaR-DNA interaction and thereby help understand the effect of antibiotic exposure on bacterial antibiotic resistance through biofilm formation.

    Organizational Affiliation: 

    Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional regulator TcaR A, B151Staphylococcus epidermidis RP62AMutation(s): 0 
Gene Names: SERP1949, SE_1937, tcaR
Find proteins for Q5HLN6 (Staphylococcus epidermidis (strain ATCC 35984 / RP62A))
Explore Q5HLN6 
Go to UniProtKB:  Q5HLN6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PNN
Query on PNN
Download Ideal Coordinates CCD File 
A, B
PENICILLIN G
C16 H18 N2 O4 S
JGSARLDLIJGVTE-MBNYWOFBSA-N		 Ligand Interaction
CAC
Query on CAC
Download Ideal Coordinates CCD File 
B
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.233 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.824α = 90
b = 106.824β = 90
c = 46.353γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance