4KDP

TcaR-ssDNA complex crystal structure reveals the novel ssDNA binding mechanism of the MarR family proteins


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.274 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

TcaR-ssDNA complex crystal structure reveals new DNA binding mechanism of the MarR family proteins.

Chang, Y.M.Ho, C.H.Chen, C.K.Maestre-Reyna, M.Chang-Chien, M.W.Wang, A.H.

(2014) Nucleic Acids Res. 42: 5314-5321

  • DOI: 10.1093/nar/gku128

  • PubMed Abstract: 
  • The teicoplanin-associated locus regulator (TcaR) regulates gene expression of proteins on the intercellular adhesion (ica) locus involved in staphylococci poly-N-acetylglucosamine biosynthesis. The absence of TcaR increases poly-N-acetylglucosamine ...

    The teicoplanin-associated locus regulator (TcaR) regulates gene expression of proteins on the intercellular adhesion (ica) locus involved in staphylococci poly-N-acetylglucosamine biosynthesis. The absence of TcaR increases poly-N-acetylglucosamine production and promotes biofilm formation. Until recently, the mechanism of multiple antibiotic resistance regulator family protein members, such as TcaR, was restricted to binding double-stranded DNA. However, we recently found that TcaR strongly interacts with single-stranded DNA, which is a new role for this family of proteins. In this study, we report Staphylococcus epidermidis TcaR-single-stranded DNA complex structures. Our model suggests that TcaR and single-stranded DNA form a 61-symmetry polymer composed of TcaR dimers with single-stranded DNA that wraps outside the polymer and 12 nt per TcaR dimer. Single-stranded DNA binding to TcaR involves a large conformational change at the DNA binding lobe. Several point mutations involving the single-stranded DNA binding surface validate interactions between single-stranded DNA and TcaR. Our results extend the novel role of multiple antibiotic resistance regulator family proteins in staphylococci.


    Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan, Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan, Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 11529, Taiwan and Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TcaR transcription regulator
A, B, C, D, E, F, G
151Staphylococcus epidermidis (strain ATCC 12228)N/A
Find proteins for A0A0H2VJZ8 (Staphylococcus epidermidis (strain ATCC 12228))
Go to UniProtKB:  A0A0H2VJZ8
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*AP*GP*CP*GP*CP*GP*CP*AP*GP*CP*CP*CP*TP*A)-3')H,J17N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
B, E, F, H
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
B, F, H, J
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.274 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 91.899α = 90.00
b = 91.899β = 90.00
c = 261.534γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
CNSphasing
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-05-14
    Type: Database references