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: 3.60 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.274 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    4KDP

  • 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 production and promotes biofilm formation ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TcaR transcription regulator
A, B, C, D, E, F, G
A, B, C, D, E, F, G
151Staphylococcus epidermidis ATCC 12228Mutation(s): 0 
Gene Names: SE_1937
UniProt
Find proteins for A0A0H2VJZ8 (Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200))
Explore A0A0H2VJZ8 
Go to UniProtKB:  A0A0H2VJZ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2VJZ8
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*GP*CP*AP*GP*CP*GP*CP*GP*CP*AP*GP*CP*CP*CP*TP*A)-3')H,
I [auth J]
17N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.274 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.899α = 90
b = 91.899β = 90
c = 261.534γ = 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: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-05-14
    Changes: Database references