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Structures of the Escherichia coli transcription activator and regulator of diauxie, XylR: an AraC DNA-binding family member with a LacI/GalR ligand-binding domain.

Publication ,  Journal Article
Ni, L; Tonthat, NK; Chinnam, N; Schumacher, MA
Published in: Nucleic Acids Res
February 1, 2013

Escherichia coli can rapidly switch to the metabolism of l-arabinose and d-xylose in the absence of its preferred carbon source, glucose, in a process called carbon catabolite repression. Transcription of the genes required for l-arabinose and d-xylose consumption is regulated by the sugar-responsive transcription factors, AraC and XylR. E. coli represents a promising candidate for biofuel production through the metabolism of hemicellulose, which is composed of d-xylose and l-arabinose. Understanding the l-arabinose/d-xylose regulatory network is key for such biocatalyst development. Unlike AraC, which is a well-studied protein, little is known about XylR. To gain insight into XylR function, we performed biochemical and structural studies. XylR contains a C-terminal AraC-like domain. However, its N-terminal d-xylose-binding domain contains a periplasmic-binding protein (PBP) fold with structural homology to LacI/GalR transcription regulators. Like LacI/GalR proteins, the XylR PBP domain mediates dimerization. However, unlike LacI/GalR proteins, which dimerize in a parallel, side-to-side manner, XylR PBP dimers are antiparallel. Strikingly, d-xylose binding to this domain results in a helix to strand transition at the dimer interface that reorients both DNA-binding domains, allowing them to bind and loop distant operator sites. Thus, the combined data reveal the ligand-induced activation mechanism of a new family of DNA-binding proteins.

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Published In

Nucleic Acids Res

DOI

EISSN

1362-4962

Publication Date

February 1, 2013

Volume

41

Issue

3

Start / End Page

1998 / 2008

Location

England

Related Subject Headings

  • Xylose
  • Transcription Factors
  • Repressor Proteins
  • Protein Structure, Tertiary
  • Protein Multimerization
  • Protein Folding
  • Protein Binding
  • Models, Molecular
  • Lac Repressors
  • Escherichia coli Proteins
 

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Ni, L., Tonthat, N. K., Chinnam, N., & Schumacher, M. A. (2013). Structures of the Escherichia coli transcription activator and regulator of diauxie, XylR: an AraC DNA-binding family member with a LacI/GalR ligand-binding domain. Nucleic Acids Res, 41(3), 1998–2008. https://doi.org/10.1093/nar/gks1207
Ni, Lisheng, Nam K. Tonthat, Nagababu Chinnam, and Maria A. Schumacher. “Structures of the Escherichia coli transcription activator and regulator of diauxie, XylR: an AraC DNA-binding family member with a LacI/GalR ligand-binding domain.Nucleic Acids Res 41, no. 3 (February 1, 2013): 1998–2008. https://doi.org/10.1093/nar/gks1207.
Ni, Lisheng, et al. “Structures of the Escherichia coli transcription activator and regulator of diauxie, XylR: an AraC DNA-binding family member with a LacI/GalR ligand-binding domain.Nucleic Acids Res, vol. 41, no. 3, Feb. 2013, pp. 1998–2008. Pubmed, doi:10.1093/nar/gks1207.
Journal cover image

Published In

Nucleic Acids Res

DOI

EISSN

1362-4962

Publication Date

February 1, 2013

Volume

41

Issue

3

Start / End Page

1998 / 2008

Location

England

Related Subject Headings

  • Xylose
  • Transcription Factors
  • Repressor Proteins
  • Protein Structure, Tertiary
  • Protein Multimerization
  • Protein Folding
  • Protein Binding
  • Models, Molecular
  • Lac Repressors
  • Escherichia coli Proteins