4FE7

structure of xylose-binding transcription activator xylR

Summary for 4FE7

• Entry DOI: 10.2210/pdb4fe7/pdb
• Descriptor: Xylose operon regulatory protein, alpha-D-xylopyranose (3 entities in total)
• Functional Keywords: hth_arac, helix-turn-helix, pbp, periplasmic binding protein, dna-binding transcription regulator, dna xylose, dna binding protein
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 47251.59

Authors

Ni, L.,Schumacher, M.A. (deposition date: 2012-05-29, release date: 2012-12-12, Last modification date: 2024-02-28)

Primary citation

Ni, L.,Tonthat, N.K.,Chinnam, N.,Schumacher, M.A.
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., 41:1998-2008, 2013

PubMed Abstract: 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.

PubMed: 23241389
DOI: 10.1093/nar/gks1207

Experimental method

X-RAY DIFFRACTION (2.9 Å)