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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

Journal Article · · Nucleic Acids Research
DOI:https://doi.org/10.1093/nar/gks1207· OSTI ID:1625499
 [1];  [2];  [2];  [2]
  1. Univ. of Texas, Houston, TX (United States); DOE/OSTI
  2. Duke Univ., Durham, NC (United States)
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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.

Research Organization:
Duke University, Durham, NC (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1625499
Journal Information:
Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: 3 Vol. 41; ISSN 0305-1048
Publisher:
Oxford University PressCopyright Statement
Country of Publication:
United States
Language:
English

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Cited By (8)

AutA and AutR, Two Novel Global Transcriptional Regulators, Facilitate Avian Pathogenic Escherichia coli Infection journal April 2016
A large family of anti‐activators accompanying XylS/AraC family regulatory proteins journal May 2016
Functional Mechanism of the Efflux Pumps Transcription Regulators From Pseudomonas aeruginosa Based on 3D Structures journal June 2018
Metabolic engineering strategies for improving xylitol production from hemicellulosic sugars journal July 2013
HipBA–promoter structures reveal the basis of heritable multidrug tolerance journal July 2015
Experimental evolution reveals an effective avenue to release catabolite repression via mutations in XylR journal June 2017
Molecular mechanisms of xylose utilization by P seudomonas fluorescens : overlapping genetic responses to xylose, xylulose, ribose and mannitol: Xylose utilization in Pseudomonas journal August 2015
Functional Characterization of the Mannitol Promoter of Pseudomonas fluorescens DSM 50106 and Its Application for a Mannitol-Inducible Expression System for Pseudomonas putida KT2440 journal July 2015

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59 BASIC BIOLOGICAL SCIENCES
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