4FE4

Crystal structure of apo E. coli XylR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 
    0.318 (Depositor), 0.320 (DCC) 
  • R-Value Work: 
    0.289 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 
    0.289 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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.

Ni, L.Tonthat, N.K.Chinnam, N.Schumacher, M.A.

(2013) Nucleic Acids Res 41: 1998-2008

  • DOI: https://doi.org/10.1093/nar/gks1207
  • Primary Citation of Related Structures:  
    4FE4, 4FE7

  • 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.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Texas, M.D. Anderson Cancer Center, Houston, TX 77030, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xylose operon regulatory protein
A, B, C
392Escherichia coli K-12Mutation(s): 0 
Gene Names: xylRb3569JW3541
UniProt
Find proteins for P0ACI3 (Escherichia coli (strain K12))
Explore P0ACI3 
Go to UniProtKB:  P0ACI3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ACI3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free:  0.318 (Depositor), 0.320 (DCC) 
  • R-Value Work:  0.289 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 0.289 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.5α = 90
b = 124.5β = 90
c = 189.8γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references
  • Version 1.2: 2013-03-06
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references