4X1E

Crystal structure of unliganded E. coli transcriptional regulator RutR, W167A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Ligand binding specificity of RutR, a member of the TetR family of transcription regulators in Escherichia coli.

Nguyen Le Minh, P.de Cima, S.Bervoets, I.Maes, D.Rubio, V.Charlier, D.

(2015) FEBS Open Bio 5: 76-84

  • DOI: 10.1016/j.fob.2015.01.002
  • Primary Citation of Related Structures:  
    4X1E

  • PubMed Abstract: 
  • RutR is a member of the large family of TetR transcriptional regulators in Escherichia coli. It was originally discovered as the regulator of the rutABCDEFG operon encoding a novel pathway for pyrimidine utilization, but its highest affinity target is the control region of the carAB operon, encoding carbamoylphosphate synthase ...

    RutR is a member of the large family of TetR transcriptional regulators in Escherichia coli. It was originally discovered as the regulator of the rutABCDEFG operon encoding a novel pathway for pyrimidine utilization, but its highest affinity target is the control region of the carAB operon, encoding carbamoylphosphate synthase. Unlike most other TetR-like regulators, RutR exerts both positive and negative effects on promoter activity. Furthermore, RutR exhibits a very narrow ligand binding specificity, unlike the broad effector specificity that characterizes some of the well-studied multidrug resistance regulators of the family. Here we focus on ligand binding and ligand specificity of RutR. We construct single alanine substitution mutants of amino acid residues of the ligand-binding pocket, study their effect on in vitro DNA binding in absence and presence of potential ligands, and analyse their effect on positive regulation of the carP1 promoter and negative autoregulation in vivo. Although RutR structures have been determined previously, they were deposited in the Protein Data Bank without accompanying publications. All of them have uracil bound in the effector-binding site, representing the inactive form of the regulator. We determined the crystal structure of an unliganded mutant RutR protein and provide a structural basis for the use of uracil as sole effector molecule and the exclusion of the very similar thymine from the ligand-binding pocket.


    Organizational Affiliation

    Research Group of Microbiology, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussel, Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HTH-type transcriptional regulator RutRA, B220Escherichia coli CFT073Mutation(s): 1 
Gene Names: rutRc1150
UniProt
Find proteins for P0ACU3 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Explore P0ACU3 
Go to UniProtKB:  P0ACU3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ACU3
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.42α = 90
b = 91.77β = 90
c = 97.71γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation Flanders (FWO-Vlaanderen)BelgiumG.0429.06
Research Council of the Vrije Universiteit Brussel (OZR-VUB)Belgium--
Vlaamse GemeenschapscommissieBelgium--
Spanish GovernmentSpainBFU2011-30407
Valencian GovernmentSpainPrometeo II/2014/029
Instituto de Salud Carlos III-CIBERERSpain--

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-03-04
    Changes: Database references