4LRY

Crystal Structure of the E.coli DhaR(N)-DhaK(T79L) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Coiled-Coil Helix Rotation Selects Repressing or Activating State of Transcriptional Regulator DhaR.

Shi, R.McDonald, L.Cygler, M.Ekiel, I.

(2014) Structure 22: 478-487

  • DOI: 10.1016/j.str.2013.11.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Escherichia coli dihydroxyacetone (Dha) kinase consists of two subunits, DhaK and DhaL. Transcription of dha operon is regulated by the DhaR transcription factor and its action is under control of the kinase subunits. DhaR is activated by interaction ...

    Escherichia coli dihydroxyacetone (Dha) kinase consists of two subunits, DhaK and DhaL. Transcription of dha operon is regulated by the DhaR transcription factor and its action is under control of the kinase subunits. DhaR is activated by interaction with DhaL while it is repressed by DhaK. We have determined the structures of DhaK and DhaL bound to the tandem GAF-like and PAS domains of the DhaR, providing an architectural model for how GAF/PAS tandem domains work together in binding protein partners. The structures reveal a mechanism of opposite transcriptional regulation by the DhaK and DhaL subunits. The kinase subunits interface with DhaR through surfaces that partially overlap with their active sites, allowing sensing of ATP- versus ADP-loaded DhaL subunit and also precluding a ternary complex between DhaK-DhaL and DhaR. The rotation of helices within the DhaR coiled-coil linker upon DhaL binding provides the mechanism for transmitting the binding signal from the GAF/PAS domains to the C-terminal DNA-binding domain.


    Organizational Affiliation

    Département de Biochimie, de Microbiologie et de Bio-informatique, PROTEO, Université Laval, Pavillon Charles-Eugene-Marchand, Québec City, QC G1V 0A6, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Pavillon Charles-Eugene-Marchand, Québec City, QC G1V 0A6, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK
A, B
356Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: dhaK (ycgT)
EC: 2.7.1.121
Find proteins for P76015 (Escherichia coli (strain K12))
Go to UniProtKB:  P76015
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PTS-dependent dihydroxyacetone kinase operon regulatory protein
C, D
318Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dhaR (ycgU)
Find proteins for P76016 (Escherichia coli (strain K12))
Go to UniProtKB:  P76016
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.201 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 231.397α = 90.00
b = 231.397β = 90.00
c = 79.763γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling
RESOLVEphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-03-26
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description