4LRZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Structures With Same Primary Citation

  • 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

    Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6, Canada; National Research Council of Canada, Life Sciences, 6100 Royalmount Avenue, Montreal, QC H4P 2R2, Canada. Electronic address: irena.ekiel@cnrc-nrc.gc.ca.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaLA, B, C, D211Escherichia coli K-12Mutation(s): 0 
Gene Names: b1199dhaLdhaRJW5186ycgS
EC: 2.7 (PDB Primary Data), 2.7.1.121 (UniProt)
Find proteins for P76014 (Escherichia coli (strain K12))
Explore P76014 
Go to UniProtKB:  P76014
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PTS-dependent dihydroxyacetone kinase operon regulatory proteinE, F, G, H318Escherichia coli K-12Mutation(s): 0 
Gene Names: b1201dhaLdhaRJW5188ycgU
Find proteins for P76016 (Escherichia coli (strain K12))
Explore P76016 
Go to UniProtKB:  P76016
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A, B, C, D
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.766α = 84.15
b = 91.5β = 72.42
c = 93.808γ = 90.01
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Data collection
  • Version 1.2: 2014-03-26
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description