4L85

Crystal structure of receiver domain of KdpE D52A mutant from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.202 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An asymmetric heterodomain interface stabilizes a response regulator-DNA complex.

Narayanan, A.Kumar, S.Evrard, A.N.Paul, L.N.Yernool, D.A.

(2014) Nat Commun 5: 3282-3282

  • DOI: 10.1038/ncomms4282
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Two-component signal transduction systems consist of pairs of histidine kinases and response regulators, which mediate adaptive responses to environmental cues. Most activated response regulators regulate transcription by binding tightly to promoter ...

    Two-component signal transduction systems consist of pairs of histidine kinases and response regulators, which mediate adaptive responses to environmental cues. Most activated response regulators regulate transcription by binding tightly to promoter DNA via a phosphorylation-triggered inactive-to-active transition. The molecular basis for formation of stable response regulator-DNA complexes that precede the assembly of RNA polymerases is unclear. Here, we present structures of DNA complexed with the response regulator KdpE, a member of the OmpR/PhoB family. The distinctively asymmetric complex in an active-like conformation reveals a unique intramolecular interface between the receiver domain (RD) and the DNA-binding domain (DBD) of only one of the two response regulators in the complex. Structure-function studies show that this RD-DBD interface is necessary to form stable complexes that support gene expression. The conservation of sequence and structure suggests that these findings extend to a large group of response regulators that act as transcription factors.


    Organizational Affiliation

    1] Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, Indiana 47907, USA [2].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
KDP operon transcriptional regulatory protein KdpE
A, B, C
123Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: kdpE
Find proteins for P21866 (Escherichia coli (strain K12))
Go to UniProtKB:  P21866
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A, B, C
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.202 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.174 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 108.918α = 90.00
b = 108.918β = 90.00
c = 74.408γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data reduction
HKL-2000data collection
SCALAdata scaling
PHENIXmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2014-03-19
    Type: Database references