4KNY

Crystal structure of the response regulator KdpE complexed to DNA in an active-like conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

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:  
    4KFC, 4KNY, 4L85

  • 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] Bindley Bioscience Center, Purdue University, 1203 West State Street, West Lafayette, Indiana 47907, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
KDP operon transcriptional regulatory protein KdpEAB227Escherichia coli K-12Mutation(s): 0 
Gene Names: b0694JW5096kdpE
Find proteins for P21866 (Escherichia coli (strain K12))
Explore P21866 
Go to UniProtKB:  P21866
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
Promoter DNAY30N/A
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
Promoter DNAZ30N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.14α = 90
b = 133.14β = 90
c = 133.67γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
PHENIXrefinement
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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