3ZQ7

The Structure of DNA-binding domain of response regulator from Escherichia coli K-12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-Function Studies of DNA Binding Domain of Response Regulator Kdpe Reveals Equal Affinity Interactions at DNA Half-Sites.

Narayanan, A.Paul, L.N.Tomar, S.Patil, D.N.Kumar, P.Yernool, D.A.

(2012) PLoS One 7: 102

  • DOI: 10.1371/journal.pone.0030102
  • Primary Citation of Related Structures:  
    3ZQ7

  • PubMed Abstract: 
  • Expression of KdpFABC, a K(+) pump that restores osmotic balance, is controlled by binding of the response regulator KdpE to a specific DNA sequence (kdpFABC(BS)) via the winged helix-turn-helix type DNA binding domain (KdpE(DBD)). Exploration of E. coli KdpE(DBD) and kdpFABC(BS) interaction resulted in the identification of two conserved, AT-rich 6 bp direct repeats that form half-sites ...

    Expression of KdpFABC, a K(+) pump that restores osmotic balance, is controlled by binding of the response regulator KdpE to a specific DNA sequence (kdpFABC(BS)) via the winged helix-turn-helix type DNA binding domain (KdpE(DBD)). Exploration of E. coli KdpE(DBD) and kdpFABC(BS) interaction resulted in the identification of two conserved, AT-rich 6 bp direct repeats that form half-sites. Despite binding to these half-sites, KdpE(DBD) was incapable of promoting gene expression in vivo. Structure-function studies guided by our 2.5 Å X-ray structure of KdpE(DBD) revealed the importance of residues R193 and R200 in the α-8 DNA recognition helix and T215 in the wing region for DNA binding. Mutation of these residues renders KdpE incapable of inducing expression of the kdpFABC operon. Detailed biophysical analysis of interactions using analytical ultracentrifugation revealed a 2∶1 stoichiometry of protein to DNA with dissociation constants of 200±100 and 350±100 nM at half-sites. Inactivation of one half-site does not influence binding at the other, indicating that KdpE(DBD) binds independently to the half-sites with approximately equal affinity and no discernable cooperativity. To our knowledge, these data are the first to describe in quantitative terms the binding at half-sites under equilibrium conditions for a member of the ubiquitous OmpR/PhoB family of proteins.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
KDP OPERON TRANSCRIPTIONAL REGULATORY PROTEIN KDPEA102Escherichia coli K-12Mutation(s): 0 
Gene Names: kdpEb0694JW5096
UniProt
Find proteins for P21866 (Escherichia coli (strain K12))
Explore P21866 
Go to UniProtKB:  P21866
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21866
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.241 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.44α = 90
b = 36.44β = 90
c = 138.47γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Data collection