4KFC

Crystal structure of a hyperactive mutant of response regulator KdpE complexed to its promoter DNA

• PDB DOI:  https://doi.org/10.2210/pdb4KFC/pdb
• NAKB: 4KFC

• Classification: TRANSCRIPTION REGULATOR/DNA
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-04-26 Released: 2014-02-19 
• Deposition Author(s): Kumar, S., Narayanan, A., Yernool, D.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.245 
• R-Value Work: 0.204 
• R-Value Observed: 0.208 

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

• PubMed: 24526190 
• DOI: https://doi.org/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 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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69.32 kDa 
• Atom Count: 4,911 
• Modelled Residue Count: 507 
• Deposited Residue Count: 514 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KDP operon transcriptional regulatory protein KdpE	A, B	227	Escherichia coli K-12	Mutation(s): 1  Gene Names: b0694, JW5096, kdpE
UniProt
Find proteins for P21866 (Escherichia coli (strain K12)) Explore P21866  Go to UniProtKB:  P21866

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Promoter DNA	C [auth Y]	30	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Promoter DNA	D [auth Z]	30	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 0.245 
• R-Value Work: 0.204 
• R-Value Observed: 0.208 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.77	α = 90
b = 132.77	β = 90
c = 134.51	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
PHASER	phasing
PHENIX	refinement
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-19 
Deposition Author(s): Kumar, S., Narayanan, A., Yernool, D.A.

Revision History  

• Version 1.0: 2014-02-19
  Type: Initial release
  
• Version 1.1: 2014-03-19
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Refinement description