2HZV

NikR-operator DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

NikR-operator complex structure and the mechanism of repressor activation by metal ions.

Schreiter, E.R.Wang, S.C.Zamble, D.B.Drennan, C.L.

(2006) Proc.Natl.Acad.Sci.Usa 103: 13676-13681

  • DOI: 10.1073/pnas.0606247103
  • Primary Citation of Related Structures:  2HZA

  • PubMed Abstract: 
  • Metal ion homeostasis is critical to the survival of all cells. Regulation of nickel concentrations in Escherichia coli is mediated by the NikR repressor via nickel-induced transcriptional repression of the nickel ABC-type transporter, NikABCDE. Here ...

    Metal ion homeostasis is critical to the survival of all cells. Regulation of nickel concentrations in Escherichia coli is mediated by the NikR repressor via nickel-induced transcriptional repression of the nickel ABC-type transporter, NikABCDE. Here, we report two crystal structures of nickel-activated E. coli NikR, the isolated repressor at 2.1 A resolution and in a complex with its operator DNA sequence from the nik promoter at 3.1 A resolution. Along with the previously published structure of apo-NikR, these structures allow us to evaluate functional proposals for how metal ions activate NikR, delineate the drastic conformational changes required for operator recognition, and describe the formation of a second metal-binding site in the presence of DNA. They also provide a rare set of structural views of a ligand-responsive transcription factor in the unbound, ligand-induced, and DNA-bound states, establishing a model system for the study of ligand-mediated effects on transcription factor function.


    Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nickel-responsive regulator
A, B, C, D, E, F, G, H
133Escherichia coli (strain K12)Gene Names: nikR (yhhG)
Find proteins for P0A6Z6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6Z6
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*AP*TP*AP*CP*TP*TP*AP*AP*AP*AP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3'I,K30N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*GP*TP*AP*TP*GP*AP*CP*GP*AP*TP*TP*TP*TP*AP*AP*GP*TP*AP*TP*TP*CP*GP*TP*CP*AP*TP*AP*CP*T)-3'J,L30N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, E, F, G, H
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A, C, D, E, F, G, H
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.261 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 197.203α = 90.00
b = 76.132β = 110.27
c = 132.092γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance