2BJ7

NIKR IN CLOSED CONFORMATION AND NICKEL BOUND TO HIGH-AFFINITY SITES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of Pyrococcus Horikoshii Nikr: Nickel Sensing and Implications for the Regulation of DNA Recognition

Chivers, P.T.Tahirov, T.H.

(2005) J Mol Biol 348: 597

  • DOI: 10.1016/j.jmb.2005.03.017
  • Primary Citation of Related Structures:  
    2BJ1, 2BJ9, 2BJ8, 2BJ7, 2BJ3

  • PubMed Abstract: 
  • The Pyrococcus horikoshii OT3 genome contains a gene (PH0601 or nikR) encoding a protein (PhNikR) that shares 33.8% amino acid sequence identity with Escherichia coli nickel responsive repressor NikR (EcNikR), including many residues that are functionally important in the E ...

    The Pyrococcus horikoshii OT3 genome contains a gene (PH0601 or nikR) encoding a protein (PhNikR) that shares 33.8% amino acid sequence identity with Escherichia coli nickel responsive repressor NikR (EcNikR), including many residues that are functionally important in the E.coli ortholog. We succeeded in crystallization and structural characterization of PhNikR in the apo form and two nickel bound forms that exhibit different conformations, open and closed. Moreover, we have identified a putative "low-affinity" nickel-binding pocket in the closed form. This binding site has unusual nickel coordination and exhibits high sensitivity to phosphate in the crystal structure. Analysis of the PhNikR structures and structure-based mutational studies with EcNikR reveals a plausible mechanism of nickel-dependent promoter recognition by the NikR family of proteins.


    Related Citations: 
    • Crystallization and Preliminary Crystallographic Analysis of the Nickel-Responsive Regulator Nikr from Pyrococcus Horikoshii
      Kitao, T., Kuroishi, C., Tahirov, T.H.
      (2005) Acta Crystallogr Sect F Struct Biol Cryst Commun 61: 43

    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NICKEL RESPONSIVE REGULATORA, B138Pyrococcus horikoshii OT3Mutation(s): 0 
Gene Names: PH0601
UniProt
Find proteins for O58316 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O58316 
Go to UniProtKB:  O58316
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.952α = 90
b = 109.952β = 90
c = 79.003γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
DMphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2005-01-31 
  • Released Date: 2005-04-08 
  • Deposition Author(s): Tahirov, T.H.

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-08
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance