2LKP

solution structure of apo-NmtR


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 19 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Solution Structure of Mycobacterium tuberculosis NmtR in the Apo State: Insights into Ni(II)-Mediated Allostery.

Lee, C.W.Chakravorty, D.K.Chang, F.M.Reyes-Caballero, H.Ye, Y.Merz, K.M.Giedroc, D.P.

(2012) Biochemistry 51: 2619-2629

  • DOI: 10.1021/bi3001402

  • PubMed Abstract: 
  • Mycobacterium tuberculosis is an obligate human respiratory pathogen that encodes approximately 10 arsenic repressor (ArsR) family regulatory proteins that allow the organism to respond to a wide range of changes in its immediate microenvironment. Ho ...

    Mycobacterium tuberculosis is an obligate human respiratory pathogen that encodes approximately 10 arsenic repressor (ArsR) family regulatory proteins that allow the organism to respond to a wide range of changes in its immediate microenvironment. How individual ArsR repressors have evolved to respond to selective stimuli is of intrinsic interest. The Ni(II)/Co(II)-specific repressor NmtR and related actinomycete nickel sensors harbor a conserved N-terminal α-NH(2)-Gly2-His3-Gly4 sequence. Here, we present the solution structure of homodimeric apo-NmtR and show that the core of the molecule adopts a typical winged-helix ArsR repressor (α1-α2-α3-αR-β1-β2-α5) "open conformation" that is similar to that of the related zinc sensor Staphylococcus aureus CzrA, but harboring long, flexible N-terminal (residues 2-16) and C-terminal (residues 109-120) extensions. Binding of Ni(II) to the regulatory sites induces strong paramagnetic broadening of the α5 helical region and the extreme N-terminal tail to residue 10. Ratiometric pulse chase amidination mass spectrometry reveals that the rate of amidination of the α-amino group of Gly2 is strongly attenuated in the Ni(II) complex relative to the apo state and noncognate Zn(II) complex. Ni(II) binding also induces dynamic disorder on the microsecond to millisecond time scale of key DNA interacting regions that likely contributes to the negative regulation of DNA binding by Ni(II). Molecular dynamics simulations and quantum chemical calculations reveal that NmtR readily accommodates a distal Ni(II) hexacoordination model involving the α-amine and His3 of the N-terminal region and α5 residues Asp91', His93', His104, and His107, which collectively define a new metal sensing site configuration in ArsR family regulators.


    Organizational Affiliation

    Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcriptional regulator, ArsR family
A, B
119Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)Mutation(s): 0 
Find proteins for Q7D4Y3 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Go to UniProtKB:  Q7D4Y3
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 19 
  • Selection Criteria: structures with the lowest energy 
  • Olderado: 2LKP Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-10-18 
  • Released Date: 2012-04-18 
  • Deposition Author(s): Lee, C., Giedroc, D.

Revision History 

  • Version 1.0: 2012-04-18
    Type: Initial release