4UA1

Crystal structure of dual function transcriptional regulator MerR form Bacillus megaterium MB1 in complex with mercury (II) ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of the mercury(II)-mediated conformational switching of the dual-function transcriptional regulator MerR

Chang, C.C.Lin, L.Y.Zou, X.W.Huang, C.C.Chan, N.L.

(2015) Nucleic Acids Res. 43: 7612-7623

  • DOI: 10.1093/nar/gkv681
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The mer operon confers bacterial resistance to inorganic mercury (Hg(2+)) and organomercurials by encoding proteins involved in sensing, transport and detoxification of these cytotoxic agents. Expression of the mer operon is under tight control by th ...

    The mer operon confers bacterial resistance to inorganic mercury (Hg(2+)) and organomercurials by encoding proteins involved in sensing, transport and detoxification of these cytotoxic agents. Expression of the mer operon is under tight control by the dual-function transcriptional regulator MerR. The metal-free, apo MerR binds to the mer operator/promoter region as a repressor to block transcription initiation, but is converted into an activator upon Hg(2+)-binding. To understand how MerR interacts with Hg(2+) and how Hg(2+)-binding modulates MerR function, we report here the crystal structures of apo and Hg(2+)-bound MerR from Bacillus megaterium, corresponding respectively to the repressor and activator conformation of MerR. To our knowledge, the apo-MerR structure represents the first visualization of a MerR family member in its intact and inducer-free form. And the Hg(2+)-MerR structure offers the first view of a triligated Hg(2+)-thiolate center in a metalloprotein, confirming that MerR binds Hg(2+) via trigonal planar coordination geometry. Structural comparison revealed the conformational transition of MerR is coupled to the assembly/disassembly of a buried Hg(2+) binding site, thereby providing a structural basis for the Hg(2+)-mediated functional switching of MerR. The pronounced Hg(2+)-induced repositioning of the MerR DNA-binding domains suggests a plausible mechanism for the transcriptional regulation of the mer operon.


    Organizational Affiliation

    Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.,Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan Agricultural Biotechnology Centre, National Chung Hsing University, Taichung 402, Taiwan nlchan@ntu.edu.tw.,Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan.,Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan Agricultural Biotechnology Centre, National Chung Hsing University, Taichung 402, Taiwan cchuang@dragon.nchu.edu.tw.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Regulatory protein
A, B
132Bacillus megateriumMutation(s): 0 
Gene Names: merR (merR1)
Find proteins for Q799U3 (Bacillus megaterium)
Go to UniProtKB:  Q799U3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download SDF File 
Download CCD File 
A
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.226 
  • Space Group: P 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 70.005α = 90.00
b = 70.556β = 90.00
c = 71.614γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
HKL-2000data processing
PHENIXrefinement
HKL-2000data scaling
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-09-16
    Type: Database references