4M1P

Crystal structure of the copper-sensing repressor CsoR with Cu(I) from Geobacillus thermodenitrificans NG80-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.564 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Cu(I)-mediated allosteric switching in a copper-sensing operon repressor (CsoR).

Chang, F.M.Coyne, H.J.Cubillas, C.Vinuesa, P.Fang, X.Ma, Z.Ma, D.Helmann, J.D.Garcia-de los Santos, A.Wang, Y.X.Dann, C.E.Giedroc, D.P.

(2014) J.Biol.Chem. 289: 19204-19217

  • DOI: 10.1074/jbc.M114.556704

  • PubMed Abstract: 
  • The copper-sensing operon repressor (CsoR) is representative of a major Cu(I)-sensing family of bacterial metalloregulatory proteins that has evolved to prevent cytoplasmic copper toxicity. It is unknown how Cu(I) binding to tetrameric CsoRs mediates ...

    The copper-sensing operon repressor (CsoR) is representative of a major Cu(I)-sensing family of bacterial metalloregulatory proteins that has evolved to prevent cytoplasmic copper toxicity. It is unknown how Cu(I) binding to tetrameric CsoRs mediates transcriptional derepression of copper resistance genes. A phylogenetic analysis of 227 DUF156 protein members, including biochemically or structurally characterized CsoR/RcnR repressors, reveals that Geobacillus thermodenitrificans (Gt) CsoR characterized here is representative of CsoRs from pathogenic bacilli Listeria monocytogenes and Bacillus anthracis. The 2.56 Å structure of Cu(I)-bound Gt CsoR reveals that Cu(I) binding induces a kink in the α2-helix between two conserved copper-ligating residues and folds an N-terminal tail (residues 12-19) over the Cu(I) binding site. NMR studies of Gt CsoR reveal that this tail is flexible in the apo-state with these dynamics quenched upon Cu(I) binding. Small angle x-ray scattering experiments on an N-terminally truncated Gt CsoR (Δ2-10) reveal that the Cu(I)-bound tetramer is hydrodynamically more compact than is the apo-state. The implications of these findings for the allosteric mechanisms of other CsoR/RcnR repressors are discussed.


    Organizational Affiliation

    the Department of Microbiology, Cornell University, Ithaca, New York 14853-8101.,From the Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102.,the Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos, México, 04510.,From the Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, giedroc@indiana.edu.,the Structural Biophysics Laboratory, Center for Cancer Research, NCI-National Institutes of Health, Frederick, Maryland 21702-1201, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Copper-sensitive operon repressor (CsoR)
A
104Geobacillus thermodenitrificans (strain NG80-2)Mutation(s): 1 
Find proteins for A4INJ9 (Geobacillus thermodenitrificans (strain NG80-2))
Go to UniProtKB:  A4INJ9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CU1
Query on CU1

Download SDF File 
Download CCD File 
A
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.564 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.214 
  • Space Group: P 6 2 2
Unit Cell:
Length (Å)Angle (°)
a = 89.204α = 90.00
b = 89.204β = 90.00
c = 57.985γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXmodel building
HKL-2000data reduction
PHENIXphasing
HKL-2000data scaling
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2014-10-08
    Type: Database references