Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.77 kDa 
• Atom Count: 1675 
• Modelled Residue Count: 182 
• Deposited Residue Count: 262 
• Unique protein chains: 1

2WTP

Crystal Structure of Cu-form Czce from C. metallidurans CH34

• PDB DOI: 10.2210/pdb2WTP/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Cupriavidus metallidurans CH34
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-09-18 Released: 2010-08-18 
• Deposition Author(s): Haertlein, I., Girard, E., Sarret, G., Hazemann, J., Gourhant, P., Kahn, R., Coves, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.189 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 

Literature

Evidence for Conformational Changes Upon Copper Binding to Cupriavidus Metallidurans Czce.

Petit-Haertlein, I., Girard, E., Sarret, G., Hazemann, J., Gourhant, P., Kahn, R., Coves, J.

(2010) Biochemistry 49: 1913

• PubMed: 20112954 
• DOI: 10.1021/bi100001z
• Primary Citation of Related Structures:  
  2WTO, 2WTP


• PubMed Abstract: 
  

CzcE is a periplasmic protein from Cupriavidus metallidurans CH34 that can bind four copper atoms per dimer. We have crystallized the apo form of the protein and determined its structure at 1.85 A resolution. Three Cu atoms were localized by soaking apo-CzcE crystals into a CuCl(2) solution. We identified His24 as a Cu(II) ligand in each protomer and Asp100 as a key residue for Cu binding at the interface of the dimer. The role of these amino acids was confirmed by site-directed mutagenesis and UV-visible spectroscopy. The fourth Cu atom was not located. The oxidized form of CzcE contains four Cu(II) atoms, while the reduced form contains four Cu(I) atoms. Average coordination spheres of four N or O atoms for Cu(II) and of one N or O atom and two S atoms for Cu(I) were determined by X-ray absorption spectroscopy. As there is no evidence for preformed metal-binding sites in apo-CzcE, we suggest that different conformational changes occurred upon Cu(II) or Cu(I) binding. These changes were further demonstrated by digestion experiments that gave different proteolysis patterns depending not only on the presence of the metal but also on its speciation. The ability of CzcE to bind copper and to adapt its conformation to different copper oxidation states could be related to a role in copper sensing for this protein.

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Related Citations: 

• Czce from Cupriavidus Metallidurans Ch34 is a Copper-Binding Protein.
  Zoropogui, A., Gambarelli, S., Coves, J.
  (2008) Biochem Biophys Res Commun 365: 735

• Overproduction, Purification and Preliminary X-Ray Diffraction Analysis of Czce from Cupriavidus Metallidurans Ch34.
  Pompidor, G., Zoropogui, A., Kahn, R., Coves, J.
  (2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 884

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Organizational Affiliation: 

Institut de Biologie Structurale-Jean-Pierre Ebel, UMR 5075 CNRS-CEA-UJF, 41, rue Jules Horowitz, 38027 Grenoble Cedex, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF131 PROTEIN	A, B	131	Cupriavidus metallidurans CH34	Mutation(s): 0  Gene Names: czcE, Rmet_5976
UniProt
Find proteins for Q1LAJ1 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34)) Explore Q1LAJ1  Go to UniProtKB:  Q1LAJ1

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	L [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	C [auth A], M [auth B], N [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CU	E [auth A], O [auth B], P [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.189 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105	α = 90
b = 29.53	β = 113.41
c = 71.17	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-09-18 
• Released Date: 2010-08-18 
Deposition Author(s): Haertlein, I., Girard, E., Sarret, G., Hazemann, J., Gourhant, P., Kahn, R., Coves, J.

Revision History  

• Version 1.0: 2010-08-18
  Type: Initial release
  
• Version 1.1: 2012-02-29
  Changes: Derived calculations, Version format compliance