4F2F

Crystal structure of the metal binding domain (MBD) of the Streptococcus pneumoniae D39 Cu(I) exporting P-type ATPase CopA with Cu(I)

• PDB DOI: https://doi.org/10.2210/pdb4F2F/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Streptococcus pneumoniae D39
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-05-07 Released: 2013-01-30 
• Deposition Author(s): Fu, Y., Dann III, C.E., Giedroc, D.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.243 
• R-Value Work: 0.213 
• R-Value Observed: 0.217 

Literature

A new structural paradigm in copper resistance in Streptococcus pneumoniae.

Fu, Y., Tsui, H.C., Bruce, K.E., Sham, L.T., Higgins, K.A., Lisher, J.P., Kazmierczak, K.M., Maroney, M.J., Dann, C.E., Winkler, M.E., Giedroc, D.P.

(2013) Nat Chem Biol 9: 177-183

• PubMed: 23354287 
• DOI: https://doi.org/10.1038/nchembio.1168
• Primary Citation of Related Structures:  
  4F2E, 4F2F


• PubMed Abstract: 
  

  Copper resistance has emerged as an important virulence determinant of microbial pathogens. In Streptococcus pneumoniae, copper resistance is mediated by the copper-responsive repressor CopY, CupA and the copper-effluxing P(1B)-type ATPase CopA. We show here that CupA is a previously uncharacterized cell membrane-anchored Cu(I) chaperone and that a Cu(I) binding-competent, membrane-localized CupA is obligatory for copper resistance. The crystal structures of the soluble domain of CupA and the N-terminal metal-binding domain (MBD) of CopA (CopA(MBD)) reveal isostructural cupredoxin-like folds that each harbor a binuclear Cu(I) cluster unprecedented in bacterial copper trafficking. NMR studies reveal unidirectional Cu(I) transfer from the low-affinity site on the soluble domain of CupA to the high-affinity site of CopA(MBD). However, copper binding by CopA(MBD) is not essential for cellular copper resistance, consistent with a primary role of CupA in cytoplasmic Cu(I) sequestration and/or direct delivery to the transmembrane site of CopA for cellular efflux.

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Organizational Affiliation: 

Department of Chemistry, Indiana University, Bloomington, Indiana, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 11.51 kDa 
• Atom Count: 909 
• Modelled Residue Count: 100 
• Deposited Residue Count: 100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation-transporting ATPase, E1-E2 family protein	A	100	Streptococcus pneumoniae D39	Mutation(s): 0  Gene Names: SPD0635, SPD_0635 EC: 3.6.3.4
UniProt
Find proteins for A0A0H2ZQ91 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)) Explore A0A0H2ZQ91  Go to UniProtKB:  A0A0H2ZQ91

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU1	B [auth A], C [auth A]	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.243 
• R-Value Work: 0.213 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.455	α = 90
b = 37.329	β = 90
c = 69.294	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-30 
Deposition Author(s): Fu, Y., Dann III, C.E., Giedroc, D.P.

Revision History  

• Version 1.0: 2013-01-30
  Type: Initial release
  
• Version 1.1: 2013-02-13
  Changes: Database references
• Version 1.2: 2013-03-06
  Changes: Database references
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations