4FAJ | pdb_00004faj

Structure and mode of peptide binding of pheromone receptor PrgZ

• PDB DOI: https://doi.org/10.2210/pdb4FAJ/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Enterococcus faecalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-22 Released: 2012-09-12 
• Deposition Author(s): Berntsson, R.P.-A., Schuurman-Wolters, G.K., Dunny, K., Slotboom, D.J., Poolman, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.193 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.156 (Depositor) 
• R-Value Observed: 
  0.158 (Depositor) 

Literature

Structure and Mode of Peptide Binding of Pheromone Receptor PrgZ.

Berntsson, R.P., Schuurman-Wolters, G.K., Dunny, G., Slotboom, D.J., Poolman, B.

(2012) J Biological Chem 287: 37165-37170

• PubMed: 22948145 
• DOI: https://doi.org/10.1074/jbc.M112.386334
• Primary Citation Related Structures: 
  4FAJ


• PubMed Abstract: 
  

  We present the crystal structure of the pheromone receptor protein PrgZ from Enterococcus faecalis in complex with the heptapeptide cCF10 (LVTLVFV), which is used in signaling between conjugative recipient and donor cells. Comparison of PrgZ with homologous oligopeptide-binding proteins (AppA and OppA) explains the high specificity of PrgZ for hydrophobic heptapeptides versus the promiscuity of peptide binding in the homologous proteins.

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Organizational Affiliation: 
• Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre, University of Groningen, 9747 AG Groningen, The Netherlands.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 64.56 kDa 
• Atom Count: 4,570 
• Modeled Residue Count: 514 
• Deposited Residue Count: 571 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PrgZ	A	564	Enterococcus faecalis	Mutation(s): 0  Gene Names: prgZ
UniProt
Find proteins for Q51643 (Enterococcus faecalis) Explore Q51643  Go to UniProtKB:  Q51643

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sex pheromone cCF10	B	7	Enterococcus faecalis	Mutation(s): 0
UniProt
Find proteins for P20104 (Enterococcus faecalis) Explore P20104  Go to UniProtKB:  P20104

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A], F [auth A], G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.193 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.156 (Depositor) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.622	α = 90
b = 74.122	β = 90
c = 112.622	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-12 
Deposition Author(s): Berntsson, R.P.-A., Schuurman-Wolters, G.K., Dunny, K., Slotboom, D.J., Poolman, B.

Revision History  

• Version 1.0: 2012-09-12
  Type: Initial release
  
• Version 1.1: 2012-11-14
  Changes: Database references, Derived calculations
• Version 1.2: 2012-12-12
  Changes: Derived calculations
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2024-02-28
  Changes: Data collection, Database references, Derived calculations