9IBN | pdb_00009ibn

Crystal structure of the peptidyl-prolyl isomerase (PPIase) from E. faecium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 
    0.250 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal structure and biophysical characterisation of the enterococcal foldase PpiC, a cross-opsonic antigen against gram-positive nosocomial pathogens.

Napolitano, V.Kramarska, E.Ghilardi, O.Romero-Saavedra, F.Del Vecchio, P.Squeglia, F.Huebner, J.Berisio, R.

(2025) FEBS J 

  • DOI: https://doi.org/10.1111/febs.70160
  • Primary Citation of Related Structures:  
    9IBN

  • PubMed Abstract: 

    Enterococcus faecium have high rates of antibiotic resistances, with vancomycin-resistant E. faecium acknowledged as the most important in the clinical setting and declared by WHO to be a threat to humankind, for which rapid actions are needed. PpiC is a membrane-bound lipoprotein of E. faecium endowed with both a peptidyl-prolyl isomerase and a foldase activity, and plays a key role in assisting the folding of many secreted enterococcal proteins. It is located at the membrane-wall interface, therefore easily accessible to inhibitors and to the immune system and an ideal target for drug and vaccine development. Despite their potential, enterococcal peptidyl-prolyl isomerases have been understudied. We previously identified PpiC as an important cross-protective vaccine antigen. To gain a better understanding of the PpiC biological role in E. faecium survival, we determined the crystal structure of PpiC and investigated its biophysical properties. Consistent with PpiC's folding activity, the biological assembly of PpiC is a bowl-shaped structure containing two parvulin-type peptidyl-prolyl cis/trans isomerase domains. We also dissected the role of N- and C-terminal regions of the molecule in its dimerisation, an event which is predicted to play an important role in the folding of client proteins. Our data point to a functional cross-talk between the foldase and peptidyl-prolyl isomerase activities of PpiC, through the protein-swapping involved in dimerisation. Also, our work provides key structural data for the design of antimicrobials and cross-protective vaccine antigens against nosocomial infections.


  • Organizational Affiliation
    • Institute of Biostructures and Bioimaging, Italian Research Council (CNR), Naples, Italy.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Foldase protein PrsA
A, B
340Enterococcus faeciumMutation(s): 0 
Gene Names: 
EC: 5.2.1.8
UniProt
Find proteins for Q3Y2Y5 (Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO))
Explore Q3Y2Y5 
Go to UniProtKB:  Q3Y2Y5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3Y2Y5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
J [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free:  0.250 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.486α = 90
b = 69.674β = 102.81
c = 87.413γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
AutoProcessdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean Union860325

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release