7L6Z | pdb_00007l6z

Crystal Structure of Peptidyl-Prolyl Cis-Trans Isomerasefrom (PpiB) Streptococcus pneumoniae R6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 
    0.212 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural analysis of extracellular ATP-independent chaperones of streptococcal species and protein substrate interactions.

Agbavor, C.Torres, M.Inniss, N.L.Latimer, S.Minasov, G.Shuvalova, L.Wawrzak, Z.Borek, D.Otwinowski, Z.Stogios, P.J.Savchenko, A.Anderson, W.F.Satchell, K.J.F.Cahoon, L.A.

(2025) mSphere 10: e0107824-e0107824

  • DOI: https://doi.org/10.1128/msphere.01078-24
  • Primary Citation of Related Structures:  
    5TVL, 7L6Y, 7L6Z, 7L75

  • PubMed Abstract: 

    During infection, bacterial pathogens rely on secreted virulence factors to manipulate the host cell. However, in gram-positive bacteria, the molecular mechanisms underlying the folding and activity of these virulence factors after membrane translocation are not clear. Here, we solved the protein structures of two secreted parvulin and two secreted cyclophilin-like peptidyl-prolyl isomerase (PPIase) ATP-independent chaperones found in gram-positive streptococcal species. The extracellular parvulin-type PPIase, PrsA in Streptococcus pneumoniae and Streptococcus mutans maintain dimeric crystal structures reminiscent of folding catalysts that consist of two domains, a PPIase and foldase domain. Structural comparison of the two cyclophilin-like extracellular chaperones from S. pneumoniae and Streptococcus pyogenes with other cyclophilins demonstrates that this group of cyclophilin-like chaperones has novel structural appendages formed by 9- and 24-residue insertions. Furthermore, we demonstrate that deletion of prsA and slrA genes impairs the secretion of the cholesterol-dependent pore-forming toxin, pneumolysin in S. pneumoniae . Using protein pull-down and biophysical assays, we demonstrate a direct interaction between PrsA and SlrA with Ply. Then, we developed chaperone-assisted folding assays that show that the S. pneumoniae PrsA and SlrA extracellular chaperones accelerate pneumolysin folding. In addition, we demonstrate that SlrA and, for the first time, S. pyogene s PpiA exhibit PPIase activity and can bind the immunosuppressive drug, cyclosporine A. Altogether, these findings suggest a mechanistic role for streptococcal PPIase chaperones in the activity and folding of secreted virulence factors such as pneumolysin. Streptococcal species are a leading cause of lower respiratory infections that annually affect millions of people worldwide. During infection, streptococcal species secrete a medley of virulence factors that allow the bacteria to colonize and translocate to deeper tissues. In many gram-positive bacteria, virulence factors are secreted from the cytosol across the bacterial membrane in an unfolded state. The bacterial membrane-cell wall interface is exposed to the potentially harsh extracellular environment, making it difficult for native virulence factors to fold before being released into the host. ATP-independent PPIase-type chaperones, PrsA and SlrA, are thought to facilitate folding and stabilization of several unfolded proteins to promote the colonization and spread of streptococci. Here, we present crystal structures of the molecular chaperones of PrsA and SlrA homologs from streptococcal species. We provide evidence that the Streptococcus pyogenes SlrA homolog, PpiA, has PPIase activity and binds to cyclosporine A. In addition, we show that Streptococcus pneumoniae PrsA and SlrA directly interact and fold the cholesterol-dependent pore-forming toxin and critical virulence determinant, pneumolysin.


  • Organizational Affiliation
    • Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
214Streptococcus pneumoniae R6Mutation(s): 0 
Gene Names: ppiAspr0679
EC: 5.2.1.8
UniProt
Find proteins for Q8DQG5 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DQG5 
Go to UniProtKB:  Q8DQG5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DQG5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
P [auth C]
Q [auth C]
S [auth D]
U [auth E]
V [auth F]
P [auth C],
Q [auth C],
S [auth D],
U [auth E],
V [auth F],
W [auth F],
Y [auth H],
Z [auth J]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
M [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth A]
L [auth A]
N [auth B]
O [auth B]
R [auth D]
K [auth A],
L [auth A],
N [auth B],
O [auth B],
R [auth D],
T [auth E],
X [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free:  0.212 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.432α = 90
b = 156.529β = 117.18
c = 90.535γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-01
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Structure summary
  • Version 1.2: 2026-02-11
    Changes: Database references