9FMA | pdb_00009fma

Structure of Porphyromonas gingivalis endopeptidase (PgPepO)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 
    0.214 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 9FMA

This is version 1.1 of the entry. See complete history

Literature

Periodontopathogens degrade angiotensin I from the human renin-angiotensin system through surface-attached proteases.

Waligorska, I.Zak, K.M.Mikrut, N.Budziaszek, J.Medviediev, V.Bielecka, E.Kantyka, T.Koziel, J.Thogersen, I.B.Enghild, J.J.Grudnik, P.Potempa, J.Ksiazek, M.

(2025) Sci Rep 15: 43309-43309

  • DOI: https://doi.org/10.1038/s41598-025-27891-0
  • Primary Citation Related Structures: 
    9EYG, 9FMA

  • PubMed Abstract: 

    The renin-angiotensin system (RAS) has its effects through biologically-active peptides, the angiotensins (Ang). The angiotensinogen-derived precursor, Ang I, is cleaved either to proinflammatory Ang II, which increases blood pressure or to Ang 1-7, which has opposite effects to Ang II. Here, we show that Porphyromonas gingivalis (Pg) and Tannerella forsythia (Tf), endogenous oral pathogens, direct the RAS to generate Ang 1-7 through the actions of the endopeptidases O PgPepO and TfPepO, respectively. The thermophilic PepOs metalloproteases preferred large hydrophobic amino acids at the carbonyl terminus of scissile peptide bonds (P1' position), and TfPepO, in contrast to all known homologous proteases, hydrolyzed substrates distant to both termini. The crystal structures revealed exceptionally wide entrances to the catalytic cleft, which explains the unique properties of TfPepO. Multiple immunoassays showed that PepOs attached to bacterial cell surfaces are released in outer membrane vesicles. Moreover, PepO was responsible for Ang I hydrolysis by Pg and Tf. Finally, PepO deletion reduced only the virulence of Tf using the Galleria mellonella model. Thus, our data show that PepOs are the only proteases of Pg and Tf, which may modulate RAS through AngI hydrolysis.


  • Organizational Affiliation
    • Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland. irena.waligorska@gmail.com.

Macromolecule Content 

  • Total Structure Weight: 76.77 kDa 
  • Atom Count: 5,800 
  • Modeled Residue Count: 652 
  • Deposited Residue Count: 667 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endopeptidase PepO667Porphyromonas gingivalisMutation(s): 0 
Gene Names: pepOPG_0159
UniProt
Find proteins for Q7MXL5 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Explore Q7MXL5 
Go to UniProtKB:  Q7MXL5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7MXL5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free:  0.214 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.222α = 90
b = 93.222β = 90
c = 182.506γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePolandUMO-2019/35/B/NZ1/03118
Polish National Science CentrePolandUMO-2018/31/N/NZ1/02891

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release
  • Version 1.1: 2026-05-13
    Changes: Database references