9EYG | pdb_00009eyg

Structure of Tannerella forsythia endopeptidase O (TfPepO)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.223 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9EYG

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: 151.88 kDa 
  • Atom Count: 11,540 
  • Modeled Residue Count: 1,299 
  • Deposited Residue Count: 1,304 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidase family M13
A, B
652Tannerella forsythiaMutation(s): 0 
Gene Names: BFO_0011
EC: 3.4.24
UniProt
Find proteins for G8UQE9 (Tannerella forsythia (strain ATCC 43037 / JCM 10827 / CCUG 21028 A / KCTC 5666 / FDC 338))
Explore G8UQE9 
Go to UniProtKB:  G8UQE9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG8UQE9
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES

Query on MES



Download:Ideal Coordinates CCD File
S [auth A],
T [auth A]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
D [auth A],
F [auth A],
X [auth B],
Y [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
IMD

Query on IMD



Download:Ideal Coordinates CCD File
GA [auth B],
O [auth A],
P [auth A],
Q [auth A],
R [auth A]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN

Query on ZN



Download:Ideal Coordinates CCD File
HA [auth B],
IA [auth B],
U [auth A],
V [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
C [auth A]
CA [auth B]
DA [auth B]
AA [auth B],
BA [auth B],
C [auth A],
CA [auth B],
DA [auth B],
E [auth A],
EA [auth B],
FA [auth B],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
W [auth A],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.223 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.414α = 90
b = 95.414β = 90
c = 301.9γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MoRDaphasing

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: 2025-10-29
    Type: Initial release
  • Version 1.1: 2026-05-13
    Changes: Database references