8EHE

Structure of Tannerella forsythia potempin C in complex with mirolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.139 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A unique network of attack, defence and competence on the outer membrane of the periodontitis pathogen Tannerella forsythia.

Ksiazek, M.Goulas, T.Mizgalska, D.Rodriguez-Banqueri, A.Eckhard, U.Veillard, F.Waligorska, I.Benedyk-Machaczka, M.Sochaj-Gregorczyk, A.M.Madej, M.Thogersen, I.B.Enghild, J.J.Cuppari, A.Arolas, J.L.de Diego, I.Lopez-Pelegrin, M.Garcia-Ferrer, I.Guevara, T.Dive, V.Zani, M.L.Moreau, T.Potempa, J.Gomis-Ruth, F.X.

(2023) Chem Sci 14: 869-888

  • DOI: https://doi.org/10.1039/d2sc04166a
  • Primary Citation of Related Structures:  
    8B2M, 8B2N, 8B2Q, 8EHB, 8EHC, 8EHD, 8EHE

  • PubMed Abstract: 

    Periodontopathogenic Tannerella forsythia uniquely secretes six peptidases of disparate catalytic classes and families that operate as virulence factors during infection of the gums, the KLIKK-peptidases. Their coding genes are immediately downstream of novel ORFs encoding the 98-132 residue potempins (Pot) A, B1, B2, C, D and E. These are outer-membrane-anchored lipoproteins that specifically and potently inhibit the respective downstream peptidase through stable complexes that protect the outer membrane of T. forsythia , as shown in vivo . Remarkably, PotA also contributes to bacterial fitness in vivo and specifically inhibits matrix metallopeptidase (MMP) 12, a major defence component of oral macrophages, thus featuring a novel and highly-specific physiological MMP inhibitor. Information from 11 structures and high-confidence homology models showed that the potempins are distinct β-barrels with either a five-stranded OB-fold (PotA, PotC and PotD) or an eight-stranded up-and-down fold (PotE, PotB1 and PotB2), which are novel for peptidase inhibitors. Particular loops insert like wedges into the active-site cleft of the genetically-linked peptidases to specifically block them either via a new "bilobal" or the classic "standard" mechanism of inhibition. These results discover a unique, tightly-regulated proteolytic armamentarium for virulence and competence, the KLIKK-peptidase/potempin system.


  • Organizational Affiliation

    Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University Gronostajowa 7 Kraków 30-387 Poland jan.potempa@icloud.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mirolase353Tannerella forsythiaMutation(s): 0 
UniProt
Find proteins for A0A0A7KVG3 (Tannerella forsythia)
Explore A0A0A7KVG3 
Go to UniProtKB:  A0A0A7KVG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A7KVG3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Potempin C (PotC)152Tannerella forsythiaMutation(s): 0 
Gene Names: CLI86_13365TFUB20_02175
UniProt
Find proteins for A0A1D3UUC0 (Tannerella forsythia)
Explore A0A1D3UUC0 
Go to UniProtKB:  A0A1D3UUC0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D3UUC0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
R [auth B],
S [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
P [auth A],
Q [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.139 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.65α = 90
b = 113.36β = 112.69
c = 50.2γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-21
    Type: Initial release
  • Version 1.1: 2023-02-22
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary