7OD0

Mirolysin in complex with compound 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.204 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Latency, thermal stability, and identification of an inhibitory compound of mirolysin, a secretory protease of the human periodontopathogen Tannerella forsythia .

Zak, K.M.Bostock, M.J.Waligorska, I.Thogersen, I.B.Enghild, J.J.Popowicz, G.M.Grudnik, P.Potempa, J.Ksiazek, M.

(2021) J Enzyme Inhib Med Chem 36: 1267-1281

  • DOI: 10.1080/14756366.2021.1937619
  • Primary Citation of Related Structures:  
    7OD0

  • PubMed Abstract: 
  • Mirolysin is a secretory protease of Tannerella forsythia , a member of the dysbiotic oral microbiota responsible for periodontitis. In this study, we show that mirolysin latency is achieved by a "cysteine-switch" mechanism exerted by Cys23 in the N-terminal profragment ...

    Mirolysin is a secretory protease of Tannerella forsythia , a member of the dysbiotic oral microbiota responsible for periodontitis. In this study, we show that mirolysin latency is achieved by a "cysteine-switch" mechanism exerted by Cys23 in the N-terminal profragment. Mutation of Cys23 shortened the time needed for activation of the zymogen from several days to 5 min. The mutation also decreased the thermal stability and autoproteolysis resistance of promirolysin. Mature mirolysin is a thermophilic enzyme and shows optimal activity at 65 °C. Through NMR-based fragment screening, we identified a small molecule (compound (cpd) 9 ) that blocks promirolysin maturation and functions as a competitive inhibitor ( K i = 3.2 µM), binding to the S1' subsite of the substrate-binding pocket. Cpd 9 shows superior specificity and does not interact with other T. forsythia proteases or Lys/Arg-specific proteases.


    Organizational Affiliation

    Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MirolysinA [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD], E [auth EEE], F [auth FFF]277Tannerella forsythiaMutation(s): 0 
UniProt
Find proteins for A0A0F7IPS1 (Tannerella forsythia)
Explore A0A0F7IPS1 
Go to UniProtKB:  A0A0F7IPS1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
V7Q (Subject of Investigation/LOI)
Query on V7Q

Download Ideal Coordinates CCD File 
G [auth AAA], HA [auth EEE], M [auth BBB], OA [auth FFF], S [auth CCC], Z [auth DDD]2,1,3-benzothiadiazol-4-ylmethanamine
C7 H7 N3 S
HMEXAOROCQLCJX-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
EA [auth DDD], J [auth AAA], LA [auth EEE], P [auth BBB], SA [auth FFF], U [auth CCC]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth DDD], DA [auth DDD], H [auth AAA], IA [auth EEE], JA [auth EEE], N [auth BBB], PA [auth FFF], QA [auth FFF]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth DDD], BA [auth DDD], I [auth AAA], KA [auth EEE], O [auth BBB], RA [auth FFF], T [auth CCC]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
FA [auth DDD] , GA [auth DDD] , K [auth AAA] , L [auth AAA] , MA [auth EEE] , NA [auth EEE] , Q [auth BBB] , R [auth BBB] , 
FA [auth DDD], GA [auth DDD], K [auth AAA], L [auth AAA], MA [auth EEE], NA [auth EEE], Q [auth BBB], R [auth BBB], TA [auth FFF], UA [auth FFF], V [auth CCC], VA [auth FFF], W [auth CCC], X [auth CCC]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
Y [auth CCC]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.204 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.593α = 92.462
b = 77.64β = 90
c = 81.995γ = 119.98
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



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: 2021-08-04
    Type: Initial release