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 

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Ligand Structure Quality Assessment 


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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
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(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
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  • 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
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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

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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