6R7V

Tannerella forsythia promirolysin mutant E225A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based mechanism of cysteine-switch latency and of catalysis by pappalysin-family metallopeptidases.

Guevara, T.Rodriguez-Banqueri, A.Ksiazek, M.Potempa, J.Gomis-Ruth, F.X.

(2020) Iucrj 7: 18-29

  • DOI: 10.1107/S2052252519013848
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • <i>Tannerella forsythia </i> is an oral dysbiotic periodontopathogen involved in severe human periodontal disease. As part of its virulence factor armamentarium, at the site of colonization it secretes mirolysin, a metallopeptidase of the unicellula ...

    Tannerella forsythia is an oral dysbiotic periodontopathogen involved in severe human periodontal disease. As part of its virulence factor armamentarium, at the site of colonization it secretes mirolysin, a metallopeptidase of the unicellular pappalysin family, as a zymogen that is proteolytically auto-activated extracellularly at the Ser54-Arg55 bond. Crystal structures of the catalytically impaired promirolysin point mutant E225A at 1.4 and 1.6 Å revealed that latency is exerted by an N-terminal 34-residue pro-segment that shields the front surface of the 274-residue catalytic domain, thus preventing substrate access. The catalytic domain conforms to the metzincin clan of metallopeptidases and contains a double calcium site, which acts as a calcium switch for activity. The pro-segment traverses the active-site cleft in the opposite direction to the substrate, which precludes its cleavage. It is anchored to the mature enzyme through residue Arg21, which intrudes into the specificity pocket in cleft sub-site S 1 '. Moreover, residue Cys23 within a conserved cysteine-glycine motif blocks the catalytic zinc ion by a cysteine-switch mechanism, first described for mammalian matrix metallopeptidases. In addition, a 1.5 Å structure was obtained for a complex of mature mirolysin and a tetradecapeptide, which filled the cleft from sub-site S 1 ' to S 6 '. A citrate molecule in S 1 completed a product-complex mimic that unveiled the mechanism of substrate binding and cleavage by mirolysin, the catalytic domain of which was already preformed in the zymogen. These results, including a preference for cleavage before basic residues, are likely to be valid for other unicellular pappalysins derived from archaea, bacteria, cyanobacteria, algae and fungi, including archetypal ulilysin from Methanosarcina acetivorans . They may further apply, at least in part, to the multi-domain orthologues of higher organisms.


    Related Citations: 
    • Mirolysin, a LysargiNase from Tannerella forsythia, proteolytically inactivates the human cathelicidin, LL-37.
      Koneru, L.,Ksiazek, M.,Waligorska, I.,Straczek, A.,Lukasik, M.,Madej, M.,Thogersen, I.B.,Enghild, J.J.,Potempa, J.
      (2017) Biol.Chem. 398: 395


    Organizational Affiliation

    Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, 501 South Preston Street, Louisville, KY 40202, USA.,Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain.,Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, Kraków 30-387, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mirolysin
A
314Tannerella forsythia (strain ATCC 43037 / JCM 10827 / FDC 338)Mutation(s): 1 
Find proteins for G8ULV1 (Tannerella forsythia (strain ATCC 43037 / JCM 10827 / FDC 338))
Go to UniProtKB:  G8ULV1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.330α = 90.00
b = 67.250β = 90.00
c = 79.640γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
BUSTERrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2020-01-29
    Type: Database references