6UKD

Co-complex of S. pyogenes 10782 streptopain bound with a nitrile-based specific covalent inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

An Irreversible Inhibitor to Probe the Role ofStreptococcus pyogenesCysteine Protease SpeB in Evasion of Host Complement Defenses.

Woehl, J.L.Kitamura, S.Dillon, N.Han, Z.Edgar, L.J.Nizet, V.Wolan, D.W.

(2020) ACS Chem Biol 15: 2060-2069

  • DOI: https://doi.org/10.1021/acschembio.0c00191
  • Primary Citation of Related Structures:  
    6UKD

  • PubMed Abstract: 

    Members of the CA class of cysteine proteases have multifaceted roles in physiology and virulence for many bacteria. Streptococcal pyrogenic exotoxin B (SpeB) is secreted by Streptococcus pyogenes and implicated in the pathogenesis of the bacterium through degradation of key human immune effector proteins. Here, we developed and characterized a clickable inhibitor, 2 S -alkyne , based on X-ray crystallographic analysis and structure-activity relationships. Our SpeB probe showed irreversible enzyme inhibition in biochemical assays and labeled endogenous SpeB in cultured S. pyogenes supernatants. Importantly, application of 2 S -alkyne decreased S. pyogenes survival in the presence of human neutrophils and supports the role of SpeB-mediated proteolysis as a mechanism to limit complement-mediated host defense. We posit that our SpeB inhibitor will be a useful chemical tool to regulate, label, and quantitate secreted cysteine proteases with SpeB-like activity in complex biological samples and a lead candidate for new therapeutics designed to sensitize S. pyogenes to host immune clearance.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Streptopain380Streptococcus pyogenes ATCC 10782Mutation(s): 1 
Gene Names: speB
EC: 3.4.22.10
UniProt
Find proteins for P0C0J0 (Streptococcus pyogenes)
Explore P0C0J0 
Go to UniProtKB:  P0C0J0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0J0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.273α = 90
b = 50.398β = 90
c = 114.497γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description