7V6K

Crystal structure of Sortase A from Streptococcus pyogenes in complex with ML346


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

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This is version 1.2 of the entry. See complete history


Literature

Covalent sortase A inhibitor ML346 prevents Staphylococcus aureus infection of Galleria mellonella.

Guan, X.N.Zhang, T.Yang, T.Dong, Z.Yang, S.Lan, L.Gan, J.Yang, C.G.

(2022) RSC Med Chem 13: 138-149

  • DOI: https://doi.org/10.1039/d1md00316j
  • Primary Citation of Related Structures:  
    7V6K

  • PubMed Abstract: 

    The housekeeping sortase A (SrtA), a membrane-associated cysteine transpeptidase, is responsible for anchoring surface proteins to the cell wall peptidoglycan in Gram-positive bacteria. This process is essential for the regulation of bacterial virulence and pathogenicity. Therefore, SrtA is considered to be an ideal target for antivirulence therapy. In this study, we report that ML346, a compound with a barbituric acid and cinnamaldehyde scaffold, functions as an irreversible inhibitor of Staphylococcus aureus SrtA ( Sa SrtA) and Streptococcus pyogenes SrtA ( Sp SrtA) in vitro at low micromolar concentrations. According to our X-ray crystal structure of the Sp SrtA ΔN81 /ML346 complex (Protein Data Bank ID: 7V6K), ML346 covalently modifies the thiol group of Cys208 in the active site of Sp SrtA. Importantly, ML346 significantly attenuated the virulence phenotypes of S. aureus and exhibited inhibitory effects on Galleria mellonella larva infection caused by S. aureus . Collectively, our results indicate that ML346 has potential for development as a covalent antivirulence agent for treating S. aureus infections, including methicillin-resistant S. aureus .


  • Organizational Affiliation

    Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China yangcg@simm.ac.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sortase
A, B
189Streptococcus pyogenesMutation(s): 0 
Gene Names: 
UniProt
Find proteins for Q99ZN4 (Streptococcus pyogenes serotype M1)
Explore Q99ZN4 
Go to UniProtKB:  Q99ZN4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99ZN4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.33α = 90
b = 34.33β = 90
c = 396.23γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21725801

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-29
    Type: Initial release
  • Version 1.1: 2022-04-27
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description