Skip to main content

 5HU4 | pdb_00005hu4

Cystal structure of listeria monocytogenes sortase A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.275 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5HU4

This is version 1.1 of the entry. See complete history. 

Literature

Inhibition of sortase A by chalcone prevents Listeria monocytogenes infection.

Li, H., Chen, Y., Zhang, B., Niu, X., Song, M., Luo, Z., Lu, G., Liu, B., Zhao, X., Wang, J., Deng, X.

(2016) Biochem Pharmacol 106: 19-29

  • DOI: https://doi.org/10.1016/j.bcp.2016.01.018
  • Primary Citation Related Structures: 
    5HU4

  • PubMed Abstract: 

    The critical role of sortase A in gram-positive bacterial pathogenicity makes this protein a good potential target for antimicrobial therapy. In this study, we report for the first time the crystal structure of Listeria monocytogenes sortase A and identify the active sites that mediate its transpeptidase activity. We also used a sortase A (SrtA) enzyme activity inhibition assay, simulation, and isothermal titration calorimetry analysis to discover that chalcone, an agent with little anti-L. monocytogenes activity, could significantly inhibit sortase A activity with an IC50 of 28.41 ± 5.34 μM by occupying the active site of SrtA. The addition of chalcone to a co-culture of L. monocytogenes and Caco-2 cells significantly inhibited bacterial entry into the cells and L. monocytogenes-mediated cytotoxicity. Additionally, chalcone treatment decreased the mortality of infected mice, the bacterial burden in target organs, and the pathological damage to L. monocytogenes-infected mice. In conclusion, these findings suggest that chalcone is a promising candidate for the development of treatment against L. monocytogenes infection.


  • Organizational Affiliation: 
    • Key Laboratory of Zoonosis, Ministry of Education, Department of Food Quality and Safety, College of Veterinary Medicine, Jilin University, Changchun, China.

Macromolecule Content 

  • Total Structure Weight: 16.11 kDa 
  • Atom Count: 1,133 
  • Modeled Residue Count: 145 
  • Deposited Residue Count: 145 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cysteine protease145Listeria monocytogenesMutation(s): 0 
Gene Names: ABE86_07720, ABE87_06300, AMC92_10805, ARD00_01217
EC: 3.4.22
UniProt
Find proteins for Q8Y8H5 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e))
Explore Q8Y8H5 
Go to UniProtKB:  Q8Y8H5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8Y8H5
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.275 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.986α = 90
b = 56.599β = 90
c = 60.548γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2017-02-01 
  • Deposition Author(s): Li, H.

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description