8QIJ | pdb_00008qij

Crystallographic Structure of a Salicylate Synthase from M. abscessus (Mab-SaS)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 
    0.217 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.177 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 8QIJ

This is version 1.1 of the entry. See complete history

Literature

Structural basis for specific inhibition of salicylate synthase from Mycobacterium abscessus.

Mori, M.Cocorullo, M.Tresoldi, A.Cazzaniga, G.Gelain, A.Stelitano, G.Chiarelli, L.R.Tomaiuolo, M.Delre, P.Mangiatordi, G.F.Garofalo, M.Cassetta, A.Covaceuszach, S.Villa, S.Meneghetti, F.

(2024) Eur J Med Chem 265: 116073-116073

  • DOI: https://doi.org/10.1016/j.ejmech.2023.116073
  • Primary Citation Related Structures: 
    8QIJ

  • PubMed Abstract: 

    Blocking iron uptake and metabolism has been emerging as a promising therapeutic strategy for the development of novel antimicrobial compounds. Like all mycobacteria, M. abscessus (Mab) has evolved several countermeasures to scavenge iron from host carrier proteins, including the production of siderophores, which play a crucial role in these processes. In this study, we solved, for the first time, the crystal structure of Mab-SaS, the first enzyme involved in the biosynthesis of siderophores. Moreover, we screened a small, focused library and identified a compound exhibiting a potent inhibitory effect against Mab-SaS (IC 50  ≈ 2 μM). Its binding mode was investigated by means of Induced Fit Docking simulations, performed on the crystal structure presented herein. Furthermore, cytotoxicity data and pharmacokinetic predictions revealed the safety and drug-likeness of this class of compounds. Finally, the crystallographic data were used to optimize the model for future virtual screening campaigns. Taken together, the findings of our study pave the way for the identification of potent Mab-SaS inhibitors, based on both established and unexplored chemotypes.


  • Organizational Affiliation
    • Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133, Milano, Italy.

Macromolecule Content 

  • Total Structure Weight: 99.21 kDa 
  • Atom Count: 7,073 
  • Modeled Residue Count: 872 
  • Deposited Residue Count: 906 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative anthranilate synthase component I TrpE2/ Salicylate synthase MbtIA,
B [auth C]
453Mycobacteroides abscessusMutation(s): 0 
Gene Names: MAB_2245
UniProt
Find proteins for B1MAQ5 (Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CCUG 20993 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543 / L948))
Explore B1MAQ5 
Go to UniProtKB:  B1MAQ5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1MAQ5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS

Query on TRS



Download:Ideal Coordinates CCD File
C [auth A],
J [auth C]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG

Query on PEG



Download:Ideal Coordinates CCD File
L [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
R [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A],
K [auth C],
M [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free:  0.217 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.177 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.34α = 90
b = 94.76β = 90
c = 102.46γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fondazione Ricerca Fibrosi CisticaItalyFFC#5/2022

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-31
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Refinement description