Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.48 kDa 
• Atom Count: 4,365 
• Modelled Residue Count: 530 
• Deposited Residue Count: 556 
• Unique protein chains: 1

 7MYG

M. tb Ag85C modified by THL-10d

• PDB DOI: 10.2210/pdb7MYG/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-05-21 Released: 2021-09-15 
• Deposition Author(s): Sudasinghe, T.D., Ronning, D.R.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.222 
• R-Value Work: 0.155 
• R-Value Observed: 0.162 

Literature

Total Synthesis of Tetrahydrolipstatin, Its Derivatives, and Evaluation of Their Ability to Potentiate Multiple Antibiotic Classes against Mycobacterium Species.

Khan, S.S., Sudasinghe, T.D., Landgraf, A.D., Ronning, D.R., Sucheck, S.J.

(2021) ACS Infect Dis 7: 2876-2888

• PubMed: 34478259 
• DOI: 10.1021/acsinfecdis.1c00283
• Primary Citation of Related Structures:  
  7MYG


• PubMed Abstract: 
  

Tetrahydrolipstatin (THL, 1a ) has been shown to inhibit both mammalian and bacterial α/β hydrolases. In the case of bacterial systems, THL is a known inhibitor of several Mycobacterium tuberculosis hydrolases involved in mycomembrane biosynthesis. Herein we report a highly efficient eight-step asymmetric synthesis of THL using a route that allows modification of the THL α-chain substituent to afford compounds 1a through 1e . The key transformation in the synthesis was use of a (TPP)CrCl/Co ₂ (CO) ₈ -catalyzed regioselective and stereospecific carbonylation on an advanced epoxide intermediate to yield a trans -β-lactone. These compounds are modest inhibitors of Ag85A and Ag85C, two α/β hydrolases of M. tuberculosis involved in the biosynthesis of the mycomembrane. Among these compounds, 10d showed the highest inhibitory effect on Ag85A (34 ± 22 μM) and Ag85C (66 ± 8 μM), and its X-ray structure was solved in complex with Ag85C to 2.5 Å resolution. In contrast, compound 1e exhibited the best-in-class MICs of 50 μM (25 μg/mL) and 16 μM (8.4 μg/mL) against M . smegmatis and M. tuberculosis H37Ra, respectively, using a microtiter assay plate. Combination of 1e with 13 well-established antibiotics synergistically enhanced the potency of few of these antibiotics in M . smegmatis and M. tuberculosis H37Ra. Compound 1e applied at concentrations 4-fold lower than its MIC enhanced the MIC of the synergistic antibiotic by 2-256-fold. In addition to observing synergy with first-line drugs, rifamycin and isoniazid, the MIC of vancomycin against M. tuberculosis H37Ra was 65 μg/mL; however, the MIC was lowered to 0.25 μg/mL in the presence of 2.1 μg/mL 1e demonstrating the potential of targeting mycobacterial hydrolases involved in mycomembrane and peptidoglycan biosynthesis.

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Organizational Affiliation: 

Department of Chemistry & Biochemistry, University of Toledo, Toledo, Ohio 43606, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diacylglycerol acyltransferase	A, B	278	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  fbpC, fbpC_1, DSI38_14625, E5M05_00190, E5M52_01085, E5M78_01085, ERS007657_00618, ERS007663_00913, ERS007665_00182, ERS007703_02124, ERS007722_01715, ERS007741_01210, ERS013471_00870, ERS024276_00850, ERS027659_01767, ERS094182_00158, F6W99_02771, FRD82_05760, GCL30_02455, SAMEA2683035_00278 EC: 2.3.1 (PDB Primary Data), 2.3.1.122 (UniProt), 2.3.1.20 (UniProt)
UniProt
Find proteins for P9WQN9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQN9  Go to UniProtKB:  P9WQN9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.222 
• R-Value Work: 0.155 
• R-Value Observed: 0.162 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.458	α = 90
b = 70.606	β = 89.97
c = 68.59	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-09-15 
Deposition Author(s): Sudasinghe, T.D., Ronning, D.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI105084

Revision History  

• Version 1.0: 2021-09-15
  Type: Initial release
  
• Version 1.1: 2021-10-20
  Changes: Database references