7JLI | pdb_00007jli

Crystal structure of Bacillus subtilis UppS

• PDB DOI: https://doi.org/10.2210/pdb7JLI/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2020-07-29 Released: 2021-08-04 
• Deposition Author(s): Workman, S.D., Strynadka, N.C.J.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR), Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.212 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Structural Insights into the Inhibition of Undecaprenyl Pyrophosphate Synthase from Gram-Positive Bacteria.

Workman, S.D., Day, J., Farha, M.A., El Zahed, S.S., Bon, C., Brown, E.D., Organ, M.G., Strynadka, N.C.J.

(2021) J Med Chem 64: 13540-13550

• PubMed: 34473495 
• DOI: https://doi.org/10.1021/acs.jmedchem.1c00941
• Primary Citation Related Structures: 
  7JLI, 7JLJ, 7JLM, 7JLR


• PubMed Abstract: 
  

  The polyprenyl lipid undecaprenyl phosphate (C ₅₅ P) is the universal carrier lipid for the biosynthesis of bacterial cell wall polymers. C ₅₅ P is synthesized in its pyrophosphate form by undecaprenyl pyrophosphate synthase (UppS), an essential cis -prenyltransferase that is an attractive target for antibiotic development. We previously identified a compound (MAC-0547630) that showed promise as a novel class of inhibitor and an ability to potentiate β-lactam antibiotics. Here, we provide a structural model for MAC-0547630's inhibition of UppS and a structural rationale for its enhanced effect on UppS from Bacillus subtilis versus Staphylococcus aureus . We also describe the synthesis of a MAC-0547630 derivative (JPD447), show that it too can potentiate β-lactam antibiotics, and provide a structural rationale for its improved potentiation. Finally, we present an improved structural model of clomiphene's inhibition of UppS. Taken together, our data provide a foundation for structure-guided drug design of more potent UppS inhibitors in the future.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.
Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.
Department of Chemistry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada.
Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.
Michael G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada.
Centre for Catalysis Research and Innovation, University of Ottawa, 30 Marie-Curie Private, Ottawa, Ontario K1N 6N5, Canada.
Department of Chemistry and Biomolecular Sciences, University of Ottawa, 150 Louis-Pasteur Private, Ottawa, Ontario K1N 6N5, Canada.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.92 kDa 
• Atom Count: 2,235 
• Modeled Residue Count: 241 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoprenyl transferase	A	260	Bacillus subtilis	Mutation(s): 0  Gene Names: uppS, A3772_08985, B4122_2664, B4417_3501, BS16045_01759, ETA10_09020, ETK61_09295, GII79_08795, SC09_Contig19orf01203 EC: 2.5.1
UniProt
Find proteins for O31751 (Bacillus subtilis (strain 168)) Explore O31751  Go to UniProtKB:  O31751

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.212 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.539	α = 90
b = 59.539	β = 90
c = 161.798	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-08-04 
Deposition Author(s): Workman, S.D., Strynadka, N.C.J.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History  

• Version 1.0: 2021-08-04
  Type: Initial release
  
• Version 1.1: 2021-09-15
  Changes: Database references
• Version 1.2: 2021-10-06
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Refinement description