3WYJ | pdb_00003wyj

Structure of E. coli undecaprenyl diphosphate synthase in complex with BPH-789

• PDB DOI: https://doi.org/10.2210/pdb3WYJ/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-29 Released: 2015-02-04 
• Deposition Author(s): Gao, J., Ko, T.P., Huang, C.H., Oldfield, E., Guo, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.241 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.198 (DCC) 

Starting Model: experimental

Literature

Antibacterial drug leads: DNA and enzyme multitargeting.

Zhu, W., Wang, Y., Li, K., Gao, J., Huang, C.H., Chen, C.C., Ko, T.P., Zhang, Y., Guo, R.T., Oldfield, E.

(2015) J Med Chem 58: 1215-1227

• PubMed: 25574764 
• DOI: https://doi.org/10.1021/jm501449u
• Primary Citation Related Structures: 
  3WYI, 3WYJ, 4U82, 4U8A, 4U8B, 4U8C


• PubMed Abstract: 
  

  We report the results of an investigation of the activity of a series of amidine and bisamidine compounds against Staphylococcus aureus and Escherichia coli. The most active compounds bound to an AT-rich DNA dodecamer (CGCGAATTCGCG)2 and using DSC were found to increase the melting transition by up to 24 °C. Several compounds also inhibited undecaprenyl diphosphate synthase (UPPS) with IC50 values of 100-500 nM, and we found good correlations (R(2) = 0.89, S. aureus; R(2) = 0.79, E. coli) between experimental and predicted cell growth inhibition by using DNA ΔTm and UPPS IC50 experimental results together with one computed descriptor. We also solved the structures of three bisamidines binding to DNA as well as three UPPS structures. Overall, the results are of general interest in the context of the development of resistance-resistant antibiotics that involve multitargeting.

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Organizational Affiliation: 
• Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.

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)

Macromolecule Content 

• Total Structure Weight: 57.91 kDa 
• Atom Count: 3,988 
• Modeled Residue Count: 441 
• Deposited Residue Count: 506 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)	A, B	253	Escherichia coli K-12	Mutation(s): 0  Gene Names: b0174, ispU, JW0169, rth, uppS, yaeS EC: 2.5.1.31
UniProt
Find proteins for P60472 (Escherichia coli (strain K12)) Explore P60472  Go to UniProtKB:  P60472

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H78	C [auth A]	[1-oxidanyl-2-[3-[3-[[3-[[3-[3-(2-oxidanyl-2,2-diphosphono-ethyl)phenyl]phenyl]sulfamoyl]phenyl]sulfonylamino]phenyl]phenyl]-1-phosphono-ethyl]phosphonic acid C34 H36 N2 O18 P4 S2 UKSQFLAKPJZXNT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.241 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.198 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.712	α = 90
b = 68.995	β = 90
c = 108.885	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-02-04 
Deposition Author(s): Gao, J., Ko, T.P., Huang, C.H., Oldfield, E., Guo, R.T.

Revision History  

• Version 1.0: 2015-02-04
  Type: Initial release
  
• Version 1.1: 2022-08-24
  Changes: Database references, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Refinement description