8ENI | pdb_00008eni

Crystal structure of Staphylococcus aureus biotin protein ligase in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8ENI/pdb

• Classification: LIGASE/LIGASE INHIBITOR
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-09-30 Released: 2022-11-30 
• Deposition Author(s): Wilce, M.C.J., Cini, D.A.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.236 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Halogenation of Biotin Protein Ligase Inhibitors Improves Whole Cell Activity against Staphylococcus aureus.

Paparella, A.S., Lee, K.J., Hayes, A.J., Feng, J., Feng, Z., Cini, D., Deshmukh, S., Booker, G.W., Wilce, M.C.J., Polyak, S.W., Abell, A.D.

(2018) ACS Infect Dis 4: 175-184

• PubMed: 29131575 
• DOI: https://doi.org/10.1021/acsinfecdis.7b00134
• Primary Citation Related Structures: 
  6APW, 6AQQ, 8ENI


• PubMed Abstract: 
  

  We report the synthesis and evaluation of 5-halogenated-1,2,3-triazoles as inhibitors of biotin protein ligase from Staphylococcus aureus. The halogenated compounds exhibit significantly improved antibacterial activity over their nonhalogenated counterparts. Importantly, the 5-fluoro-1,2,3-triazole compound 4c displays antibacterial activity against S. aureus ATCC49775 with a minimum inhibitory concentration (MIC) of 8 μg/mL.

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Organizational Affiliation: 
• Department of Molecular and Cellular Biology, University of Adelaide , North Tce, Adelaide, South Australia 5005, Australia.
Department of Chemistry, University of Adelaide , North Tce, Adelaide, South Australia 5005, Australia.
Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide , North Tce, Adelaide, South Australia 5005, Australia.
School of Biomedical Science, Monash University , Wellington Road, Clayton, Victoria 3800, Australia.

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: SAXS

Macromolecule Content 

• Total Structure Weight: 38.52 kDa 
• Atom Count: 2,696 
• Modeled Residue Count: 321 
• Deposited Residue Count: 329 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional ligase/repressor BirA	A	329	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: birA, SAV1456 EC: 6.3.4.15
UniProt
Find proteins for A0A0H3JRH8 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3JRH8  Go to UniProtKB:  A0A0H3JRH8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WNE (Subject of Investigation/LOI)	B [auth A]	3-[4-(5-fluoro-4-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentyl}-1H-1,2,3-triazol-1-yl)butyl]-5-methyl-1,3-benzoxazol-2(3H)-one C24 H31 F N6 O3 S DLFQUZRTJJWUQY-YYWHXJBOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.236 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.24	α = 90
b = 94.24	β = 90
c = 131.19	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-30 
Deposition Author(s): Wilce, M.C.J., Cini, D.A.

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Funding Organization	Location	Grant Number
Other government		--

Revision History  

• Version 1.0: 2022-11-30
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description