6APW

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

• PDB DOI: https://doi.org/10.2210/pdb6APW/pdb

• Classification: LIGASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-08-18 Released: 2018-02-07 
• Deposition Author(s): Cini, D.A., Wilce, M.C.J.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.228 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

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 of 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.

---

Organizational Affiliation: 

Department of Molecular and Cellular Biology, University of Adelaide , North Tce, Adelaide, South Australia 5005, Australia.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 38.43 kDa 
• Atom Count: 2,649 
• Modelled Residue Count: 322 
• 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	Mutation(s): 0  Gene Names: birA, BER48_001399, SAMEA2236422_00088, SAMEA2236459_00088, SAMEA2384800_00088, SAMEA2384856_00382, SAMEA2445640_00088 EC: 6.3.4.15

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTV	B [auth A]	4-[(4-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentyl}-1H-1,2,3-triazol-1-yl)methyl]benzoic acid C20 H25 N5 O3 S WFMFNVSBAHDHPE-BZSNNMDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.228 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.454	α = 90
b = 94.454	β = 90
c = 130.978	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-02-07 
Deposition Author(s): Cini, D.A., Wilce, M.C.J.

---

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History  

• Version 1.0: 2018-02-07
  Type: Initial release
  
• Version 1.1: 2018-02-14
  Changes: Author supporting evidence
• Version 1.2: 2018-02-21
  Changes: Database references
• Version 1.3: 2020-01-08
  Changes: Author supporting evidence
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references