3V7R

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Selective inhibition of biotin protein ligase from Staphylococcus aureus.

Soares da Costa, T.P., Tieu, W., Yap, M.Y., Pendini, N.R., Polyak, S.W., Sejer Pedersen, D., Morona, R., Turnidge, J.D., Wallace, J.C., Wilce, M.C., Booker, G.W., Abell, A.D.

(2012) J Biol Chem 287: 17823-17832

  • DOI: 10.1074/jbc.M112.356576
  • Primary Citation of Related Structures:  
    3V7R, 3V7S, 3V7C, 3V8J, 3V8K, 3V8L, 4DQ2

  • PubMed Abstract: 

    • There is a well documented need to replenish the antibiotic pipeline with new agents to combat the rise of drug resistant bacteria. One strategy to combat resistance is to discover new chemical classes immune to current resistance mechanisms that inhibit essential metabolic enzymes ...

    There is a well documented need to replenish the antibiotic pipeline with new agents to combat the rise of drug resistant bacteria. One strategy to combat resistance is to discover new chemical classes immune to current resistance mechanisms that inhibit essential metabolic enzymes. Many of the obvious drug targets that have no homologous isozyme in the human host have now been investigated. Bacterial drug targets that have a closely related human homologue represent a new frontier in antibiotic discovery. However, to avoid potential toxicity to the host, these inhibitors must have very high selectivity for the bacterial enzyme over the human homolog. We have demonstrated that the essential enzyme biotin protein ligase (BPL) from the clinically important pathogen Staphylococcus aureus could be selectively inhibited. Linking biotin to adenosine via a 1,2,3 triazole yielded the first BPL inhibitor selective for S. aureus BPL over the human equivalent. The synthesis of new biotin 1,2,3-triazole analogues using click chemistry yielded our most potent structure (K(i) 90 nM) with a >1100-fold selectivity for the S. aureus BPL over the human homologue. X-ray crystallography confirmed the mechanism of inhibitor binding. Importantly, the inhibitor showed cytotoxicity against S. aureus but not cultured mammalian cells. The biotin 1,2,3-triazole provides a novel pharmacophore for future medicinal chemistry programs to develop this new antibiotic class.

    Organizational Affiliation: 

    School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Biotin ligaseA329Staphylococcus aureus A9781Mutation(s): 0 
Gene Names: SAOG_00031
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
32G
Query on 32G
Download Ideal Coordinates CCD File 
 B [auth A](3aS,4S,6aR)-4-(5-{1-[4-(6-amino-9H-purin-9-yl)butyl]-1H-1,2,3-triazol-4-yl}pentyl)tetrahydro-1H-thieno[3,4-d]imidazol-2(3H)-one
C21 H30 N10 O S
GCOZLSRXMOWRSO-ULQDDVLXSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
32GKi:  660   nM  BindingDB
32GIC50:  4000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.6α = 90
b = 94.6β = 90
c = 130.68γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references