4YRD

Crystal structure of CapF with inhibitor 3-isopropenyl-tropolone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery and characterization of natural tropolones as inhibitors of the antibacterial target CapF from Staphylococcus aureus.

Nakano, K.Chigira, T.Miyafusa, T.Nagatoishi, S.Caaveiro, J.M.Tsumoto, K.

(2015) Sci Rep 5: 15337-15337

  • DOI: 10.1038/srep15337

  • PubMed Abstract: 
  • The rapid spread of antibiotic-resistance among pathogenic bacteria poses a serious risk for public health. The search for novel therapeutic strategies and antimicrobial compounds is needed to ameliorate this menace. The bifunctional metalloenzyme Ca ...

    The rapid spread of antibiotic-resistance among pathogenic bacteria poses a serious risk for public health. The search for novel therapeutic strategies and antimicrobial compounds is needed to ameliorate this menace. The bifunctional metalloenzyme CapF is an antibacterial target produced by certain pathogenic bacteria essential in the biosynthetic route of capsular polysaccharide, a mucous layer on the surface of bacterium that facilitates immune evasion and infection. We report the first inhibitor of CapF from Staphylococcus aureus, which was identified by employing fragment-based methodologies. The hit compound 3-isopropenyl-tropolone inhibits the first reaction catalyzed by CapF, disrupting the synthesis of a key precursor of capsular polysaccharide. Isothermal titration calorimetry demonstrates that 3-isopropenyl-tropolone binds tightly (KD = 27 ± 7 μM) to the cupin domain of CapF. In addition, the crystal structure of the enzyme-inhibitor complex shows that the compound engages the essential Zn(2+) ion necessary for the first reaction catalyzed by the enzyme, explaining its inhibitory effect. Moreover, the tropolone compound alters the coordination sphere of the metal, leading to the overall destabilization of the enzyme. We propose 3-isopropenyl-tropolone as a precursor to develop stronger inhibitors for this family of enzymes to impair the synthesis of capsular polysaccharide in Staphylococcus aureus.


    Organizational Affiliation

    Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsular polysaccharide synthesis enzyme Cap5F
A, B
359Staphylococcus aureus (strain Mu50 / ATCC 700699)Mutation(s): 1 
Gene Names: capF
Find proteins for A0A0H3JP37 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Go to UniProtKB:  A0A0H3JP37
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3IT
Query on 3IT

Download SDF File 
Download CCD File 
A, B
2-hydroxy-3-(prop-1-en-2-yl)cyclohepta-2,4,6-trien-1-one
3-isopropenyl-tropolone
C10 H10 O2
AYEFINNLGCCCNK-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3ITKd: 27000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.229 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 78.580α = 90.00
b = 194.620β = 90.00
c = 158.360γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-11-04
    Type: Database references