6VO2

Crystal structure of Staphylococcus aureus ketol-acid reductoisomerase in complex with Mg, NADPH and inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

Starting Model: experimental
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Literature

Discovery, Synthesis and Evaluation of a Ketol-Acid Reductoisomerase Inhibitor.

Bayaraa, T.Kurz, J.L.Patel, K.M.Hussein, W.M.Bilyj, J.K.West, N.P.Schenk, G.McGeary, R.P.Guddat, L.W.

(2020) Chemistry 26: 8958-8968

  • DOI: https://doi.org/10.1002/chem.202000899
  • Primary Citation of Related Structures:  
    6VO2

  • PubMed Abstract: 

    Ketol-acid reductoisomerase (KARI), the second enzyme in the branched-chain amino acid biosynthesis pathway, is a potential drug target for bacterial infections including Mycobacterium tuberculosis. Here, we have screened the Medicines for Malaria Venture Pathogen Box against purified M. tuberculosis (Mt) KARI and identified two compounds that have K i values below 200 nm. In Mt cell susceptibility assays one of these compounds exhibited an IC 50 value of 0.8 μm. Co-crystallization of this compound, 3-((methylsulfonyl)methyl)-2H-benzo[b][1,4]oxazin-2-one (MMV553002), in complex with Staphylococcus aureus KARI, which has 56 % identity with Mt KARI, NADPH and Mg 2+ yielded a structure to 1.72 Å resolution. However, only a hydrolyzed product of the inhibitor (i.e. 3-(methylsulfonyl)-2-oxopropanic acid, missing the 2-aminophenol attachment) is observed in the active site. Surprisingly, Mt cell susceptibility assays showed that the 2-aminophenol product is largely responsible for the anti-TB activity of the parent compound. Thus, 3-(methylsulfonyl)-2-oxopropanic acid was identified as a potent KARI inhibitor that could be further explored as a potential biocidal agent and we have shown 2-aminophenol, as an anti-TB drug lead, especially given it has low toxicity against human cells. The study highlights that careful analysis of broad screening assays is required to correctly interpret cell-based activity data.


  • Organizational Affiliation

    School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ketol-acid reductoisomerase (NADP(+))
A, B
334Staphylococcus aureusMutation(s): 0 
Gene Names: ilvCDB727_12700E4U00_11130ERS072840_02559NCTC6133_02793NCTC7878_02786NCTC7988_02129
EC: 1.1.1.86
UniProt
Find proteins for Q2FWK4 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FWK4 
Go to UniProtKB:  Q2FWK4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FWK4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
R67 (Subject of Investigation/LOI)
Query on R67

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
3-(methylsulfonyl)-2-oxopropanoic acid
C4 H6 O5 S
KHOMRFGIBYBMCN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B],
H [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.039α = 90
b = 80.825β = 92.61
c = 66.803γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia114729

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references
  • Version 1.2: 2020-08-05
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description