5ELZ

Staphylococcus aureus Type II pantothenate kinase in complex with a pantothenate analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of Potent Pantothenamide Inhibitors of Staphylococcus aureus Pantothenate Kinase through a Minimal SAR Study: Inhibition Is Due to Trapping of the Product.

Hughes, S.J.Barnard, L.Mottaghi, K.Tempel, W.Antoshchenko, T.Hong, B.S.Allali-Hassani, A.Smil, D.Vedadi, M.Strauss, E.Park, H.W.

(2016) ACS Infect Dis 2: 627-641

  • DOI: 10.1021/acsinfecdis.6b00090
  • Primary Citation of Related Structures:  
    5JIC, 5ELZ, 4M7X, 4M7Y

  • PubMed Abstract: 
  • The potent antistaphylococcal activity of N-substituted pantothenamides (PanAms) has been shown to at least partially be due to the inhibition of Staphylococcus aureus's atypical type II pantothenate kinase (SaPanK II ), the first enzyme of coenzyme A biosynthesis ...

    The potent antistaphylococcal activity of N-substituted pantothenamides (PanAms) has been shown to at least partially be due to the inhibition of Staphylococcus aureus's atypical type II pantothenate kinase (SaPanK II ), the first enzyme of coenzyme A biosynthesis. This mechanism of action follows from SaPanK II having a binding mode for PanAms that is distinct from those of other PanKs. To dissect the molecular interactions responsible for PanAm inhibitory activity, we conducted a mini SAR study in tandem with the cocrystallization of SaPanK II with two classic PanAms (N5-Pan and N7-Pan), culminating in the synthesis and characterization of two new PanAms, N-Pip-PanAm and MeO-N5-PanAm. The cocrystal structures showed that all of the PanAms are phosphorylated by SaPanK II but remain bound at the active site; this occurs primarily through interactions with Tyr240' and Thr172'. Kinetic analysis showed a strong correlation between k cat (slow PanAm turnover) and IC 50 (inhibition of pantothenate phosphorylation) values, suggesting that SaPanK II inhibition occurs via a delay in product release. In-depth analysis of the PanAm-bound structures showed that the capacity for accepting a hydrogen bond from the amide of Thr172' was a stronger determinant for PanAm potency than the capacity to π-stack with Tyr240'. The two new PanAms, N-Pip-PanAm and MeO-N5-PanAm, effectively combine both hydrogen bonding and hydrophobic interactions, resulting in the most potent SaPanK II inhibition described to date. Taken together, our results are consistent with an inhibition mechanism wherein PanAms act as SaPanK II substrates that remain bound upon phosphorylation. The phospho-PanAm-SaPanK II interactions described herein may help future antistaphylococcal drug development.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Tulane School of Medicine , New Orleans, Louisiana 70112, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Type II pantothenate kinase A273Staphylococcus aureus subsp. aureus MW2Mutation(s): 0 
Gene Names: coaWMW2054
EC: 2.7.1.33
Find proteins for Q2FWC7 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FWC7 
Go to UniProtKB:  Q2FWC7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3V9
Query on 3V9

Download Ideal Coordinates CCD File 
A
N-(1,3-benzodioxol-5-ylmethyl)-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide
C17 H25 N2 O9 P
BHYGBZMPSWVNBD-HNNXBMFYSA-N
 Ligand Interaction
ADP
Query on ADP

Download Ideal Coordinates CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
A
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.967α = 90
b = 136.771β = 90
c = 73.87γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
SCALAdata scaling
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-11-09
    Changes: Database references