5H9D

Crystal structure of Heptaprenyl Diphosphate Synthase from Staphylococcus aureus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.243 

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Literature

Structure, Function, and Inhibition of Staphylococcus aureus Heptaprenyl Diphosphate Synthase

Desai, J., Liu, Y.L., Wei, H., Liu, W., Ko, T.P., Guo, R.T., Oldfield, E.

(2016) ChemMedChem 11: 1915-1923

  • DOI: 10.1002/cmdc.201600311
  • Primary Citation of Related Structures:  
    5H9D

  • PubMed Abstract: 

    • We report the first structure of heptaprenyl diphosphate synthase from Staphylococcus aureus (SaHepPPS), together with an investigation of its mechanism of action and inhibition. The protein is involved in the formation of menaquinone, a key electron transporter in many bacteria, including pathogens ...

    We report the first structure of heptaprenyl diphosphate synthase from Staphylococcus aureus (SaHepPPS), together with an investigation of its mechanism of action and inhibition. The protein is involved in the formation of menaquinone, a key electron transporter in many bacteria, including pathogens. SaHepPPS consists of a "catalytic " subunit (SaHepPPS-2) having two "DDXXD" motifs and a "regulatory" subunit (SaHepPPS-1) that lacks these motifs. High concentrations of the substrates, isopentenyl diphosphate and farnesyl diphosphate, inhibit the enzyme, which is also potently inhibited by bisphosphonates. The most active inhibitors (Ki ∼200 nm) were N-alkyl analogues of zoledronate containing ∼C6 alkyl side chains. They were modestly active against S. aureus cell growth, and growth inhibition was partially "rescued" by the addition of menaquinone-7. Because SaHepPPS is essential for S. aureus cell growth, its structure is of interest in the context of the development of menaquinone biosynthesis inhibitors as potential antibiotic leads.

    Organizational Affiliation: 

    Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Matthews Avenue, Urbana, IL, 61801, USA. eo@chad.scs.uiuc.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Farnesyl pyrophosphate synthetaseA, B319Staphylococcus aureusMutation(s): 0 
Gene Names: 
EC: 2.5.1.1 (PDB Primary Data), 2.5.1.30 (PDB Primary Data)
UniProt
Find proteins for Q2FYG6 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FYG6 
Go to UniProtKB:  Q2FYG6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FYG6
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1 family proteinC, D190Staphylococcus aureusMutation(s): 0 
Gene Names: 
UniProt
Find proteins for W8TTD5 (Staphylococcus aureus)
Explore W8TTD5 
Go to UniProtKB:  W8TTD5
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UniProt GroupW8TTD5
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
C-terminal peptide from Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1 family proteinE [auth K],
F [auth L]		17Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for Q2FYG4 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FYG4 
Go to UniProtKB:  Q2FYG4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FYG4
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.243 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.394α = 90
b = 137.642β = 90
c = 144.05γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-05-31
    Changes: Database references