4PZV

Crystal structure of Francisella tularensis HPPK-DHPS in complex with bisubstrate analog HPPK inhibitor J1D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.704 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural enzymology and inhibition of the bi-functional folate pathway enzyme HPPK-DHPS from the biowarfare agent Francisella tularensis.

Shaw, G.X.Li, Y.Shi, G.Wu, Y.Cherry, S.Needle, D.Zhang, D.Tropea, J.E.Waugh, D.S.Yan, H.Ji, X.

(2014) Febs J. 281: 4123-4137

  • DOI: 10.1111/febs.12896

  • PubMed Abstract: 
  • Two valid targets for antibiotic development, 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) and dihydropteroate synthase (DHPS), catalyze consecutive reactions in folate biosynthesis. In Francisella tularensis (Ft), these two activities ...

    Two valid targets for antibiotic development, 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) and dihydropteroate synthase (DHPS), catalyze consecutive reactions in folate biosynthesis. In Francisella tularensis (Ft), these two activities are contained in a single protein, FtHPPK-DHPS. Although Pemble et al. (PLoS One 5, e14165) determined the structure of FtHPPK-DHPS, they were unable to measure the kinetic parameters of the enzyme. In this study, we elucidated the binding and inhibitory activities of two HPPK inhibitors (HP-18 and HP-26) against FtHPPK-DHPS, determined the structure of FtHPPK-DHPS in complex with HP-26, and measured the kinetic parameters for the dual enzymatic activities of FtHPPK-DHPS. The biochemical analyses showed that HP-18 and HP-26 have significant isozyme selectivity, and that FtHPPK-DHPS is unique in that the catalytic efficiency of its DHPS activity is only 1/260,000 of that of Escherichia coli DHPS. Sequence and structural analyses suggest that HP-26 is an excellent lead for developing therapeutic agents for tularemia, and that the very low DHPS activity is due, at least in part, to the lack of a key residue that interacts with the substrate p-aminobenzoic acid (pABA). A BLAST search of the genomes of ten F. tularensis strains indicated that the bacterium contains a single FtHPPK-DHPS. The marginal DHPS activity and the single copy existence of FtHPPK-DHPS in F. tularensis make this bacterium more vulnerable to DHPS inhibitors. Current sulfa drugs are ineffective against tularemia; new inhibitors targeting the unique pABA-binding pocket may be effective and less subject to resistance because any mutations introducing resistance may make the marginal DHPS activity unable to support the growth of F. tularensis.


    Related Citations: 
    • Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: New design with improved properties.
      Shi, G.,Shaw, G.,Liang, Y.H.,Subburaman, P.,Li, Y.,Wu, Y.,Yan, H.,Ji, X.
      (2012) Bioorg.Med.Chem. 20: 47
    • Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: synthesis and biochemical and crystallographic studies.
      Shi, G.,Blaszczyk, J.,Ji, X.,Yan, H.
      (2001) J.Med.Chem. 44: 1364
    • Bisubstrate analog inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: new lead exhibits a distinct binding mode.
      Shi, G.,Shaw, G.,Li, Y.,Wu, Y.,Yan, H.,Ji, X.
      (2012) Bioorg.Med.Chem. 20: 4303


    Organizational Affiliation

    Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase/dihydropteroate synthase
A
421Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)Mutation(s): 0 
Gene Names: folK
EC: 2.5.1.15, 2.7.6.3
Find proteins for Q5NGA7 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4))
Go to UniProtKB:  Q5NGA7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J1D
Query on J1D

Download SDF File 
Download CCD File 
A
5'-{[2-({N-[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)carbonyl]glycyl}amino)ethyl]sulfonyl}-5'-deoxyadenosine
C23 H30 N12 O8 S
QCWCABDSXQYDST-GWKRVTOESA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
J1DKd: 2000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.704 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.945α = 90.00
b = 74.434β = 93.20
c = 69.758γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data reduction
PHENIXphasing
SCALEPACKdata scaling
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-10-01
    Type: Database references