5CKS

DAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase in complex with DAHP Oxime.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1181 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Potent Inhibition of 3-Deoxy-d-arabinoheptulosonate-7-phosphate (DAHP) Synthase by DAHP Oxime, a Phosphate Group Mimic.

Balachandran, N.Heimhalt, M.Liuni, P.To, F.Wilson, D.J.Junop, M.S.Berti, P.J.

(2016) Biochemistry 55: 6617-6629

  • DOI: 10.1021/acs.biochem.6b00930

  • PubMed Abstract: 
  • 3-Deoxy-d-arabinoheptulosonate-7-phosphate (DAHP) synthase catalyzes the first step in the shikimate pathway. It catalyzes an aldol-like reaction of phosphoenolpyruvate (PEP) with erythrose 4-phosphate (E4P) to form DAHP. The kinetic mechanism was ra ...

    3-Deoxy-d-arabinoheptulosonate-7-phosphate (DAHP) synthase catalyzes the first step in the shikimate pathway. It catalyzes an aldol-like reaction of phosphoenolpyruvate (PEP) with erythrose 4-phosphate (E4P) to form DAHP. The kinetic mechanism was rapid equilibrium sequential ordered ter ter, with the essential divalent metal ion, Mn2+, binding first, followed by PEP and E4P. DAHP oxime, in which an oxime group replaces the keto oxygen, was a potent inhibitor, with Ki = 1.5 ± 0.4 μM, though with residual activity at high inhibitor concentrations. It displayed slow-binding inhibition with a residence time, tR, of 83 min. The crystal structure revealed that the oxime functional group, combined with two crystallographic waters, bound at the same location in the catalytic center as the phosphate group of the tetrahedral intermediate. DAHP synthase has a dimer-of-dimers homotetrameric structure, and DAHP oxime bound to only one subunit of each tight dimer. Inhibitor binding was competitive with respect to all three substrates in the subunits to which it bound. DAHP oxime did not overlap with the metal binding site, so the cause of their mutually exclusive binding was not clear. Similarly, there was no obvious structural reason for inhibitor binding in only two subunits; however, changes in global hydrogen/deuterium exchange showed large scale changes in protein dynamics upon inhibitor binding. The kcat value for the residual activity at high inhibitor concentrations was 3-fold lower, and the apparent KM,E4P value decreased at least 10-fold. This positive cooperativity of binding between DAHP oxime in subunits B and C, and E4P in subunits A and D appears to be the dominant cause for incomplete inhibition at high inhibitor concentrations. In spite of its lack of obvious structural similarity to phosphate, the oxime and crystallographic waters acted as a small, neutral phosphate mimic.


    Organizational Affiliation

    Department of Chemistry, York University , Toronto, Ontario M3J 1P3, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive
A, B, C, D
351Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: aroG
EC: 2.5.1.54
Find proteins for P0AB91 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AB91
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAL
Query on GAL

Download SDF File 
Download CCD File 
A, B, C
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
52L
Query on 52L

Download SDF File 
Download CCD File 
B, C
DAHP Oxime
(2E,4R,5S,6R)-4,5,6-trihydroxy-2-(hydroxyimino)-7-(phosphonooxy)heptanoic acid
C7 H14 N O10 P
KFGHSGKOOHKNEU-WVMCLEPLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1181 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 209.990α = 90.00
b = 53.360β = 115.44
c = 150.655γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanadaMOP-64422
Canadian Institutes of Health ResearchCanadaMOP-89903

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2017-01-04
    Type: Database references
  • Version 1.2: 2017-11-01
    Type: Author supporting evidence