double complex of the tyrosine sensitive DAHP Synthase from S. cerevisiae with Co2+, PEP and the E4P analogoue G3P

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.127 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Substrate and Metal Complexes of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase from Saccharomyces Cerevisiae Provide New Insights Into the Catalytic Mechanism

Koenig, V.Pfeil, A.Braus, G.H.Schneider, T.R.

(2004) J Mol Biol 337: 675

  • DOI: https://doi.org/10.1016/j.jmb.2004.01.055
  • Primary Citation of Related Structures:  
    1OAB, 1OF8, 1OFA, 1OFB, 1OFO, 1OFP, 1OFQ, 1OFR

  • PubMed Abstract: 

    3-Deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthases are metal-dependent enzymes that catalyse the first committed step in the biosynthesis of aromatic amino acids in microorganisms and plants, the condensation of 2-phophoenolpyruvate (PEP) and d-erythrose 4-phosphate (E4P) to DAHP. The DAHP synthases are possible targets for fungicides and represent a model system for feedback regulation in metabolic pathways. To gain further insight into the role of the metal ion and the catalytic mechanism in general, the crystal structures of several complexes between the tyrosine-regulated form of DAHP synthase from Saccharomyces cerevisiae and different metal ions and ligands have been determined. The crystal structures provide evidence that the simultaneous presence of a metal ion and PEP result in an ordering of the protein into a conformation that is prepared for binding the second substrate E4P. The site and binding mode of E4P was derived from the 1.5A resolution crystal structure of DAHP synthase in complex with PEP, Co2+, and the E4P analogue glyceraldehyde 3-phosphate. Our data suggest that the oxygen atom of the reactive carbonyl group of E4P replaces a water molecule coordinated to the metal ion, strongly favouring a reaction mechanism where the initial step is a nucleophilic attack of the double bond of PEP on the metal-activated carbonyl group of E4P. Mutagenesis experiments substituting specific amino acids coordinating PEP, the divalent metal ion or the second substrate E4P, result in stable but inactive Aro4p-derivatives and show the importance of these residues for the catalytic mechanism.

  • Organizational Affiliation

    Department of Structural Chemistry, University of Göttingen, Tammannstr. 4, D-37077 Göttingen, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
370Saccharomyces cerevisiaeMutation(s): 0 
EC: (PDB Primary Data), (UniProt)
Find proteins for P32449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32449 
Go to UniProtKB:  P32449
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32449
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on G3P

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
C3 H9 O6 P
Query on PEP

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
C3 H5 O6 P
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth B]
C3 H8 O3
Query on CO

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.127 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 196.462α = 90
b = 50.788β = 106.39
c = 64.7γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-08
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2019-05-22
    Changes: Data collection, Other, Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection