PDBsum entry 1ofq

Lyase

PDB id: 1ofq

Contents

Protein chains

343 a.a. *

Metals

_MN ×4

Waters ×285

* Residue conservation analysis

PDB id:

1ofq

Name:

Lyase

Title:

Crystal structure of the tyrosine-regulated 3-deoxy-d-arabino- heptulosonate-7-phosphate synthase from saccharomyces cerevisiae in complex with manganese(ii)

Structure:

Phospho-2-dehydro-3-deoxyheptonate aldolase. Chain: a, b, c, d. Synonym: phospho-2-keto-3-deoxyheptonate aldolase dahp synthetase, 3- deoxy-d-arabino-heptulosonate 7-phosphate synthase, phospho-2- dehydro- 3-deoxyheptonate aldolase. Engineered: yes. Other_details: metal ion\: manganese(ii)

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: rh1326. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932

Biol. unit:

Dimer (from PDB file)

Resolution:

2.70Å R-factor: 0.221 R-free: 0.245

Authors:

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

Key ref:

V.König et al. (2004). Substrate and metal complexes of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Saccharomyces cerevisiae provide new insights into the catalytic mechanism. J Mol Biol, 337, 675-690. PubMed id: 15019786 DOI: 10.1016/j.jmb.2004.01.055

Date:

17-Apr-03 Release date: 15-Apr-04

Protein chains

P32449  (AROG_YEAST) -  Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 370 a.a.

Struc: 343 a.a.

Enzyme reactions

• Enzyme class: E.C.2.5.1.54 - 3-deoxy-7-phosphoheptulonate synthase.
• Pathway: Shikimate and Chorismate Biosynthesis
• Reaction: D-erythrose 4-phosphate + phosphoenolpyruvate + H2O = 7-phospho-2- dehydro-3-deoxy-D-arabino-heptonate + phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2004.01.055

J Mol Biol 337:675-690 (2004)

PubMed id: 15019786

Substrate and metal complexes of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Saccharomyces cerevisiae provide new insights into the catalytic mechanism.

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

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.

Selected figure(s)

Figure 3.
Figure 3. (a) Topology plot of DAHPS. The b-strands and a-helices belonging to the canonical ba-barrel are shown in light blue and dark blue, respectively; non-canonical modules are shown in cyan. Regions of the structure that were found to be flexible or disordered in any of the crystal forms are marked by a grey background. The location of residues interacting with PEP, G3P, and the metal is indicated using different flags (red for PEP, yellow for G3P, grey for metal). (b) Schematic view of the crystal structure of DAHPS in complex with PEP (red), G3P (yellow), and Co2+ (grey) with phosphorus atoms shown in magenta. (c) The same as (b) but the view is towards the C-terminal face of the barrel.

Figure 8.
Figure 8. Stereoview of the active site in the DAHPS·Co2+·PEP·G3P-complex showing the water molecules on the re-side of PEP in green. In this view, the si-side of PEP is on top of PEP, the re-side on the bottom.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 337, 675-690) copyright 2004.

Figures were selected by an automated process.