1OFP

CRYSTAL STRUCTURE OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE

PDB DOI: 10.2210/pdb1OFP/pdb

Classification: LYASE
Organism(s): Saccharomyces cerevisiae
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2003-04-17 Released: 2004-04-15
Deposition Author(s): Koenig, V., Pfeil, A., Heinrich, G., Braus, G.H., Schneider, T.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.260
R-Value Work: 0.205

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

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

PubMed: 15019786 Search on PubMed
DOI: 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.

Related Citations:

Evolution of Feedback-Inhibited Beta /Alpha Barrel Isoenzymes by Gene Duplication and a Single Mutation
Hartmann, M., Schneider, T., Pfeil, A., Heinrich, G., Lipscomb, W., Braus, G.
(2003) Proc Natl Acad Sci U S A 100: 862

Organizational Affiliation:

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE	A, B, C, D	370	Saccharomyces cerevisiae	Mutation(s): 0 EC: 4.1.2.15 (PDB Primary Data), 2.5.1.54 (UniProt)
UniProt
Find proteins for P32449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32449 Go to UniProtKB: P32449
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32449
Protein Feature View Expand
Reference Sequence