The red numbers in the chart represent enzymes that catalyze those steps; the blue arrows are transformations that we will not discuss explicitly.

Things to think about:

• How do we know what biosynthetic pathways are?

• How are biosynthetic pathways regulated?

• How does Mother Nature's way relate to the organic chemists' way?

• How do biosynthetic pathways evolve?

We'll take a look at a few of the enzymes of this path in enough detail to work out mechanisms for their catalysis.

To get us started, here are the first few steps and the enzymes that catalyze the steps:

Most organisms express multiple isozymes of DAHP synthase

• The reaction catalyzed is an aldol condensation

• Each isozyme is inhibited by a different aromatic amino acid

• For example, E. coli expresses three, inhibited by phenylalanine, tyrosine, and tryptophan

• A metal ion, Zn⁺⁺, Cu⁺⁺, or Fe⁺⁺ is necessary

• The active form is a tight dimer, as shown, each chain an (ba)₈ barrel

DAHP Synthetase (E. coli; 1kfl), Phe Bound	DAHP Synthetase (Yeast; 1of6), Tyrosine Bound

Substantial similarity exists among the enzymes from different species

• The two enzymes above have 54% identity and 67% similarity of residues

• They superpose with rmsd of 0.57 A!

Sequence Alignment of 1kfl and 1of6	Structure Alignment of 1kfl and 1of6

The implication is that this is a very old biosynthetic pathway.

DQ synthetase also is a dimer in the biologically active state, requiring a Zn⁺⁺ (purple) and an NAD⁺ in each unit to function.

It catalyzes a multi-step reaction sequence:

• alcohol oxidation

• phosphate b-elimination

• carbonyl reduction

• ring opening

• intramolecular aldol condensation

Proposed Mechanism of Dehydroquinate Synthetase

What was that about enzymes catalyzing single, specific reactions?

Dehydroquinate Synthetase, with NAD+and Inhibitor	Catalytic Site of Dehydroquinate Synthetase