Biology:DAHP synthase

Short description: Class of enzymes

3-deoxy-7-phosphoheptulonate synthase
Identifiers
EC number	2.5.1.54
CAS number	9026-94-2
Databases
IntEnz	IntEnz view
BRENDA	BRENDA entry
ExPASy	NiceZyme view
KEGG	KEGG entry
MetaCyc	metabolic pathway
PRIAM	profile
PDB structures	RCSB PDB PDBe PDBsum
Gene Ontology	AmiGO / QuickGO
Search PMC articles PubMed articles NCBI proteins

DAHP synthetase I domain
Structure of Aquifex aeolicus kdo8ps in complex with z-methyl-pep 2-dehydro-3-deoxyphosphooctonate aldolase.
Identifiers
Symbol	DAHP_synth_1
Pfam	PF00793
Pfam clan	CL0036
InterPro	IPR006218
SCOP2	51569 / SCOPe / SUPFAM
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

3-Deoxy-D-arabinoheptulosonate 7-phosphate (DAHP) synthase (EC 2.5.1.54) is the first enzyme in a series of metabolic reactions known as the shikimate pathway, which is responsible for the biosynthesis of the amino acids phenylalanine, tyrosine, and tryptophan. Since it is the first enzyme in the shikimate pathway, it controls the amount of carbon entering the pathway. Enzyme inhibition is the primary method of regulating the amount of carbon entering the pathway. Forms of this enzyme differ between organisms, but can be considered DAHP synthase based upon the reaction that is catalyzed by this enzyme.

In enzymology, a DAHP synthase (EC 2.5.1.54) is an enzyme that catalyzes the chemical reaction

phosphoenolpyruvate + D-erythrose 4-phosphate + H₂O [math]\displaystyle{ \rightleftharpoons }[/math] 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate + phosphate

The three substrates of this enzyme are phosphoenolpyruvate, D-erythrose 4-phosphate, and H₂O, whereas its two products are 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate and phosphate.

Nomenclature

This enzyme belongs to the family of transferases, to be specific those transferring aryl or alkyl groups other than methyl groups. The systematic name of this enzyme class is phosphoenolpyruvate:D-erythrose-4-phosphate C-(1-carboxyvinyl)transferase (phosphate-hydrolysing, 2-carboxy-2-oxoethyl-forming). Other names in common use include 2-dehydro-3-deoxy-phosphoheptonate aldolase, 2-keto-3-deoxy-D-arabino-heptonic acid 7-phosphate synthetase, 3-deoxy-D-arabino-2-heptulosonic acid 7-phosphate synthetase, 3-deoxy-D-arabino-heptolosonate-7-phosphate synthetase, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase, 7-phospho-2-keto-3-deoxy-D-arabino-heptonate D-erythrose-4-phosphate, lyase (pyruvate-phosphorylating), 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate, D-erythrose-4-phosphate lyase (pyruvate-phosphorylating), D-erythrose-4-phosphate-lyase, D-erythrose-4-phosphate-lyase (pyruvate-phosphorylating), DAH7-P synthase, DAHP synthase, DS-Co, DS-Mn, KDPH synthase, KDPH synthetase, deoxy-D-arabino-heptulosonate-7-phosphate synthetase, phospho-2-dehydro-3-deoxyheptonate aldolase, phospho-2-keto-3-deoxyheptanoate aldolase, phospho-2-keto-3-deoxyheptonate aldolase, phospho-2-keto-3-deoxyheptonic aldolase, and phospho-2-oxo-3-deoxyheptonate aldolase.

Biological function

The primary function of DAHP synthase is to catalyze the reaction of phosphoenolpyruvate and D-erythrose 4-phosphate to DAHP and phosphate. However, another biological function of the enzyme is to regulate the amount of carbon that enters the shikimate pathway. This is accomplished primarily through two different methods, feedback inhibition and transcriptional control. Feedback inhibition and transcriptional control are both mechanisms of regulating carbon in bacteria, but the only mechanism of regulation found in DAHP synthase found in plants is transcriptional control.

In Escherichia coli, a species of bacteria, DAHP synthase is found as three isoenzymes, each of which sensitive to one of the amino acids produced in the shikimate pathway. In a study of DAHP synthase sensitive to tyrosine in E. coli, it was determined that the enzyme is inhibited by tyrosine through noncompetitive inhibition with respect to phosphoenolpyruvate, the first substrate of the reaction catalyzed by DAHP synthase, while the enzyme is inhibited by tyrosine through competitive inhibition with respect to D-erythrose 4-phosphate, the second substrate of the reaction catalyzed by DAHP synthase when the concentration of tyrosine is above 10 μM. It was also determined that the enzyme is inhibited by inorganic phosphate through noncompetitive inhibition with respect to both substrates and inhibited by DAHP through competitive inhibition with respect to phosphoenolpyruvate and noncompetitive inhibition with respect to D-erythrose 4-phosphate. Studies of product inhibition have shown that phosphoenolpyruvate is the first substrate to bind to the enzyme complex, inorganic phosphate is the first product to dissociate from the enzyme complex. Thus the amount of carbon entering the shikimate pathway can be controlled by inhibiting DAHP synthase from catalyzing the reaction that forms DAHP.

Carbon flow into the shikimate pathway in plants is regulated by transcriptional control. This method is also found in bacteria, but feedback inhibition is more prevalent. In plants, as the plants progressed through the growth cycle, the activity of DAHP synthase changed.

Catalytic activity

Metal ions are required in order for DAHP synthase to catalyze reactions. In DAHP synthase, it has been shown that binding site contains patterns of cysteine and histidine residues bound to metal ions in a Cys-X-X-His fashion.

It has been shown that, in general, DAHP synthases require a bivalent metal ion cofactor in order for the enzyme to function properly. Metal ions that can function as cofactors include Mn²⁺, Fe²⁺, Co²⁺, Zn²⁺, Cu²⁺, and Ca²⁺. Studies have suggested that one metal ion bonds to each monomer of DAHP synthase.

The reaction catalyzed by DAHP synthase is shown below.

This is the reaction catalyzed by DAHP synthase.

Structure

This image shows the quaternary structure of DAHP synthase.

This image shows the quaternary structure of DAHP synthase, with the secondary and tertiary structures illustrated in cartoon form.

The quaternary structure of DAHP synthase consists of two tightly bound dimers, which means that DAHP synthase is a tetramer.

To the right is an image of DAHP synthase that shows the quaternary structure of DAHP synthase. This image shows that DAHP synthase consists of two tightly bound dimers. Each of the monomer chains is colored differently.

Below the first image to the right is an image of DAHP synthase that also shows quaternary structure, however this image is in a cartoon view. This view also shows each of the four monomers colored differently. In addition, this view can also be used to show secondary and tertiary structures. As shown, two of the monomers have beta sheets that interact on one side of the enzyme, while the other two monomers have beta sheets that interact on the opposite side.

Structural studies

As of late 2007, four structures have been solved for this class of enzymes, with PDB accession codes 1RZM, 1VR6, 1VS1, and 2B7O.

Class-II DAHP synthetase family
Identifiers
Symbol	DAHP_synth_2
Pfam	PF01474
Pfam clan	CL0036
InterPro	IPR002480
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

Further reading

• "2-Keto-3-deoxy-D-arabo-heptonic acid 7-phosphate synthetase". The Journal of Biological Chemistry 234 (4): 716–22. April 1959. PMID 13654249. 
• "Characterization of a new feedback-resistant 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroF of Escherichia coli". FEMS Microbiology Letters 202 (1): 145–8. August 2001. doi:10.1111/j.1574-6968.2001.tb10795.x. PMID 11506923. 
• "Crystallization and preliminary X-ray analysis of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (tyrosine inhibitable) from Saccharomyces cerevisiae". Acta Crystallographica D 55 (Pt 9): 1586–8. September 1999. doi:10.1107/S0907444999007830. PMID 10489454.