Rhea - reaction knowledgebase

Enzymes

UniProtKB ^help_outline	48,174 proteins
Enzyme class ^help_outline	EC 2.5.1.54 3-deoxy-7-phosphoheptulonate synthase
GO Molecular Function ^help_outline	GO:0003849 3-deoxy-7-phosphoheptulonate synthase activity

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Name ^help_outline D-erythrose 4-phosphate Identifier CHEBI:16897 (Beilstein: 9129751) ^help_outline Charge -2 Formula C4H7O7P InChIKey^help_outline NGHMDNPXVRFFGS-IUYQGCFVSA-L SMILES^help_outline [H]C(=O)[C@H](O)[C@H](O)COP([O-])([O-])=O 2D coordinates Mol file for the small molecule Search links Involved in 12 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline phosphoenolpyruvate Identifier CHEBI:58702 (Beilstein: 3951723) ^help_outline Charge -3 Formula C3H2O6P InChIKey^help_outline DTBNBXWJWCWCIK-UHFFFAOYSA-K SMILES^help_outline [O-]C(=O)C(=C)OP([O-])([O-])=O 2D coordinates Mol file for the small molecule Search links Involved in 40 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline H₂O Identifier CHEBI:15377 (CAS: 7732-18-5) ^help_outline Charge 0 Formula H2O InChIKey^help_outline XLYOFNOQVPJJNP-UHFFFAOYSA-N SMILES^help_outline [H]O[H] 2D coordinates Mol file for the small molecule Search links Involved in 6,418 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate Identifier CHEBI:58394 Charge -3 Formula C7H10O10P InChIKey^help_outline PJWIPEXIFFQAQZ-PUFIMZNGSA-K SMILES^help_outline O[C@H](COP([O-])([O-])=O)[C@@H](O)[C@H](O)CC(=O)C([O-])=O 2D coordinates Mol file for the small molecule Search links Involved in 2 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline phosphate Identifier CHEBI:43474 Charge -2 Formula HO4P InChIKey^help_outline NBIIXXVUZAFLBC-UHFFFAOYSA-L SMILES^help_outline OP([O-])([O-])=O 2D coordinates Mol file for the small molecule Search links Involved in 1,024 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule

Cross-references

	RHEA:14717	RHEA:14718	RHEA:14719	RHEA:14720
Reaction direction	undefined	left-to-right	right-to-left	bidirectional
UniProtKB ^help_outline	48,174 proteins	2 proteins
EC numbers ^help_outline	2.5.1.54
Gene Ontology ^help_outline	GO:0003849
KEGG ^help_outline				R01826
MetaCyc ^help_outline				DAHPSYN-RXN
EcoCyc ^help_outline				DAHPSYN-RXN

Publications

Evolution of feedback-inhibited beta/alpha barrel isoenzymes by gene duplication and a single mutation.

Hartmann M., Schneider T.R., Pfeil A., Heinrich G., Lipscomb W.N., Braus G.H.

The betaalpha barrel is the common protein fold of numerous enzymes and was proposed recently to be the result of gene duplication and fusion of an ancient half-barrel. The initial enzyme of shikimate biosynthesis possesses the additional feature of feedback regulation. The crystal structure and k ... >> More

The betaalpha barrel is the common protein fold of numerous enzymes and was proposed recently to be the result of gene duplication and fusion of an ancient half-barrel. The initial enzyme of shikimate biosynthesis possesses the additional feature of feedback regulation. The crystal structure and kinetic studies on chimera and mutant proteins of yeast 3-deoxy-d-arabino-heptulosonate-7-phosphate (DAHP) synthase from Saccharomyces cerevisiae inhibited by phenylalanine (Aro3p) and DAHP synthase S. cerevisiae inhibited by tyrosine (Aro4p) give insight into important regions for regulation in the enzyme: The loop, which is connecting the two half-barrels, and structural elements added to the barrel are prerequisites for regulation and form a cavity on the N-terminal side of the betaalpha barrel. In the cavity of Aro4p at position 226 is a glycine residue, which is highly conserved in all other tyrosine-regulated DAHP synthases as well. Sequence alignments with phenylalanine-regulated DAHP synthases including Aro3p show a highly conserved serine residue at this position. An exchange of glycine to serine and vice versa leads to a complete change in the regulation pattern. Therefore the evolution of these differently feedback-inhibited isoenzymes required gene duplication and a single mutation within the internal extra element. Numerous additional amino acid substitutions present in the contemporary isoenzymes are irrelevant for regulation and occurred independently. << Less

Proc. Natl. Acad. Sci. U.S.A. 100:862-867(2003) [PubMed] [EuropePMC]
Characterization of a new feedback-resistant 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroF of Escherichia coli.

Jossek R., Bongaerts J., Sprenger G.A.

Tyrosine feedback-inhibits the 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase isoenzyme AroF of Escherichia coli. Here we show that an Asn-8 to Lys-8 substitution in AroF leads to a tyrosine-insensitive DAHP synthase. This mutant enzyme exhibited similar activities (v=30-40 U mg(-1)) ... >> More

Tyrosine feedback-inhibits the 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase isoenzyme AroF of Escherichia coli. Here we show that an Asn-8 to Lys-8 substitution in AroF leads to a tyrosine-insensitive DAHP synthase. This mutant enzyme exhibited similar activities (v=30-40 U mg(-1)) and substrate affinities (K(m)(erythrose-4-phosphate)=0.5 mM, positive cooperativity with respect to phospho(enol)pyruvate) as the wild-type AroF, but showed decreased thermostability. An engineered AroF enzyme lacking the seven N-terminal residues also was tyrosine-resistant. These results strongly suggest that the N-terminus of AroF is involved in the molecular interactions occurring in the feedback-inhibition mechanism. << Less

FEMS Microbiol Lett 202:145-148(2001) [PubMed] [EuropePMC]
Crystal structure of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli.

Shumilin I.A., Kretsinger R.H., Bauerle R.H.

<h4>Background</h4>In microorganisms and plants the first step in the common pathway leading to the biosynthesis of aromatic compounds is the stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) ... >> More

<h4>Background</h4>In microorganisms and plants the first step in the common pathway leading to the biosynthesis of aromatic compounds is the stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP). This reaction is catalyzed by DAHP synthase (DAHPS), a metal-activated enzyme, which in microorganisms is the target for negative-feedback regulation by pathway intermediates or by end products. In Escherichia coli there are three DAHPS isoforms, each specifically inhibited by one of the three aromatic amino acids.<h4>Results</h4>The crystal structure of the phenylalanine-regulated form of DAHPS complexed with PEP and Pb2+ (DAHPS(Phe)-PEP-Pb) was determined by multiple wavelength anomalous dispersion phasing utilizing the anomalous scattering of Pb2+. The tetramer consists of two tight dimers. The monomers of the tight dimer are coupled by extensive interactions including a pair of three-stranded, intersubunit beta sheets. The monomer (350 residues) is a (beta/alpha)8 barrel with several additional beta strands and alpha helices. The PEP and Pb2+ are at the C-ends of the beta strands of the barrel, as is SO4(2-), inferred to occupy the position of the phosphate of E4P. Mutations that reduce feedback inhibition cluster about a cavity near the twofold axis of the tight dimer and are centered approximately 15 A from the active site, indicating the location of a separate regulatory site.<h4>Conclusions</h4>The crystal structure of DAHPS(Phe)-PEP-Pb reveals the active site of this key enzyme of aromatic biosynthesis and indicates the probable site of inhibitor binding. This is the first reported structure of a DAHPS; the structure of its two paralogs and of a variety of orthologs should now be readily determined by molecular replacement. << Less

Structure 7:865-875(1999) [PubMed] [EuropePMC]
The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis reveals a common catalytic scaffold and ancestry for type I and type II enzymes.

Webby C.J., Baker H.M., Lott J.S., Baker E.N., Parker E.J.

The shikimate pathway, responsible for the biosynthesis of aromatic compounds, is essential for the growth of Mycobacterium tuberculosis and is a potential target for the design of new anti-tuberculosis drugs. The first step of this pathway is catalyzed by 3-deoxy-d-arabino-heptulosonate 7-phospha ... >> More

The shikimate pathway, responsible for the biosynthesis of aromatic compounds, is essential for the growth of Mycobacterium tuberculosis and is a potential target for the design of new anti-tuberculosis drugs. The first step of this pathway is catalyzed by 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS). The DAH7PSs have been classified into two apparently unrelated types and, whereas structural data have been obtained for the type I DAH7PSs, no structural information is available for their type II counterparts. The type II DAH7PS from M.tuberculosis has been expressed in Escherichia coli, purified, functionally characterized and crystallized. It is found to be metal ion-dependent and subject to feedback inhibition by phenylalanine, tryptophan, tyrosine and chorismate, with a significant synergistic effect when tryptophan is used in combination with phenylalanine. The crystal structure of M.tuberculosis DAH7PS has been determined by single-wavelength anomalous diffraction and refined at 2.3A in complex with substrate phosphoenolpyruvate and Mn(2+). The structure reveals a tightly associated dimer of (beta/alpha)(8) TIM barrels. The monomer fold, the arrangement of key residues in the active site, and the binding modes of PEP and Mn(2+), all match those of the type I enzymes, and indicate a common ancestry for the type I and type II DAH7PSs, despite their minimal sequence identity. In contrast, the structural elements that decorate the core (beta/alpha)(8) fold differ from those in the type I enzymes, consistent with their different regulatory and oligomeric properties. << Less

J. Mol. Biol. 354:927-939(2005) [PubMed] [EuropePMC]
Crystallization and preliminary X-ray analysis of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (tyrosine inhibitable) from Saccharomyces cerevisiae.

Schneider T.R., Hartmann M., Braus G.H.

3-Deoxy-D-arabino-heptulosonate-7-phosphate synthase (E.C. 4.1.2.15) catalyses the first step in the biosynthesis of aromatic amino acids: the condensation of phophoenolpyruvate and erythrose 4-phosphate to 3-deoxy-D-arabino-heptulosonate-7-phosphate. Diffraction-quality crystals of the tyrosine-i ... >> More

3-Deoxy-D-arabino-heptulosonate-7-phosphate synthase (E.C. 4.1.2.15) catalyses the first step in the biosynthesis of aromatic amino acids: the condensation of phophoenolpyruvate and erythrose 4-phosphate to 3-deoxy-D-arabino-heptulosonate-7-phosphate. Diffraction-quality crystals of the tyrosine-inhibitable form of the enzyme from Saccharomyces cerevisiae have been obtained by the hanging-drop vapour-diffusion method in the presence of polyethylene glycol. The crystals belong to the triclinic space group P1, with unit-cell parameters a = 81.5, b = 94.0, c = 104.6 A, alpha = 65.5, beta = 85.2, gamma = 75.0 degrees, and can be flash-cooled using glycerol as a cryoprotectant. A data set to 2.3 A has been collected at 120 K. << Less

Acta Crystallogr D Biol Crystallogr 55:1586-1588(1999) [PubMed] [EuropePMC]

RHEA:14717 D-erythrose 4-phosphate + phosphoenolpyruvate + H2O = 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate + phosphate

Enzymes

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Cross-references

Publications

Evolution of feedback-inhibited beta/alpha barrel isoenzymes by gene duplication and a single mutation.

Characterization of a new feedback-resistant 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroF of Escherichia coli.

Crystal structure of phenylalanine-regulated 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli.

The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis reveals a common catalytic scaffold and ancestry for type I and type II enzymes.

Crystallization and preliminary X-ray analysis of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (tyrosine inhibitable) from Saccharomyces cerevisiae.