Cofactors

Thiamine diphosphate.

Reaction Mechanism

1-deoxy-D-xylulose 5-phosphate synthase By Reference

1-Deoxy-D-xylulose-5-phosphate synthase (DXS ) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. DXP synthase is a thiamine diphosphate-dependent enzyme related to transketolase and the pyruvate dehydrogenase E1-beta subunit. DXS is found in bacteria (gene:dxs) and plants (gene:CLA1) which catalyses the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP), a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6). DXS is evolutionary related to TK. This reaction is the first and rate limiting step of the mevalonate-independent pathway for the biosynthesis of isopentyl pyrophosphate, a process undertaken only in fungi, algae and bacteria. DXS differs from related thiamine diphosphate dependent enzymes by virtue of its domain arrangement: the active site is not situated on a chain interface, as seen in related enzymes, but instead resides between two domain faces within the same monomer of a homodimeric complex [PMID:17135236].




• Summary
• Step 1
• Step 2
• Step 3
• Step 4
• Step 5
• Step 6
• Step 7
• Products

Glu373 deprotonates the N1 position of TDP. Charge delocalisation across the conjugated molecule results in concomitant deprotonation of the thiazole ring, activating the cofactor for the next steps in catalysis. The TDP carbanion, stabilised as an ylid, attacks the carbonyl of pyruvate forming a covalently bound intermediate. The oxyanion intermediate collapses to generate carbon dioxide and a TDP-enol intermediate. The carbanion attacks at the glyceraldehyde group to form a tetrahedral oxyanion intermediate. The tetrahedral intermediate collapses releasing the TDP ylid and 1-deoxy-D-xylulose 5-phosphate, the product which enters the isoprenoid biosynthesis pathway [PMID:19778006]. The cofactor is reprotonated to regenerate the active site.

Catalytic Residues

AA	Uniprot	Uniprot Resid	PDB	PDB Resid
Lys	Q9RUB5	289	2o1x	289
Glu	Q9RUB5	373	2o1x	373
Arg	Q9RUB5	401	2o1x	401

Step Components

overall reactant used, proton transfer, overall product formed, unimolecular elimination by the conjugate base, intramolecular elimination, bimolecular nucleophilic addition, native state of cofactor regenerated, intermediate formation, native state of enzyme regenerated, inferred reaction step, cofactor used, charge delocalisation, intermediate collapse, elimination (not covered by the Ingold mechanisms)



Step 1.

Glu373 deprotonates the N1 position of TDP. Charge delocalisation across the conjugated molecule results in concomitant deprotonation of the thiazole ring, activating the cofactor for the next steps in catalysis. The ionisation of TDP is fast compared to enzymatic turnover, and is therefore not rate determining [PMID:19476486].



Step 2.

The TDP carbanion, stabilised as an ylid, attacks the carbonyl of pyruvate forming a covalently bound intermediate.



Step 3.

The oxyanion intermediate collapses to generate carbon dioxide and a TDP-enol intermediate.



Step 4.

The carbanion attacks at the glyceraldehyde group to form a tetrahedral oxyanion intermediate. Electron delocalisation across the thiazole ring allows for several resonance structures.



Step 5.

The tetrahedral intermediate collapses releasing the TDP ylid and 1-deoxy-D-xylulose 5-phosphate, the product which enters the isoprenoid biosynthesis pathway [PMID:19778006].



Step 6.

The cofactor is reprotonated.



Step 7.

The cofactor is reprotonated in an inferred return step.



Products.

The products of the reaction.

View Reaction Mechanisms in M-CSA

Reaction Parameters

There are no kinetic parameters information for this Enzyme

Associated Proteins

Citations

• Molecular cloning and heterologous expression analysis of 1-Deoxy-D-Xylulose-5-Phosphate Synthase gene in Centella asiatica L.
• 1-deoxy-D-xylulose-5-phosphate synthase from Pseudomonas aeruginosa and Klebsiella pneumoniae reveals conformational changes upon cofactor binding.
• Differential roles of Cassia tora 1-deoxy-D-xylulose-5-phosphate synthase and 1-deoxy-D-xylulose-5-phosphate reductoisomerase in trade-off between plant growth and drought tolerance.
• Not Every Hit-Identification Technique Works on 1-Deoxy-d-Xylulose 5-Phosphate Synthase (DXPS): Making the Most of a Virtual Screening Campaign.
• Genetic diversity of 1-deoxy-D-xylulose 5-phosphate synthase gene (SmDXS) among the cultivated Danshen (Salvia miltiorrhiza) populations
• Characterization of the 1-Deoxy-D-xylulose 5-Phosphate synthase Genes in Toona ciliata Suggests Their Role in Insect Defense.
• Cloning and functional analysis of 1-deoxy-d-xylulose-5-phosphate synthase (DXS) in Santalum album L.
• Over-expression of a cyanobacterial gene for 1-deoxy-d-xylulose-5-phosphate synthase in the chloroplast of Chlamydomonas reinhardtii perturbs chlorophyll: carotenoid ratios.
• Structural and functional characterization of 1-deoxy-D-xylulose-5-phosphate synthase (DXS) from Acinetobacter baumannii: identification of promising lead molecules from virtual screening, molecular docking and molecular dynamics simulations.
• First crystal structures of 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Mycobacterium tuberculosis indicate a distinct mechanism of intermediate stabilization.
• Structural analysis of 1-deoxy-D-xylulose 5-phosphate synthase from Pseudomonas aeruginosa and Klebsiella pneumoniae reveals conformational changes upon cofactor binding