Structure, mechanism and catalytic duality of thiamine-dependent enzymes

  title={Structure, mechanism and catalytic duality of thiamine-dependent enzymes},
  author={Ren{\'e} A.W. Frank and Finian J. Leeper and B F Luisi},
  journal={Cellular and Molecular Life Sciences},
Abstract.Thiamine is an essential cofactor that is required for processes of general metabolism amongst all organisms, and it is likely to have played a role in the earliest stages of the evolution of life. Here, we review from a structural perspective the enzymatic mechanisms that involve this cofactor. We explore asymmetry within homodimeric thiamine diphosphate (ThDP)-dependent enzyme structures and discuss how this may be correlated with the kinetic properties of half-of-the-sites… 

Alternating sites reactivity is a common feature of thiamin diphosphate-dependent enzymes as evidenced by isothermal titration calorimetry studies of substrate binding.

The results unambiguously show that only one active center of the functional dimers accomplishes covalent binding of the substrate analogue methyl acetylphosphonate to three different ThDP-dependent enzymes acting on substrate pyruvate, supporting the proposed alternating sites reactivity as a common feature of all ThDP enzymes and resolving the recent controversy in the field.

Regulation of enzymes with identical subunits on the example of Transketolase

  • Solovjeva Olga N
  • Biology, Chemistry
    Open Journal of Analytical and Bioanalytical Chemistry
  • 2022
It is shown that the functional non-equivalence of the active sites of transketolase from Saccharomyces cerevisiae is initially formed upon the binding of the first cofactor, a divalent cation, not thiamine diphosphate, as previously thought.

Systematic analysis of the sequence-structure-function relationships of thiamine diphosphate-dependent enzymes

Thiamine diphosphate (ThDP)-dependent enzymes form a vast and diverse protein family, both in the sequence space and in their functional potential. Of particular interest are the enantioselective C-C

Catalysis in Enzymatic Decarboxylations: Comparison of Selected Cofactor-dependent and Cofactor-independent Examples.

The enzyme OMPDC has posed a challenge to the enzymologist attempting to explain a 1017-fold rate acceleration in the absence of cofactors or even metal ions, so a comparison of the available evidence on the three types of decarboxylases underlines some common features and more differences.

Allosteric Regulation of Vitamin K2 Biosynthesis in a Human Pathogen

The last cytosolicmetabolite in the menaquinone biosynthesis pathway (1,4-dihydroxy-2-napthoic acid, DHNA) binds to domain II of Mtb-MenD and inhibits enzyme activity, unravelling a protein level regulatory mechanism for control ofMenaquinone levels within the cell.

7.16 – Thiamin Enzymology




Current mechanistic understanding of thiamin diphosphate-dependent enzymatic reactions.

  • F. Jordan
  • Chemistry, Biology
    Natural product reports
  • 2003
The current view is that the two aromatic rings both contribute to catalysis, perhaps carrying out an intramolecular proton transfer to initiate the various reactions, an ability that makes this coenzyme virtually unique among coenzymes.

The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography

X-ray structures of key intermediates in the oxidative decarboxylation of pyruvate, a central reaction in carbon metabolism catalyzed by the ThDP- and flavin-dependent enzyme pyruVate oxidase (POX)3 from Lactobacillus plantarum, provide profound insights into the chemical mechanisms and the stereochemical course of thiamin catalysis.

Sixty years of thiamin diphosphate biochemistry.

How Thiamine Diphosphate Is Activated in Enzymes

The protein component accelerated the deprotonation of the C2 atom by several orders of magnitude, beyond the rate of the overall enzyme reaction, and the earlier proposed concerted mechanism or stabilization of a C2 carbanion can be excluded.

Multiple modes of active center communication in thiamin diphosphate-dependent enzymes.

Evidence for active-center interactions will be presented for the following thiamin diphosphate-dependent enzymes: yeast pyruvate decarboxylase, benzoylformatedecarboxyase, and examples from the 2-oxoacid dehydrogenase multienzyme complex class.

Malic dehydrogenase. VII. The catalytic mechanism and possible role of identical protein subunits.

Initial rate kinetic studies of mitochondrial malate dehydrogenase show that the zero order maximum initial velocity and the oxidized coenzyme dissociation constant decrease concomitantly when ketomalonate is substituted for oxalacetate as the substrate, and a more complex "reciprocating compulsory order mechanism" is proposed.

A Molecular Switch and Proton Wire Synchronize the Active Sites in Thiamine Enzymes

Evidence is presented that the ThDPs in the two active sites of the E1 (EC component of the pyruvate dehydrogenase complex communicate over a distance of 20 angstroms by reversibly shuttling a proton through an acidic tunnel in the protein.

Studies on thiamine diphosphate-dependent enzymes.

The 3-deaza analogue of TPP (thiamine diphosphate), a close mimic of the ylid intermediate, has been synthesized and is an extremely potent inhibitor of a variety of TPP-dependent enzymes, binding

Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase

The data, along with evidence from the literature, suggest that acetyl-CoA synthesis by PFOR proceeds via a condensation mechanism involving acetyl (PFOR-based) and thiyl (CoA- based) radicals.

Three‐dimensional structure of transketolase, a thiamine diphosphate dependent enzyme, at 2.5 A resolution.

The structure analysis identifies amino acids critical for cofactor binding and provides mechanistic insights into thiamine catalysis.