Enzymic Racemization of Allantoin

Okumura, Itsuo; Yamamoto, Takehiko

doi:10.1093/oxfordjournals.jbchem.a132201

Cited by 9 publications

(11 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…employ HpxA allantoin racemase, related to hydantoin racemases (72,94), as well as the HpxB (PuuE) allantoinase, related to polysaccharide deacetylases and described recently by Ramazzina and coworkers (76). Our work in progress indicates further that other previously undescribed enzymes are involved in allantoate catabolism (Fig.…”

Section: Nal Fmn Binding Domain (Consensus Sequences R-x-y-s-l and Gsupporting

confidence: 75%

“…The S. cerevisiae DCG1 gene was identified as a nitrogen-regulated gene within the DAL cluster, encoding allantoinase, allantoin permease, and allantoicase (106), but the function of the Dcg1p protein has not been determined. Allantoin racemase activity has been characterized for Candida utilis (72). The analysis presented here indicates that Dcg1p may function as allantoin racemase.…”

Section: Nal Fmn Binding Domain (Consensus Sequences R-x-y-s-l and Gmentioning

confidence: 83%

“…However, the nonenzymatic conversion of HIU to allantoin creates a racemic mixture of R-and S-allantoin (45), and allantoin is present as the racemic mixture in decaying organic matter (94). Allantoin racemase has been characterized for bacteria (94) and for Candida utilis (72). To our knowledge, the structural gene for an allantoin racemease has not been identified.…”

Section: Nal Fmn Binding Domain (Consensus Sequences R-x-y-s-l and Gmentioning

confidence: 99%

See 2 more Smart Citations

Purine Utilization byKlebsiella oxytocaM5al: Genes for Ring-Oxidizing and -Opening Enzymes

2009

View full text Add to dashboard Cite

The enterobacterium Klebsiella oxytoca uses a variety of inorganic and organic nitrogen sources, including purines, nitrogen-rich compounds that are widespread in the biosphere. We have identified a 23-gene cluster that encodes the enzymes for utilizing purines as the sole nitrogen source. Growth and complementation tests with insertion mutants, combined with sequence comparisons, reveal functions for the products of these genes. Here, we report our characterization of 12 genes, one encoding guanine deaminase and the others encoding enzymes for converting (hypo)xanthine to allantoate. Conventionally, xanthine dehydrogenase, a broadly distributed molybdoflavoenzyme, catalyzes sequential hydroxylation reactions to convert hypoxanthine via xanthine to urate. Our results show that these reactions in K. oxytoca are catalyzed by a two-component oxygenase (HpxE-HpxD enzyme) homologous to Rieske nonheme iron aromatic-ring-hydroxylating systems, such as phthalate dioxygenase. Our results also reveal previously undescribed enzymes involved in urate oxidation to allantoin, catalyzed by a flavoprotein monooxygenase (HpxO enzyme), and in allantoin conversion to allantoate, which involves allantoin racemase (HpxA enzyme). The pathway also includes the recently described PuuE allantoinase (HpxB enzyme). The HpxE-HpxD and HpxO enzymes were discovered independently by de la Riva et al.

show abstract

Section: Nal Fmn Binding Domain (Consensus Sequences R-x-y-s-l and Gsupporting

confidence: 75%

Section: Nal Fmn Binding Domain (Consensus Sequences R-x-y-s-l and Gmentioning

confidence: 83%

Section: Nal Fmn Binding Domain (Consensus Sequences R-x-y-s-l and Gmentioning

confidence: 99%

See 1 more Smart Citation

Purine Utilization byKlebsiella oxytocaM5al: Genes for Ring-Oxidizing and -Opening Enzymes

2009

View full text Add to dashboard Cite

show abstract

“…[179,180] Consequently,A llanR (EC 5.1.99.3) plays the vital role of converting (R)-allanotin formed through nonenzymatic processes to (S)-allantoin for further catabolism. [181,182] This cofactor-independent racemase utilizes at wobase mechanismwith either Cys184 and Cys79 (Klebsiella pneumoniae enzyme) [183] or Glu180 and Cys78 (Pseudomonasfluorescens enzyme) [184] acting as the enantiospecific Brønsted bases to abstract the a-proton from (R)-and (S)-allantoin, respectively,w ith the oxygen of the enolate intermediate being stabilized by an oxyanion hole (Scheme10).…”

Section: Allantoin Racemase (Allanr)mentioning

confidence: 99%

Through the Looking Glass: Chiral Recognition of Substrates and Products at the Active Sites of Racemases and Epimerases

Bearne

2020

Chemistry A European J

View full text Add to dashboard Cite

Unlike most enzymes, which exhibit stereospecific substrate binding, racemases and epimerases bind and catalyze the reversible interconversion of enantiomeric and epimeric pairs of substrates. Over the past 15 years, a growing number of racemase and epimerase structures have been solved, furnishing insights into the nature of chiral recognition of substrates by these enzymes. Those enzymes catalyzing stereoinversion of a carbon acid substrate through a direct 1,1‐proton transfer mechanism all bind their substrates in a mirror‐image packing orientation. This does not apply generally to racemases and epimerases that use other mechanisms, such as NADH‐dependent epimerases that employ a “flipping” mechanism. In general, polar groups are bound and fixed at the three binding determinants on the protein defining a pseudo‐mirror plane, while nonpolar groups may be mobile. The hydrogen atoms on each stereocenter are positioned antipodal with respect to the pseudo‐mirror plane, making a two‐base mechanism imperative. Recognition that mirror‐image packing is the common binding mode for enantiomeric or epimeric substrates of these enzymes should inform modelling/docking studies and protein engineering.

show abstract

“…We thus started with the reasonable assumption that a thiole/thiolate dyad is present upon formation of the Michaelis complex between AllR and allantoin. As a corollary, we suppose that the initial protonation state of the dyad is restored upon product release through exchange with the solvent, as suggested by deuterium exchange experiments …”

Section: Introductionmentioning

confidence: 99%

Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase

et al. 2014

View full text Add to dashboard Cite

The stereospecific oxidative decomposition of urate into allantoin is the core of purine catabolism in many organisms. The spontaneous decomposition of upstream intermediates and the nonenzymatic racemization of allantoin lead to an accumulation of (R)-allantoin, because the enzymes converting allantoin into allantoate are specific for the (S) isomer. The enzyme allantoin racemase catalyzes the reversible conversion between the two allantoin enantiomers, thus ensuring the overall efficiency of the catabolic pathway and preventing allantoin accumulation. On the basis of recent crystallographic and biochemical evidence, allantoin racemase has been assigned to the family of cofactor-independent racemases, together with other amino acid racemases. A detailed computational investigation of allantoin racemase has been carried out to complement the available experimental data and to provide atomistic insight into the enzymatic action. Allantoin, the natural substrate of the enzyme, has been investigated at the quantum mechanical level, in order to rationalize its conformational and tautomeric equilibria, playing a key role in protein-ligand recognition and in the following catalytic steps. The reaction mechanism of the enzyme has been elucidated through quantum mechanics/molecular mechanics (QM/MM) calculations. The potential energy surface investigation, carried out at the QM/MM level, revealed a stepwise reaction mechanism. A pair of cysteine residues promotes the stereoinversion of a carbon atom of the ligand without the assistance of cofactors. Electrostatic fingerprint calculations are used to discuss the role of the active site residues in lowering the pK of the substrate. The planar unprotonated intermediate is compared with the enolic allantoin tautomer observed in the active site of the crystallized enzyme. Finally, the enzymatic catalysis featured by allantoin racemase (AllR) is compared with that of other enzymes belonging to the same family.

show abstract

Enzymic Racemization of Allantoin

Cited by 9 publications

References 0 publications

Purine Utilization byKlebsiella oxytocaM5al: Genes for Ring-Oxidizing and -Opening Enzymes

Purine Utilization byKlebsiella oxytocaM5al: Genes for Ring-Oxidizing and -Opening Enzymes

Through the Looking Glass: Chiral Recognition of Substrates and Products at the Active Sites of Racemases and Epimerases

Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase

Contact Info

Product

Resources

About