Structure and substrate docking of a hydroxy(phenyl)pyruvate reductase from the higher plant Coleus blumei Benth

Hydroxy(phenyl)pyruvic acid reductase in Actaea racemosa L.: a putative enzyme in cimicifugic and fukinolic acid biosynthesis

MAIN CONCLUSION

Hydroxy(phenyl)pyruvic acid reductase from Actaea racemosa catalyzes dual reactions in reducing 4-hydroxyphenylpyruvic acid as well as β-hydroxypyruvic acid. It thus qualifies to be part of fukinolic and cimicifugic acid biosynthesis and also photorespiration. The accumulation of fukinolic acid and cimicifugic acids is mainly restricted to Actaea racemosa (Ranunculaceae) and other species of the genus Actaea/Cimicifuga. Cimicifugic and fukinolic acids are composed of a hydroxycinnamic acid part esterified with a benzyltartaric acid moiety. The biosynthesis of the latter is unclear. We isolated cDNA encoding a hydroxy(phenyl)pyruvic acid reductase (GenBank OR393286) from suspension-cultured material of A. racemosa (ArH(P)PR) and expressed it in E. coli for protein production. The heterologously synthesized enzyme had a mass of 36.51 kDa and catalyzed the NAD(P)H-dependent reduction of 4-hydroxyphenylpyruvic acid to 4-hydroxyphenyllactic acid or β-hydroxypyruvic acid to glyceric acid, respectively. The optimal temperature was at 38 °C and the pH optimum at pH 7.5. NADPH is the preferred cosubstrate (Km 23 ± 4 µM). Several substrates are accepted by ArH(P)PR with β-hydroxypyruvic acid (Km 0.26 ± 0.12 mM) followed by 4-hydroxyphenylpyruvic acid (Km 1.13 ± 0.12 mM) as the best ones. Thus, ArH(P)PR has properties of β-hydroxypyruvic acid reductase (involved in photorespiration) as well as hydroxyphenylpyruvic acid reductase (possibly involved in benzyltartaric acid formation).

Comparative analysis of three SmHPPR genes encoding hydroxyphenylpyruvate reductases in Salvia miltiorrhiza

Hydroxyphenylpyruvate reductase (HPPR) is an enzyme that is involved in the biosynthesis of hydrophilic phenolic acids in Salvia miltiorrhiza, which is a model medicinal plant. Three SmHPPR genes have been identified in the S. miltiorrhiza genome; however, only one has been functionally analyzed. Here, we cloned three SmHPPR genes (SmHPPR1, SmHPPR2, and SmHPPR3) from the cDNA of S. miltiorrhiza, and their expression profiles were studied. The expression levels of SmHPPR1 were significantly higher than those of SmHPPR2 and SmHPPR3, where SmHPPR1 revealed the highest level in stems, while SmHPPR2 and SmHPPR3 exhibited the highest level in flowers. SmHPPR1, SmHPPR2, and SmHPPR3 are localized in the cytoplasm. All three recombinant enzymes had HPPR activities and catalyzed the reduction of 4-hydroxyphenylpyruvic acid (pHPP) to 4-hydroxyphenyllactic acid (pHPL), with SmHPPR1 showing the highest activity. The transient over-expression of SmHPPR1, SmHPPR2, and SmHPPR3 in the leaves of Nicotiana benthamiana promoted the production of pHPL, which indicated that all three SmHPPRs had in vivo activities. Overall, between the three homologs, SmHPPR1 plays a dominant role in catalyzing pHPP to pHPL, which provides new insights into the biosynthesis of phenolic acids in S. miltiorrhiza.

Rosmarinic acid and its derivatives: Current insights on anticancer potential and other biomedical applications

Cancer is still the leading cause of death worldwide, burdening the global medical system. Rosmarinic acid (RA) is among the first secondary metabolites discovered and it is a bioactive compound identified in plants such as Boraginaceae and Nepetoideae subfamilies of the Lamiaceae family, including Thymus masticmasti chinaythia koreana, Ocimum sanctum, and Hyptis pectinate. This updated review is to highlight the chemopreventive and chemotherapeutic effects of RA and its derivatives, thus providing valuable clues for the potential development of some complementary drugs in the treatment of cancers. Relevant information about RA's chemopreventive and chemotherapeutic effects and its derivatives were collected from electronic scientific databases, such as PubMed/Medline, Scopus, TRIP database, Web of Science, and Science Direct. The results of the studies showed numerous significant biological effects such as antiviral, antibacterial, anti-inflammatory, anti-tumour, antioxidant and antiangiogenic effects. Most of the studies on the anticancer potential with the corresponding mechanisms are still in the experimental preclinical stage and are missing evidence from clinical trials to support the research. To open new anticancer therapeutic perspectives of RA and its derivatives, future clinical studies must elucidate the molecular mechanisms and targets of action in more detail, the human toxic potential and adverse effects.

An aldo-keto reductase with 2-keto-l-gulonate reductase activity functions in l-tartaric acid biosynthesis from vitamin C in Vitis vinifera

Tartaric acid has high economic value as an antioxidant and flavorant in food and wine industries. l-Tartaric acid biosynthesis in wine grape (Vitis vinifera) uses ascorbic acid (vitamin C) as precursor, representing an unusual metabolic fate for ascorbic acid degradation. Reduction of the ascorbate breakdown product 2-keto-l-gulonic acid to l-idonic acid constitutes a critical step in this l-tartaric acid biosynthetic pathway. However, the underlying enzymatic mechanisms remain obscure. Here, we identified a V. vinifera aldo-keto reductase, Vv2KGR, with 2-keto-l-gulonic acid reductase activity. Vv2KGR belongs to the d-isomer-specific 2-hydroxyacid dehydrogenase superfamily and displayed the highest similarity to the hydroxyl pyruvate reductase isoform 2 in Arabidopsis thaliana Enzymatic analyses revealed that Vv2KGR efficiently reduces 2-keto-l-gulonic acid to l-idonic acid and uses NADPH as preferred coenzyme. Moreover, Vv2KGR exhibited broad substrate specificity toward glyoxylate, pyruvate, and hydroxypyruvate, having the highest catalytic efficiency for glyoxylate. We further determined the X-ray crystal structure of Vv2KGR at 1.58 Å resolution. Comparison of the Vv2KGR structure with those of d-isomer-specific 2-hydroxyacid dehydrogenases from animals and microorganisms revealed several unique structural features of this plant hydroxyl pyruvate reductase. Substrate structural analysis indicated that Vv2KGR uses two modes (A and B) to bind different substrates. 2-Keto-l-gulonic acid displayed the lowest predicted free-energy binding to Vv2KGR among all docked substrates. Hence, we propose that Vv2KGR functions in l-tartaric acid biosynthesis. To the best of our knowledge, this is the first report of a d-isomer-specific 2-hydroxyacid dehydrogenase that reduces 2-keto-l-gulonic acid to l-idonic acid in plants.

A Phenylpyruvic Acid Reductase Is Required for Biosynthesis of Tropane Alkaloids

Solanaceous medicinal plants produce tropane alkaloids (TAs). We discovered a novel gene from Atropa belladonna, AbPPAR, which encodes a phenylpyruvic acid reductase required for TA biosynthesis. AbPPAR was specifically expressed in root pericycles and endodermis. AbPPAR was shown to catalyze reduction of phenylpyruvic acid to phenyllactic acid, a precursor of TAs. Suppression of AbPPAR disrupted TA biosynthesis through reduction of phenyllactic acid levels. In summary, we identified a novel enzyme involved in TA biosynthesis.

The Glycerate and Phosphorylated Pathways of Serine Synthesis in Plants: The Branches of Plant Glycolysis Linking Carbon and Nitrogen Metabolism

Serine metabolism in plants has been studied mostly in relation to photorespiration where serine is formed from two molecules of glycine. However, two other pathways of serine formation operate in plants and represent the branches of glycolysis diverging at the level of 3-phosphoglyceric acid. One branch (the glycerate - serine pathway) is initiated in the cytosol and involves glycerate formation from 3-phosphoglycerate, while the other (the phosphorylated serine pathway) operates in plastids and forms phosphohydroxypyruvate as an intermediate. Serine formed in these pathways becomes a precursor of glycine, formate and glycolate accumulating in stress conditions. The pathways can be linked to GABA shunt via transamination reactions and via participation of the same reductase for both glyoxylate and succinic semialdehyde. In this review paper we present a hypothesis of the regulation of redox balance in stressed plant cells via participation of the reactions associated with glycerate and phosphorylated serine pathways. We consider these pathways as important processes linking carbon and nitrogen metabolism and maintaining cellular redox and energy levels in stress conditions.

Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies

The d-2-hydroxyacid dehydrogenase (2HADH) family illustrates a complex evolutionary history with multiple lateral gene transfers and gene duplications and losses. As a result, the exact functional annotation of individual members can be extrapolated to a very limited extent. Here, we revise the previous simplified view on the classification of the 2HADH family; specifically, we show that the previously delineated glyoxylate/hydroxypyruvate reductase (GHPR) subfamily consists of two evolutionary separated GHRA and GHRB subfamilies. We compare two representatives of these subfamilies from Sinorhizobium meliloti (SmGhrA and SmGhrB), employing a combination of biochemical, structural, and bioinformatics approaches. Our kinetic results show that both enzymes reduce several 2-ketocarboxylic acids with overlapping, but not equivalent, substrate preferences. SmGhrA and SmGhrB show highest activity with glyoxylate and hydroxypyruvate, respectively; in addition, only SmGhrB reduces 2-keto-d-gluconate, and only SmGhrA reduces pyruvate (with low efficiency). We present nine crystal structures of both enzymes in apo forms and in complexes with cofactors and substrates/substrate analogues. In particular, we determined a crystal structure of SmGhrB with 2-keto-d-gluconate, which is the biggest substrate cocrystallized with a 2HADH member. The structures reveal significant differences between SmGhrA and SmGhrB, both in the overall structure and within the substrate-binding pocket, offering insight into the molecular basis for the observed substrate preferences and subfamily differences. In addition, we provide an overview of all GHRA and GHRB structures complexed with a ligand in the active site.

Activity prediction of substrates in NADH-dependent carbonyl reductase by docking requires catalytic constraints and charge parameterization of catalytic zinc environment

Molecular docking of substrates is more challenging compared to inhibitors as the reaction mechanism has to be considered. This becomes more pronounced for zinc-dependent enzymes since the coordination state of the catalytic zinc ion is of greater importance. In order to develop a predictive substrate docking protocol, we have performed molecular docking studies of diketone substrates using the catalytic state of carbonyl reductase 2 from Candida parapsilosis (CPCR2). Different docking protocols using two docking methods (AutoDock Vina and AutoDock4.2) with two different sets of atomic charges (AM1-BCC and HF-RESP) for catalytic zinc environment and substrates as well as two sets of vdW parameters for zinc ion were examined. We have selected the catalytic binding pose of each substrate by applying mechanism based distance criteria. To compare the performance of the docking protocols, the correlation plots for the binding energies of these catalytic poses were obtained against experimental Vmax values of the 11 diketone substrates for CPCR2. The best correlation of 0.73 was achieved with AutoDock4.2 while treating catalytic zinc ion in optimized non-bonded (NBopt) state with +1.01 charge on the zinc ion, compared to 0.36 in non-bonded (+2.00 charge on the zinc ion) state. These results indicate the importance of catalytic constraints and charge parameterization of catalytic zinc environment for the prediction of substrate activity in zinc-dependent enzymes by molecular docking. The developed predictive docking protocol described here is in principle generally applicable for the efficient in silico substrate spectra characterization of zinc-dependent ADH.

Characterization and crystal structure of a first fungal glyoxylate reductase from Paecilomyes thermophila

A glyoxylate reductase gene (PtGR) from the fungus Paecilomyces thermophila was cloned and expressed in Escherichia coli. PtGR was biochemically and structurally characterized. PtGR has an open reading frame of 993bp encoding 330 amino acids. The deduced amino acid sequence has low similarities to the reported glyoxylate reductases. The purified PtGR forms a homodimer. PtGR displayed an optimum pH of 7.5 and broad pH stability (pH 4.5-10). It exhibited an optimal temperature of 50°C and was stable up to 50°C. PtGR was found to be highly specific for glyoxylate, but it showed no detectable activity with 4-methyl-2-oxopentanoate, phenylglyoxylate, pyruvate, oxaloacetate and α-ketoglutarate. PtGR prefered NADPH rather than NADH as an electron donor. Moreover, the crystal structure of PtGR was determined at 1.75Å resolution. The overall structure of apo-PtGR monomer adopts the typical d-2-hydroxy-acid dehydrogenase fold with a "closed" conformation unexpectedly. The coenzyme specificity is provided by a cationic cluster consisting of N184, R185, and N186 structurally. These structural observations could explain its different coenzyme and substrate specificity.

Crystallization and structural analysis of 2-hydroxyacid dehydrogenase from Ketogulonicigenium vulgare

L-2-Hydroxyacid dehydrogenase (HDH) from Ketogulonicigenium vulgare Y25 was cloned and overexpressed in Escherichia coli. The protein was purified and crystallized by the sitting-drop vapour-diffusion method with polyethylene glycol 3350 as precipitant. The crystal structure of HDH was determined at 1.64 Å resolution using the molecular replacement method with the crystal structure of hydroxyl (phenyl) pyruvate reductase from Coleus blumei Benth as the search model. The overall structure of HDH was similar to that of hydroxyl(phenyl)pyruvate reductase, consisting of two compact domains separated by a deep active cleft. The most significant structural divergence is located around the pocket gate comprising residues A210, T211 and R212, which is located on top of the catalytic triad.

Cloning and characterisation of rosmarinic acid synthase from Melissa officinalis L

Lemon balm (Melissa officinalis L.; Lamiaceae) is a well-known medicinal plant mainly due to two groups of compounds, the essential oil and the phenylpropanoid derivatives. The prominent phenolic compound is rosmarinic acid (RA), an ester of caffeic acid and 3,4-dihydroxyphenyllactic acid. RA shows a number of interesting biological activities. Rosmarinic acid synthase (RAS; 4-coumaroyl-CoA:hydroxyphenyllactic acid hydroxycinnamoyltransferase) catalyses the ester formation. Cell cultures of M. officinalis have been established in order to characterise the formation of RA in an important diploid medicinal plant. RAS activity as well as the expression of the RAS gene are closely correlated with the accumulation of RA in suspension cultures of M. officinalis. The RAS cDNA and gene (MoRAS) were isolated. The RAS gene was shown to be intron-free. MoRAS belongs to the BAHD superfamily of acyltransferases. Southern-blot analysis suggests the presence of only one RAS gene copy in the M. officinalis genome. The enzyme was characterised with respect to enzyme properties, substrate preferences and kinetic data in crude plant extracts and as heterologously synthesised protein from Escherichia coli.

Characterisation and Expression Analysis of Hydroxyphenylpyruvate Reductase derived from Orthosiphon aristatus

Herbal products are getting more popular as alternative medicines and food supplements. The therapeutic effects of herbal medicines are mainly attributed to their bioactive secondary metabolites. Orthosiphon aristatus, locally known as ‘Misai Kucing’, is known for its various health benefits. One of the main chemical constituent of O. aristatus is rosmarinic acid, a plant polyphenol that has been proven to have antioxidant, anti-inflammatory and antimicrobial activities. Hydroxyphenylpyruvate reductase (HPPR) is one of the enzymes involved in rosmarinic acid biosynthetic pathway. Here we report the effect of UV on HPPR expression and the isolation of a full-length hppr cDNA from O. aristatus via rapid amplification of cDNA ends polymerase chain reaction. An increase in the expression was detected when the plant was exposed to UV and detected via the expression of hppr transcript. A 1116 bp nucleotide putative cDNA was isolated corresponding to 307 predicted amino acid. We have also isolated the 5’ and 3’ untranslated regions with a length of 54 bp and 123 bp, respectively. Sequence similarity analysis was performed against NCBI genebank and the BLAST result showed that the putative hppr cDNA isolated from O. aristatus exhibited high similarities with other hppr cDNA of the members of the Lamiaceae family such as Perilla frutescens, Salvia officinalis, Salvia miltiorrhiza and Solenostemon scutellarioides.