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1.
Biochim Biophys Acta Mol Cell Biol Lipids ; 1869(3): 159452, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38244676

ABSTRACT

Very long-chain fatty acids (VLCFAs) are degraded exclusively in peroxisomes, as evidenced by the accumulation of VLCFAs in patients with certain peroxisomal disorders. Although accumulation of VLCFAs is considered to be associated with health issues, including neuronal degeneration, the mechanisms underlying VLCFAs-induced tissue degeneration remain unclear. Here, we report the toxic effect of VLCFA and protective effect of C18: 1 FA in peroxisome-deficient CHO cells. We examined the cytotoxicity of saturated and monounsaturated VLCFAs with chain-length at C20-C26, and found that longer and saturated VLCFA showed potent cytotoxicity at lower accumulation levels. Furthermore, the extent of VLCFA-induced toxicity was found to be associated with a decrease in cellular C18:1 FA levels. Notably, supplementation with C18:1 FA effectively rescued the cells from VLCFA-induced apoptosis without reducing the cellular VLCFAs levels, implying that peroxisome-deficient cells can survive in the presence of accumulated VLCFA, as long as the cells keep sufficient levels of cellular C18:1 FA. These results suggest a therapeutic potential of C18:1 FA in peroxisome disease and may provide new insights into the pharmacological effect of Lorenzo's oil, a 4:1 mixture of C18:1 and C22:1 FA.


Subject(s)
Oleic Acid , Peroxisomes , Animals , Cricetinae , Humans , Oleic Acid/pharmacology , Oleic Acid/metabolism , Peroxisomes/metabolism , Fatty Acids/metabolism , Cricetulus , CHO Cells , Fatty Acids, Nonesterified/metabolism , Apoptosis
2.
J Biochem ; 175(1): 115-124, 2023 Dec 20.
Article in English | MEDLINE | ID: mdl-37827526

ABSTRACT

A convenient method for the determination of plant sphingolipids (glycosylinositol phosphoceramide, GIPC; glucosylceramide, GluCer; phytoceramide 1-phosphate, PC1P and phytoceramide, PCer) was developed. This method includes the extraction of lipids using 1-butanol, alkali hydrolysis with methylamine and separation by TLC. The amounts of sphingolipids in the sample were determined based on the relative intensities of standard sphingolipids visualized by primulin/UV on TLC. Using this method, we found that almost all GIPCs were degraded in response to tissue homogenization in cruciferous plants (cabbage, broccoli and Arabidopsis thaliana). The decrease in GIPCs was compensated for by increases in PC1P and PCer, indicating that GIPC was degraded by hydrolysis at the D and C positions of GIPC, respectively. In carrot roots and leaves, most of GIPC degradation was compensated for by an increase in PCer. In rice roots, the decrease in GIPCs was not fully explained by the increases in PC1P and PCer, indicating that enzymes other than phospholipase C and D activities operated. As the visualization of lipids on TLC is useful for detecting the appearance or disappearance of lipids, this method will be available for the characterization of metabolism of sphingolipids in plants.


Subject(s)
Arabidopsis , Brassica , Glycosphingolipids/metabolism , Sphingolipids/metabolism , Plants/metabolism , Arabidopsis/metabolism
3.
Int J Biol Macromol ; 249: 126070, 2023 Sep 30.
Article in English | MEDLINE | ID: mdl-37524275

ABSTRACT

Crystal structures of Pseudomonas veroniil-arginine dehydrogenase (l-ArgDH), belonging to the µ-crystallin/ornithine cyclodeaminase family, were determined for the enzyme in complex with l-lysine and NADP+ and with l-arginine and NADPH. The main chain coordinates of the P. veroniil-ArgDH monomer showed notable similarity to those of Archaeoglobus fulgidusl-AlaDH, belonging to the same family, and pro-R specificity similar to l-AlaDH for hydride transfer to NADP+ was postulated. However, the residues recognizing the α-amino group of the substrates differed between the two enzymes. Based on a substrate modeling study, it was proposed that in A. fulgidusl-AlaDH, the amino group of l-alanine interacts via a water molecule (W510) with the side chains of Lys41 and Arg52. By contrast, the α-amino group of l-arginine formed hydrogen bonds with the side chains of Thr224 and Asn225 in P. veroniil-ArgDH. Moreover, the guanidino group of l-arginine was fixed into the active site via hydrogen bonds with the side chain of Asp54. Site-directed mutagenesis suggested that Asp54 plays an important role in maintaining high reactivity against the substrate and that Tyr58 and Lys71 play critical roles in enzyme catalysis.


Subject(s)
NADPH Dehydrogenase , mu-Crystallins , NADP/metabolism , Amino Acid Sequence , Arginine , Binding Sites , Crystallography, X-Ray , Substrate Specificity
4.
Article in English | MEDLINE | ID: mdl-36460260

ABSTRACT

One of the major functions of peroxisomes in mammals is oxidation of very long-chain fatty acids (VLCFAs). Genetic defects in peroxisomal ß-oxidation result in the accumulation of VLCFAs and lead to a variety of health problems, such as demyelination of nervous tissues. However, the mechanisms by which VLCFAs cause tissue degeneration have not been fully elucidated. Recently, we found that the addition of small amounts of isopropanol can enhance the solubility of saturated VLCFAs in an aqueous medium. In this study, we characterized the biological effect of extracellular VLCFAs in peroxisome-deficient Chinese hamster ovary (CHO) cells, neural crest-derived pheochromocytoma cells (PC12), and immortalized adult Fischer rat Schwann cells (IFRS1) using this solubilizing technique. C20:0 FA was the most toxic of the C16-C26 FAs tested in all cells. The basis of the toxicity of C20:0 FA was apoptosis and was observed at 5 µM and 30 µM in peroxisome-deficient and wild-type CHO cells, respectively. The sensitivity of wild-type CHO cells to cytotoxic C20:0 FA was enhanced in the presence of a peroxisomal ß-oxidation inhibitor. Further, a positive correlation was evident between cell toxicity and the extent of intracellular accumulation of toxic FA. These results suggest that peroxisomes are pivotal in the detoxification of apoptotic VLCFAs by preventing their accumulation.


Subject(s)
Fatty Acids , Peroxisomes , Cricetinae , Animals , Peroxisomes/metabolism , Fatty Acids/metabolism , CHO Cells , Cricetulus , Oxidation-Reduction
5.
FEBS Lett ; 596(23): 3024-3036, 2022 Dec.
Article in English | MEDLINE | ID: mdl-36266963

ABSTRACT

Glycosylinositol phosphoceramide (GIPC) is a major sphingolipid in the plasma membranes of plants. Previously, we found an enzyme activity that produces phytoceramide 1-phosphate (PC1P) by hydrolysis of the D position of GIPC in cabbage and named this activity as GIPC-phospholipase D (PLD). Here, we purified GIPC-PLD by sequential chromatography from radish roots. Peptide mass fingerprinting analysis revealed that the potential candidate for GIPC-PLD protein was nonspecific phospholipase C3 (NPC3), which has not been characterized as a PLD. The recombinant NPC3 protein obtained by heterologous expression system in Escherichia coli produced PC1P from GIPC and showed essentially the same enzymatic properties as those we characterized as GIPC-PLD in cabbage, radish and Arabidopsis thaliana. From these results, we conclude that NPC3 is one of the enzymes that degrade GIPC.


Subject(s)
Arabidopsis , Brassica , Phospholipase D , Raphanus , Phospholipase D/genetics , Phospholipase D/chemistry , Raphanus/metabolism , Phospholipases/metabolism , Sphingolipids/metabolism , Brassica/genetics , Brassica/chemistry , Arabidopsis/genetics , Arabidopsis/metabolism
6.
Int J Biol Macromol ; 208: 731-740, 2022 May 31.
Article in English | MEDLINE | ID: mdl-35337912

ABSTRACT

Ornithine δ-aminotransferase (Orn-AT) activity was detected for the enzyme annotated as a γ-aminobutyrate aminotransferase encoded by PH1423 gene from Pyrococcus horikoshii OT-3. Crystal structures of this novel archaeal ω-aminotransferase were determined for the enzyme in complex with pyridoxal 5'-phosphate (PLP), in complex with PLP and l-ornithine (l-Orn), and in complex with N-(5'-phosphopyridoxyl)-l-glutamate (PLP-l-Glu). Although the sequence identity was relatively low (28%), the main-chain coordinates of P. horikoshii Orn-AT monomer showed notable similarity to those of human Orn-AT. However, the residues recognizing the α-amino group of l-Orn differ between the two enzymes. In human Orn-AT, Tyr55 and Tyr85 recognize the α-amino group, whereas the side chains of Thr92* and Asp93*, which arise from a loop in the neighboring subunit, form hydrogen bonds with the α-amino group of the substrate in P. horikoshii enzyme. Site-directed mutagenesis suggested that Asp93* plays critical roles in maintaining high affinity for the substrate. This study provides new insight into the substrate binding of a novel type of Orn-AT. Moreover, the structure of the enzyme with the reaction-intermediate analogue PLP-l-Glu bound provides the first structural evidence for the "Glu switch" mechanism in the dual substrate specificity of Orn-AT.


Subject(s)
Pyrococcus horikoshii , Archaea/metabolism , Crystallography, X-Ray , Humans , Models, Molecular , Ornithine/chemistry , Pyridoxal Phosphate/chemistry , Pyrococcus horikoshii/metabolism , Substrate Specificity , Transaminases/chemistry
7.
Article in English | MEDLINE | ID: mdl-34848380

ABSTRACT

Fatty acids (FAs) longer than C20 are classified as very long-chain fatty acids (VLCFAs). Although biosynthesis and degradation of VLCFAs are important for the development and integrity of the myelin sheath, knowledge on the incorporation of extracellular VLCFAs into the cells is limited due to the experimental difficulty of solubilizing them. In this study, we found that a small amount of isopropanol solubilized VLCFAs in aqueous medium by facilitating the formation of the VLCFA/albumin complex. Using this solubilizing technique, we examined the role of the peroxisome in the uptake and metabolism of VLCFAs in Chinese hamster ovary (CHO) cells. When wild-type CHO cells were incubated with saturated VLCFAs (S-VLCFAs), such as C23:0 FA, C24:0 FA, and C26:0 FA, extensive uptake was observed. Most of the incorporated S-VLCFAs were oxidatively degraded without acylation into cellular lipids. In contrast, in peroxisome-deficient CHO cells uptake of S-VLCFAs was marginal and oxidative metabolism was not observed. Extensive uptake and acylation of monounsaturated (MU)-VLCFAs, such as C24:1 FA and C22:1 FA, were observed in both types of CHO cells. However, oxidative metabolism was evident only in wild-type cells. Similar manners of uptake and metabolism of S-VLCFAs and MU-VLCFAs were observed in IFRS1, a Schwan cell-derived cell line. These results indicate that peroxisome-deficient cells limit intracellular S-VLCFAs at a low level by halting uptake, and as a result, peroxisome-deficient cells almost completely lose the clearance ability of S-VLCFAs accumulated outside of the cells.


Subject(s)
Peroxisomes
8.
Biosci Biotechnol Biochem ; 85(7): 1650-1657, 2021 Jun 24.
Article in English | MEDLINE | ID: mdl-33942867

ABSTRACT

The amino acid sequence of the OCC_10945 gene product from the hyperthermophilic archaeon Thermococcus litoralis DSM5473, originally annotated as γ-aminobutyrate aminotransferase, is highly similar to that of the uncharacterized pyridoxal 5'-phosphate (PLP)-dependent amino acid racemase from Pyrococcus horikoshii. The OCC_10945 enzyme was successfully overexpressed in Escherichia coli by coexpression with a chaperone protein. The purified enzyme demonstrated PLP-dependent amino acid racemase activity primarily toward Met and Leu. Although PLP contributed to enzyme stability, it only loosely bound to this enzyme. Enzyme activity was strongly inhibited by several metal ions, including Co2+ and Zn2+, and nonsubstrate amino acids such as l-Arg and l-Lys. These results suggest that the underlying PLP-binding and substrate recognition mechanisms in this enzyme are significantly different from those of the other archaeal and bacterial amino acid racemases. This is the first description of a novel PLP-dependent amino acid racemase with moderate substrate specificity in hyperthermophilic archaea.


Subject(s)
Amino Acid Isomerases/metabolism , Archaeal Proteins/metabolism , Thermococcus/enzymology , Amino Acid Isomerases/chemistry , Amino Acid Sequence , Archaeal Proteins/chemistry , Electrophoresis, Polyacrylamide Gel , Genes, Archaeal , Molecular Chaperones/metabolism , Phylogeny , Substrate Specificity , Thermococcus/genetics
9.
Lipids ; 56(2): 181-188, 2021 03.
Article in English | MEDLINE | ID: mdl-32996178

ABSTRACT

Sphingomyelin (SM) with N-α-hydroxy fatty acyl residues (hSM) has been shown to occur in mammalian skin and digestive epithelia. However, the metabolism and physiological relevance of this characteristic SM species have not been fully elucidated yet. Here, we show methods for mass spectrometric characterization and quantification of hSM. The hSM in mouse skin was isolated by TLC. The hydroxy hexadecanoyl residue was confirmed by electron impact ionization-induced fragmentation in gas chromatography-mass spectrometry. Mass shift analysis of acetylated hSM by time of flight mass spectrometry revealed the number of hydroxyl groups in the molecule. After correcting the difference in detection efficacy, hSM in mouse skin and intestinal mucosa were quantified by liquid chromatography-tandem mass spectrometry, and found to be 16.5 ± 2.0 and 0.8 ± 0.4 nmol/µmol phospholipid, respectively. The methods described here are applicable to biological experiments on hSM in epithelia of the body surface and digestive tract.


Subject(s)
Fatty Acids/analysis , Skin/chemistry , Sphingomyelins/analysis , Animals , Chromatography, Gas , Male , Mass Spectrometry , Mice , Mice, Inbred ICR
10.
Article in English | MEDLINE | ID: mdl-32615533

ABSTRACT

Glycosylinositol phosphoceramide (GIPC) is a sphingophospholipid in plants. Recently, we identified that GIPC is hydrolyzed to phytoceramide 1-phosphate (PC1P) by an uncharacterized phospholipase D activity following homogenization of certain plant tissues. We now developed methods for isolation of GIPC and PC1P from plant tissues and characterized their chemical stabilities. Hydrophilic solvents, namely a lower layer of a mixed solvent system consisting of isopropanol/hexane/water (55:20:25, v/v/v) was efficient solvent for extraction and eluent in column chromatography. GIPC was isolated by Sephadex column chromatography followed by TLC. A conventional method, such as the Bligh and Dyer method, was applicable for PC1P extraction. Specifically, PC1P was isolated by TLC following mild alkali treatment of lipid extracts of plants. The yields of GIPC and PC1P in our methods were both around 50-70%. We found that PC1P is tolerant against heat (up to 125 °C), strong acid (up to 10 M HCl), and mild alkali (0.1 M KOH). In contrast, significant degradation of GIPC occurred at 100 °C and 1.0 M HCl treatment, suggesting the instability of the inositol glycan moiety in these conditions. These data will be useful for further biochemical and nutritional studies on these sphingolipids.


Subject(s)
Ceramides/isolation & purification , Glycosphingolipids/isolation & purification , Phytochemicals/isolation & purification , Ceramides/analysis , Ceramides/chemistry , Chromatography, Thin Layer , Drug Stability , Glycosphingolipids/analysis , Glycosphingolipids/chemistry , Hydrophobic and Hydrophilic Interactions , Inositol/analogs & derivatives , Inositol/chemistry , Phytochemicals/analysis , Phytochemicals/chemistry , Polysaccharides/chemistry , Solvents
11.
J Nutr Sci Vitaminol (Tokyo) ; 65(Supplement): S175-S179, 2019.
Article in English | MEDLINE | ID: mdl-31619623

ABSTRACT

Previously, we found an unidentified sphingolipid in cabbage, and determined it as phytoceramide 1-phosphate (PC1P). PC1P is found to be produced from glycosylinositol phosphoceramide (GIPC) by the action of phospholipase D (PLD) activity. Although GIPC is abundant sphingolipid, especially in cruciferous vegetables, amount of daily intake, digestibility and nutritional activity of GIPC are not well understood. Here, we investigated amounts of GIPC and PC1P in vegetables. GIPC was found in all vegetables examined (13 kinds) at levels 3-20 mg/100 g (wet weight). On the other hand, PC1P was present in limited vegetables which show higher GIPC-PLD activity, such as inner cabbage leaves (5.2 mg/100 g). Because PC1P is formed during homogenization by activated GIPC-PLD, level of PC1P in boiled cabbage leaves was very low. Although digestibility of GIPC is unknown at present, a portion of dietary GIPC is considered to be converted to PC1P during mastication by plant-derived GIPC-PLD activity in some vegetables.


Subject(s)
Ceramides/analysis , Glycosphingolipids/analysis , Inositol/analysis , Phosphates/analysis , Vegetables/chemistry , Brassica/chemistry , Inositol/analogs & derivatives , Phospholipase D/metabolism , Plant Leaves/chemistry , Sphingolipids/chemistry
12.
J Biochem ; 166(5): 441-448, 2019 Nov 01.
Article in English | MEDLINE | ID: mdl-31504617

ABSTRACT

Glycosylinositol phosphoceramide (GIPC) is the most abundant sphingolipid in plants and fungi. Recently, we detected GIPC-specific phospholipase D (GIPC-PLD) activity in plants. Here, we found that GIPC-PLD activity in young cabbage leaves catalyzes transphosphatidylation. The available alcohol for this reaction is a primary alcohol with a chain length below C4. Neither secondary alcohol, tertiary alcohol, choline, serine nor glycerol serves as an acceptor for transphosphatidylation of GIPC-PLD. We also found that cabbage GIPC-PLD prefers GIPC containing two sugars. Neither inositol phosphoceramide, mannosylinositol phosphoceramide nor GIPC with three sugar chains served as substrate. GIPC-PLD will become a useful catalyst for modification of polar head group of sphingophospholipid.


Subject(s)
Biocatalysis , Brassica/enzymology , Ceramides/metabolism , Inositol/metabolism , Phosphatidylcholines/metabolism , Phospholipase D/metabolism , Plant Leaves/enzymology , Brassica/chemistry , Ceramides/chemistry , Inositol/analogs & derivatives , Inositol/chemistry , Molecular Structure , Phosphatidylcholines/chemistry , Phospholipase D/chemistry , Plant Leaves/chemistry
13.
Front Microbiol ; 9: 1481, 2018.
Article in English | MEDLINE | ID: mdl-30038603

ABSTRACT

We recently identified and characterized a novel broad substrate specificity amino acid racemase (BAR) from the hyperthermophilic archaeon Pyrococcus horikoshii OT-3. Three genes, PH0782, PH1423, and PH1501, encoding homologs exhibiting about 45% sequence identity with BAR were present in the P. horikoshii genome. In this study, we detected pyridoxal 5'-phosphate (PLP)-dependent amino acid racemase activity in the protein encoded by PH0782. The enzyme showed activity toward Ala, Ser, Thr, and Val, but the catalytic efficiency with Thr or Val was much lower than with Ala or Ser. The enzyme was therefore designated Ala/Ser racemase (ASR). Like BAR, ASR was highly stable at high temperatures and over a wide range of pHs, though its hexameric structure differed from the dimeric structure of BAR. No activity was detected in K291A or D234A ASR mutants. This suggests that, as in Ile 2-epimerase (ILEP) from Lactobacillus buchneri JCM1115, these residues are involved in Schiff base formation and substrate interaction, respectively. Unlike BAR, enhanced ASR activity was not detected in P. horikoshii cells cultivated in the presence of D-Ala or D-Ser. This is the first description of a PLP-dependent fold type I ASR in archaea.

14.
J Biosci Bioeng ; 124(1): 23-27, 2017 Jul.
Article in English | MEDLINE | ID: mdl-28343923

ABSTRACT

A novel amino acid racemase with broad substrate specificity (BAR) was recently isolated from the hyperthermophilic archaeon Pyrococcus horikoshii OT-3. Characterization of this enzyme has been difficult, however, because the recombinant enzyme is produced mainly as an inclusion body in Escherichia coli. In this study, expression of the recombinant protein into the soluble fraction was markedly improved by co-expression with chaperone molecules. The purified enzyme retained its full activity after incubation at 80°C for at least 2 h in buffer (pH 7-10), making this enzyme the most thermostable amino acid racemase so far known. Besides the nine amino acids containing hydrophobic and aromatic amino acids previously reported (Kawakami et al., Amino Acids, 47, 1579-1587, 2015), the enzyme exhibited substantial activity toward Thr (about 42% of relative activity toward Phe) and showed no activity toward Arg, His, Gln, and Asn. The substrate specificity of this enzyme thus differs markedly from those of other known amino acid racemases. In particular, the high reaction rate with Trp and Tyr, in addition to Leu, Met and Phe as substrates is a noteworthy feature of this enzyme. The high reactivity toward Trp and Tyr, as well as extremely high thermostability, is likely a major advantage of using BAR for biochemical conversion of these aromatic amino acids.


Subject(s)
Amino Acid Isomerases/metabolism , Pyrococcus horikoshii/enzymology , Temperature , Amino Acid Sequence , Hydrophobic and Hydrophilic Interactions , Pyrococcus horikoshii/physiology , Substrate Specificity
15.
Protein Expr Purif ; 126: 62-68, 2016 10.
Article in English | MEDLINE | ID: mdl-27215670

ABSTRACT

2-Deoxy-d-ribose-5-phosphate aldolase (DERA) catalyzes the aldol reaction between two aldehydes and is thought to be a potential biocatalyst for the production of a variety of stereo-specific materials. A gene encoding DERA from the extreme halophilic archaeon, Haloarcula japonica, was overexpressed in Escherichia coli. The gene product was successfully purified, using procedures based on the protein's halophilicity, and characterized. The expressed enzyme was stable in a buffer containing 2 M NaCl and exhibited high thermostability, retaining more than 90% of its activity after heating at 70 °C for 10 min. The enzyme was also tolerant to high concentrations of organic solvents, such as acetonitrile and dimethylsulfoxide. Moreover, H. japonica DERA was highly resistant to a high concentration of acetaldehyde and retained about 35% of its initial activity after 5-h' exposure to 300 mM acetaldehyde at 25 °C, the conditions under which E. coli DERA is completely inactivated. The enzyme exhibited much higher activity at 25 °C than the previously characterized hyperthermophilic DERAs (Sakuraba et al., 2007). Our results suggest that the extremely halophilic DERA has high potential to serve as a biocatalyst in organic syntheses. This is the first description of the biochemical characterization of a halophilic DERA.


Subject(s)
Aldehyde-Lyases , Archaeal Proteins , Haloarcula , Sodium Chloride/chemistry , Aldehyde-Lyases/biosynthesis , Aldehyde-Lyases/chemistry , Aldehyde-Lyases/genetics , Aldehyde-Lyases/isolation & purification , Archaeal Proteins/biosynthesis , Archaeal Proteins/chemistry , Archaeal Proteins/genetics , Archaeal Proteins/isolation & purification , Enzyme Stability , Escherichia coli/genetics , Escherichia coli/metabolism , Haloarcula/enzymology , Haloarcula/genetics , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification
16.
Amino Acids ; 47(8): 1579-87, 2015 Aug.
Article in English | MEDLINE | ID: mdl-25963389

ABSTRACT

To date, there have been few reports analyzing the amino acid requirement for growth of hyperthermophilic archaea. We here found that the hyperthermophilic archaeon Pyrococcus horikoshii OT-3 requires Thr, Leu, Val, Phe, Tyr, Trp, His and Arg in the medium for growth, and shows slow growth in medium lacking Met or Ile. This largely corresponds to the presence, or absence, of genes related to amino acid biosynthesis in its genome, though there are exceptions. The amino acid requirements were dramatically lost by addition of D-isomers of Met, Leu, Val, allo-Ile, Phe, Tyr, Trp and Arg. Tracer analysis using (14)C-labeled D-Trp showed that D-Trp in the medium was used as a protein component in the cells, suggesting the presence of D-amino acid metabolic enzymes. Pyridoxal 5'-phosphate (PLP)-dependent racemase activity toward Met, Leu and Phe was detected in crude extract of P. horikoshii and was enhanced in cells grown in the medium supplemented with D-amino acids, especially D-allo-Ile. The gene encoding the racemase was narrowed down to one open reading frame on the basis of enzyme purification from P. horikoshii cells, and the recombinant enzyme exhibited PLP-dependent racemase activity toward several amino acids, including Met, Leu and Phe, but not Pro, Asp or Glu. This is the first report showing the presence in a hyperthermophilic archaeon of a PLP-dependent amino acid racemase with broad substrate specificity that is likely responsible for utilization of D-amino acids for growth.


Subject(s)
Amino Acid Isomerases/metabolism , Pyrococcus horikoshii/enzymology , Amino Acid Isomerases/analysis , Amino Acids/administration & dosage , Amino Acids/biosynthesis , Amino Acids/metabolism , Genome, Archaeal , Pyrococcus horikoshii/genetics , Pyrococcus horikoshii/growth & development , Pyrococcus horikoshii/metabolism
17.
Biosci Biotechnol Biochem ; 78(12): 2045-50, 2014.
Article in English | MEDLINE | ID: mdl-25126984

ABSTRACT

We previously found a very large NAD-dependent glutamate dehydrogenase with approximately 170 kDa subunit from Janthinobacterium lividum (Jl-GDH) and predicted that GDH reaction occurred in the central domain of the subunit. To gain further insights into the role of the central domain, several single point mutations were introduced. The enzyme activity was completely lost in all single mutants of R784A, K810A, K820A, D885A, and S1142A. Because, in sequence alignment analysis, these residues corresponded to the residues responsible for glutamate binding in well-known small GDH with approximately 50 kDa subunit, very large GDH and well-known small GDH may share the same catalytic mechanism. In addition, we demonstrated that C1141, one of the three cysteine residues in the central domain, was responsible for the inhibition of enzyme activity by HgCl2, and HgCl2 functioned as an activating compound for a C1141T mutant. At low concentrations, moreover, HgCl2 was found to function as an activating compound for a wild-type Jl-GDH. This suggests that the mechanism for the activation is entirely different from that for the inhibition.


Subject(s)
Bacterial Proteins/chemistry , Burkholderiaceae/enzymology , Glutamate Dehydrogenase/chemistry , Glutamic Acid/chemistry , Mutation , Protein Subunits/chemistry , Amino Acid Sequence , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Binding Sites , Biocatalysis , Burkholderiaceae/genetics , Cysteine/chemistry , Cysteine/metabolism , Enzyme Assays , Gene Expression , Glutamate Dehydrogenase/genetics , Glutamate Dehydrogenase/metabolism , Glutamic Acid/metabolism , Kinetics , Mercuric Chloride/chemistry , Molecular Sequence Data , Mutagenesis, Site-Directed , Protein Binding , Protein Structure, Tertiary , Protein Subunits/genetics , Protein Subunits/metabolism , Sequence Homology, Amino Acid , Structure-Activity Relationship
18.
Appl Microbiol Biotechnol ; 97(8): 3419-27, 2013 Apr.
Article in English | MEDLINE | ID: mdl-22752365

ABSTRACT

Two types of hetero-oligomeric dye-linked L-proline dehydrogenases (α4ß4 and αßγδ types) are expressed in the hyperthermophilic archaea belonging to Thermococcales. In both enzymes, the ß subunit (PDHß) is responsible for catalyzing L-proline dehydrogenation. The genes encoding the two enzyme types form respective clusters that are completely conserved among Pyrococcus and Thermococcus strains. To compare the enzymatic properties of PDHßs from α4ß4- and αßγδ-type enzyme complexes, eight PDHßs (four of each type) from Pyrococcus furiosus DSM3638, Pyrococcus horikoshii OT-3, Thermococcus kodakaraensis KOD1 JCM12380 and Thermococcus profundus DSM9503 were expressed in Escherichia coli cells and purified to homogeneity using one-step Ni-chelating chromatography. The α4ß4-type PDHßs showed greater thermostability than most of the αßγδ-type PDHßs: the former retained more than 80 % of their activity after heating at 70 °C for 20 min, while the latter showed different thermostabilities under the same conditions. In addition, the α4ß4-type PDHßs utilized ferricyanide as the most preferable electron acceptor, whereas αßγδ-type PDHßs preferred 2, 6-dichloroindophenol, with one exception. These results indicate that the differences in the enzymatic properties of the PDHßs likely reflect whether they were from an αßγδ- or α4ß4-type complex, though the wider divergence observed within αßγδ-type PDHßs based on the phylogenetic analysis may also be responsible for their inconsistent enzymatic properties. By contrast, differences in the kinetic parameters among the PDHßs did not reflect the complex type. Interestingly, the k cat value for free α4ß4-type PDHß from P. horikoshii was much larger than the value for the same subunit within the α4ß4-complex. This indicates that the isolated PDHß could be a useful element for an electrochemical system for detection of L-proline.


Subject(s)
Proline Oxidase/metabolism , Proline/metabolism , Pyrococcus/enzymology , Thermococcus/enzymology , 2,6-Dichloroindophenol/metabolism , Chromatography, Affinity , Cloning, Molecular , Enzyme Stability , Escherichia coli/genetics , Escherichia coli/metabolism , Ferricyanides/metabolism , Gene Expression , Hot Temperature , Kinetics , Proline Oxidase/genetics , Protein Stability , Pyrococcus/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Thermococcus/genetics , Time Factors
19.
J Biol Chem ; 287(24): 20070-80, 2012 Jun 08.
Article in English | MEDLINE | ID: mdl-22511758

ABSTRACT

Two types of dye-linked L-proline dehydrogenase (PDH1, α4ß4-type hetero-octamer, and PDH2, αßγδ-type heterotetramer) have been identified so far in hyperthermophilic archaea. Here, we report the crystal structure of a third type of L-proline dehydrogenase, found in the aerobic hyperthermophilic archaeon Aeropyrum pernix, whose structure (homodimer) is much simpler than those of previously studied L-proline dehydrogenases. The structure was determined at a resolution of 1.92 Å. The asymmetric unit contained one subunit, and a crystallographic 2-fold axis generated the functional dimer. The overall fold of the subunit showed similarity to that of the PDH1 ß-subunit, which is responsible for catalyzing L-proline dehydrogenation. However, the situation at the subunit-subunit interface of the A. pernix enzyme was totally different from that in PDH1. The presence of additional surface elements in the A. pernix enzyme contributes to a unique dimer association. Moreover, the C-terminal Leu(428), which is provided by a tail extending from the FAD-binding domain, shielded the active site, and an L-proline molecule was entrapped within the active site cavity. The K(m) value of a Leu(428) deletion mutant for L-proline was about 800 times larger than the K(m) value of the wild-type enzyme, although the k(cat) values did not differ much between the two enzymes. This suggests the C-terminal Leu(428) is not directly involved in catalysis, but it is essential for maintaining a high affinity for the substrate. This is the first description of an LPDH structure with L-proline bound, and it provides new insight into the substrate binding of LPDH.


Subject(s)
Aeropyrum/enzymology , Archaeal Proteins/chemistry , Proline Oxidase/chemistry , Protein Multimerization , Crystallography, X-Ray , Protein Structure, Quaternary , Protein Structure, Tertiary
20.
Article in English | MEDLINE | ID: mdl-22442236

ABSTRACT

A galactose 1-phosphate uridylyltransferase from the hyperthermophilic archaeon Pyrobaculum aerophilum was crystallized using the sitting-drop vapour-diffusion method with polyethylene glycol 8000 as the precipitant. The crystals belonged to the tetragonal space group P4(1), with unit-cell parameters a = b = 73.3, c = 126.1 Å, and diffracted to 2.73 Å resolution on beamline BL5A at the Photon Factory. The overall R(merge) was 7.3% and the data completeness was 99.8%.


Subject(s)
Pyrobaculum/enzymology , UTP-Hexose-1-Phosphate Uridylyltransferase/chemistry , Crystallization , Crystallography, X-Ray , Gene Expression , UTP-Hexose-1-Phosphate Uridylyltransferase/genetics , UTP-Hexose-1-Phosphate Uridylyltransferase/isolation & purification
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