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1.
Biosci Biotechnol Biochem ; 85(7): 1650-1657, 2021 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-33942867

RESUMO

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.


Assuntos
Isomerases de Aminoácido/metabolismo , Proteínas Arqueais/metabolismo , Thermococcus/enzimologia , Isomerases de Aminoácido/química , Sequência de Aminoácidos , Proteínas Arqueais/química , Eletroforese em Gel de Poliacrilamida , Genes Arqueais , Chaperonas Moleculares/metabolismo , Filogenia , Especificidade por Substrato , Thermococcus/genética
2.
Protein Expr Purif ; 126: 62-68, 2016 10.
Artigo em Inglês | MEDLINE | ID: mdl-27215670

RESUMO

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.


Assuntos
Aldeído Liases , Proteínas Arqueais , Haloarcula , Cloreto de Sódio/química , Aldeído Liases/biossíntese , Aldeído Liases/química , Aldeído Liases/genética , Aldeído Liases/isolamento & purificação , Proteínas Arqueais/biossíntese , Proteínas Arqueais/química , Proteínas Arqueais/genética , Proteínas Arqueais/isolamento & purificação , Estabilidade Enzimática , Escherichia coli/genética , Escherichia coli/metabolismo , Haloarcula/enzimologia , Haloarcula/genética , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação
3.
Amino Acids ; 47(8): 1579-87, 2015 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-25963389

RESUMO

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.


Assuntos
Isomerases de Aminoácido/metabolismo , Pyrococcus horikoshii/enzimologia , Isomerases de Aminoácido/análise , Aminoácidos/administração & dosagem , Aminoácidos/biossíntese , Aminoácidos/metabolismo , Genoma Arqueal , Pyrococcus horikoshii/genética , Pyrococcus horikoshii/crescimento & desenvolvimento , Pyrococcus horikoshii/metabolismo
4.
Biosci Biotechnol Biochem ; 78(12): 2045-50, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25126984

RESUMO

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.


Assuntos
Proteínas de Bactérias/química , Burkholderiaceae/enzimologia , Glutamato Desidrogenase/química , Ácido Glutâmico/química , Mutação , Subunidades Proteicas/química , Sequência de Aminoácidos , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Biocatálise , Burkholderiaceae/genética , Cisteína/química , Cisteína/metabolismo , Ensaios Enzimáticos , Expressão Gênica , Glutamato Desidrogenase/genética , Glutamato Desidrogenase/metabolismo , Ácido Glutâmico/metabolismo , Cinética , Cloreto de Mercúrio/química , Dados de Sequência Molecular , Mutagênese Sítio-Dirigida , Ligação Proteica , Estrutura Terciária de Proteína , Subunidades Proteicas/genética , Subunidades Proteicas/metabolismo , Homologia de Sequência de Aminoácidos , Relação Estrutura-Atividade
5.
Biochim Biophys Acta Mol Cell Biol Lipids ; 1869(3): 159452, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38244676

RESUMO

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.


Assuntos
Ácido Oleico , Peroxissomos , Animais , Cricetinae , Humanos , Ácido Oleico/farmacologia , Ácido Oleico/metabolismo , Peroxissomos/metabolismo , Ácidos Graxos/metabolismo , Cricetulus , Células CHO , Ácidos Graxos não Esterificados/metabolismo , Apoptose
6.
J Biol Chem ; 287(24): 20070-80, 2012 Jun 08.
Artigo em Inglês | MEDLINE | ID: mdl-22511758

RESUMO

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.


Assuntos
Aeropyrum/enzimologia , Proteínas Arqueais/química , Prolina Oxidase/química , Multimerização Proteica , Cristalografia por Raios X , Estrutura Quaternária de Proteína , Estrutura Terciária de Proteína
7.
Appl Microbiol Biotechnol ; 97(8): 3419-27, 2013 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-22752365

RESUMO

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.


Assuntos
Prolina Oxidase/metabolismo , Prolina/metabolismo , Pyrococcus/enzimologia , Thermococcus/enzimologia , 2,6-Dicloroindofenol/metabolismo , Cromatografia de Afinidade , Clonagem Molecular , Estabilidade Enzimática , Escherichia coli/genética , Escherichia coli/metabolismo , Ferricianetos/metabolismo , Expressão Gênica , Temperatura Alta , Cinética , Prolina Oxidase/genética , Estabilidade Proteica , Pyrococcus/genética , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Thermococcus/genética , Fatores de Tempo
8.
Int J Biol Macromol ; 249: 126070, 2023 Sep 30.
Artigo em Inglês | MEDLINE | ID: mdl-37524275

RESUMO

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.


Assuntos
NADPH Desidrogenase , Cristalinas mu , NADP/metabolismo , Sequência de Aminoácidos , Arginina , Sítios de Ligação , Cristalografia por Raios X , Especificidade por Substrato
9.
Artigo em Inglês | MEDLINE | ID: mdl-36460260

RESUMO

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.


Assuntos
Ácidos Graxos , Peroxissomos , Cricetinae , Animais , Peroxissomos/metabolismo , Ácidos Graxos/metabolismo , Células CHO , Cricetulus , Oxirredução
10.
J Biochem ; 175(1): 115-124, 2023 Dec 20.
Artigo em Inglês | MEDLINE | ID: mdl-37827526

RESUMO

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.


Assuntos
Arabidopsis , Brassica , Glicoesfingolipídeos/metabolismo , Esfingolipídeos/metabolismo , Plantas/metabolismo , Arabidopsis/metabolismo
11.
Artigo em Inglês | MEDLINE | ID: mdl-22442236

RESUMO

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%.


Assuntos
Pyrobaculum/enzimologia , UTP-Hexose-1-Fosfato Uridililtransferase/química , Cristalização , Cristalografia por Raios X , Expressão Gênica , UTP-Hexose-1-Fosfato Uridililtransferase/genética , UTP-Hexose-1-Fosfato Uridililtransferase/isolamento & purificação
12.
Appl Microbiol Biotechnol ; 93(1): 83-93, 2012 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-22089387

RESUMO

Dye-linked L-proline dehydrogenase (ProDH) catalyzes the oxidation of L-proline to ∆(1)-pyrroline-5-carboxylate (P5C) in the presence of artificial electron acceptors. The enzyme is known to be widely distributed in bacteria and eukarya, together with nicotinamide adenine dinucleotide (phosphate)-dependent P5C dehydrogenase, and to function in the metabolism of L-proline to L-glutamate. In addition, over the course of the last decade, three other types of ProDH with molecular compositions completely different from previously known ones have been identified in hyperthermophilic archaea. The first is a heterotetrameric αßγδ-type ProDH, which exhibits both ProDH and reduced nicotinamide adenine dinucleotide dehydrogenase activity and includes two electron transfer proteins. The second is a heterooctameric α(4)ß(4)-type ProDH, which uses flavin adenine dinucleotide, flavin mononucleotide, adenosine triphosphate, and Fe as cofactors and creates a new electron transfer pathway. The third is a recently identified homodimeric ProDH, which exhibits the greatest thermostability among these archaeal ProDHs. This minireview focuses on the functional and structural properties of these three types of archaeal ProDH and their distribution in archaea. In addition, we will describe the specific application of hyperthermostable ProDH for use in a biosensor and for DNA sensing.


Assuntos
Archaea/enzimologia , Prolina Oxidase/metabolismo , Prolina/metabolismo , Pirróis/metabolismo , Sequência de Aminoácidos , Archaea/genética , Coenzimas/metabolismo , Modelos Moleculares , Dados de Sequência Molecular , Prolina Oxidase/química , Prolina Oxidase/genética , Multimerização Proteica , Subunidades Proteicas/metabolismo
13.
Int J Biol Macromol ; 208: 731-740, 2022 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-35337912

RESUMO

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.


Assuntos
Pyrococcus horikoshii , Archaea/metabolismo , Cristalografia por Raios X , Humanos , Modelos Moleculares , Ornitina/química , Fosfato de Piridoxal/química , Pyrococcus horikoshii/metabolismo , Especificidade por Substrato , Transaminases/química
14.
Artigo em Inglês | MEDLINE | ID: mdl-34848380

RESUMO

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.


Assuntos
Peroxissomos
15.
FEBS Lett ; 596(23): 3024-3036, 2022 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-36266963

RESUMO

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.


Assuntos
Arabidopsis , Brassica , Fosfolipase D , Raphanus , Fosfolipase D/genética , Fosfolipase D/química , Raphanus/metabolismo , Fosfolipases/metabolismo , Esfingolipídeos/metabolismo , Brassica/genética , Brassica/química , Arabidopsis/genética , Arabidopsis/metabolismo
16.
Acta Crystallogr Sect F Struct Biol Cryst Commun ; 67(Pt 11): 1425-7, 2011 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-22102248

RESUMO

A dye-linked D-lactate dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix was crystallized using the hanging-drop vapour-diffusion method with polyethylene glycol 8000 as the precipitant. The crystals belonged to the monoclinic space group P2(1), with unit-cell parameters a = 63.4, b = 119.4, c = 70.2 Å, ß = 112.0°, and diffracted to 2.0 Å resolution on the BL26B1 beamline at SPring-8. The overall R(merge) was 4.5% and the completeness was 99.8%.


Assuntos
Aeropyrum/enzimologia , Lactato Desidrogenases/química , Cristalização , Cristalografia por Raios X
17.
Lipids ; 56(2): 181-188, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-32996178

RESUMO

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.


Assuntos
Ácidos Graxos/análise , Pele/química , Esfingomielinas/análise , Animais , Cromatografia Gasosa , Masculino , Espectrometria de Massas , Camundongos , Camundongos Endogâmicos ICR
18.
Biochim Biophys Acta ; 1794(10): 1496-504, 2009 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-19555779

RESUMO

Tartrate oxidation activity was found in the crude extract of an aerobic hyperthermophilic archaeon Aeropyrum pernix, and the enzyme was identified as (S)-malate dehydrogenase (MDH), which, when produced in Escherichia coli, was mainly obtained as an inactive inclusion body. The inclusion body was dissolved in 6 M guanidine-HCl and gradually refolded to the active enzyme through dilution of the denaturant. The purified recombinant enzyme consisted of four identical subunits with a molecular mass of about 110 kDa. NADP was preferred as a coenzyme over NAD for (S)-malate oxidation and, unlike MDHs from other sources, this enzyme readily catalyzed the oxidation of (2S,3S)-tartrate and (2S,3R)-tartrate. The tartrate oxidation activity was also observed in MDHs from the hyperthermophilic archaea Methanocaldococcus jannaschii and Archaeoglobus fulgidus, suggesting these hyperthermophilic MDHs loosely bind their substrates. The refolded A. pernix MDH was also crystallized, and the structure was determined at a resolution of 2.9 A. Its overall structure was similar to those of the M. jannaschii, Chloroflexus aurantiacus, Chlorobium vibrioforme and Cryptosporidium parvum [lactate dehydrogenase-like] MDHs with root-mean-square-deviation values between 1.4 and 2.1 A. Consistent with earlier reports, Ala at position 53 was responsible for coenzyme specificity, and the next residue, Arg, was important for NADP binding. Structural comparison revealed that the hyperthermostability of the A. pernix MDH is likely attributable to its smaller cavity volume and larger numbers of ion pairs and ion-pair networks, but the molecular strategy for thermostability may be specific for each enzyme.


Assuntos
Aeropyrum/enzimologia , Malato Desidrogenase/química , Aeropyrum/genética , Sequência de Aminoácidos , Sequência de Bases , Domínio Catalítico/genética , Cristalografia por Raios X , Primers do DNA/genética , DNA Arqueal/genética , Estabilidade Enzimática , Genes Arqueais , Malato Desidrogenase/genética , Malato Desidrogenase/metabolismo , Modelos Moleculares , Dados de Sequência Molecular , Peso Molecular , Dobramento de Proteína , Subunidades Proteicas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Homologia de Sequência de Aminoácidos , Especificidade por Substrato , Termodinâmica
19.
Biosci Biotechnol Biochem ; 74(4): 884-7, 2010.
Artigo em Inglês | MEDLINE | ID: mdl-20378971

RESUMO

The kinetics of a very large NAD-dependent glutamate dehydrogenase from Janthinobacterium lividum showed positive cooperativity toward alpha-ketoglutarate and NADH, and the Michaelis-Menten type toward ammonium chloride in the absence of the catalytic activator, L-aspartate. An increase in the maximum activity accompanied the decrease in the S(0.5) values for alpha-ketoglutarate and NADH with the addition of L-aspartate, and the kinetic response for alpha-ketoglutarate changed completely to a typical Michaelis-Menten type in the presence of 10 mM L-aspartate.


Assuntos
Glutamato Desidrogenase/metabolismo , Ácido Aspártico , Catálise , Chromobacterium/metabolismo , Ácido Glutâmico , Ácidos Cetoglutáricos , Cinética , NAD/metabolismo , Oxalobacteraceae/metabolismo
20.
Artigo em Inglês | MEDLINE | ID: mdl-32615533

RESUMO

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.


Assuntos
Ceramidas/isolamento & purificação , Glicoesfingolipídeos/isolamento & purificação , Compostos Fitoquímicos/isolamento & purificação , Ceramidas/análise , Ceramidas/química , Cromatografia em Camada Fina , Estabilidade de Medicamentos , Glicoesfingolipídeos/análise , Glicoesfingolipídeos/química , Interações Hidrofóbicas e Hidrofílicas , Inositol/análogos & derivados , Inositol/química , Compostos Fitoquímicos/análise , Compostos Fitoquímicos/química , Polissacarídeos/química , Solventes
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