Recent study on nonketotic hyperglycinemia, an inborn error of glycine metabolism, is reviewed from clinical, metabolic, molecular, and neuropathological points of view. This disorder is caused by an inherited deficiency of the mitochondrial glycine cleavage system (GCS), which causes accumulation of glycine in such body fluids as plasma, cerebrospinal fluid, and urine. There are four disease types: neonatal, infantile, late-onset, and transient types. The genetic backgrounds of the neonatal and infantile types have been largely clarified by a comprehensive mutational screening of genes encoding three components of the GCS, while the molecular pathogenesis of the late-onset and transient types are largely unknown. In the central nervous system of vertebrates, the GCS has been identified in astrocytes and neural stem cells. The GCS in astrocytes is co-localized with N-methyl-D-aspartate receptors, and is thought to maintain the glycine level around the receptors, while the physiological and pathological roles of the GCS in neural stem cells remains to be elucidated.
Based on the successful use of human milk oligosaccharide patterns for elucidation of the biochemical basis of ABO and Lewis blood types in humans, a strategy to establish reliable techniques to analyze the structures and functions of the N-linked sugar chains of glycoproteins was devised. N-Linked sugar chains were first released quantitatively as oligosaccharides by enzymatic or chemical means, and labeled by reduction with NaB3H4. After fractionation by gel-permeation chromatography and lectin-affinity chromatography, structure of each radioactive oligosaccharide was determined by a series of sensitive methods, which were developed for the structural study of oligosaccharides. By using these techniques, structural rules of the N-linked sugar chains were found. Furthermore, occurrence of site-specific, organ-specific and species-specific N-glycosylation of proteins, which served as important bases for the development of Glycobiology, was revealed.
Chalcone synthase (CHS), the pivotal enzyme in the biosynthesis of flavonoids, is a plant-specific type III polyketide synthase (PKS) that catalyzes a sequential condensation of 4-coumaroyl-CoA with three molecules of malonyl-CoA to produce naringenin chalcone. Two novel CHSs were for the first time cloned and sequenced from rhubarb (Rheum palmatum), a medicinal plant rich in aromatic polyketides. Recombinant CHS1 and CHS2, sharing 90% amino acid sequence identity, showed KM = 61.1 M, kcat = 1.12 min-1, and KM = 36.1 M, kcat = 0.79 min-1 for 4-coumaroyl-CoA, respectively. Interestingly, CHS's conserved Thr197, the residue lining the active-site cavity, is uniquely replaced with Cys in CHS1 and CHS2. It was remarkable that both enzymes accepted long-chain fatty acyl CoAs up to the C20 chain length as a starter substrate to efficiently produce triketide and tetraketide α-pyrones.
Aspergilloglutamic peptidase from Aspergillus niger (formerly called aspergillopepsin II) is a novel pepstatin-insensitive acid endopeptidase distinct from the well-studied aspartic peptidases, and thus is an interesting target for protein structure/function studies. Our recent X-ray crystallographic and site-directed mutagenesis studies showed that the enzyme is a glutamic peptidase in which glutamic acid-110 and glutamine-24 in the heavy chain are involved in the active site, forming a catalytic dyad. In the present study, we have investigated the pH-dependence of the enzyme activity and performed docking calculations to shed light on the catalytic mechanism of the enzyme. The results suggest a novel catalytic mechanism where glutamic acid-110 acts as a general acid in the first phase of catalysis.
A novel prolyl endopeptidase has been purified to homogeneity and characterized from the crude extract powder of the culture filtrate of Aspergillus niger var. macrosporus. It was shown to be a monomeric protein with a molecular weight of approximately 54,500, cleaving Pro-X bonds not only in oligopeptides but also in proteins. It has a pH optimum at around 3.7 and is strongly inhibited by diisopropylfluorophosphate, thus being an acid serine endopeptidase. Comparison of the amino acid sequences of related peptidases in the database indicates that it belongs, not to the serine peptidase family S9 which includes prolyl oligopeptidase, but to the serine peptidase family S28 which includes Pro-specific exopeptidases, such as lysosomal Pro-X carboxypeptidase and dipeptidyl peptidase II.
Proton nuclear magnetic resonance (NMR) titration shifts are a very sensitive indication of proton dissociation from carboxyl groups and of hydrogen-bond formation between carboxylate groups and backbone amide protons. As a model protein, we selected bromelain inhibitor VI (BI-VI), which is a unique double-chain molecule (Mr = 5888), and characterized almost all the proton resonances in the pH range of 1.5-9.9 by two-dimensional NMR. In this study, we first examined the ionization effects of Asp13H(β-CO2H) and Glu24H(γ-CO 2H) (superscript letters H and L indicate heavy and light chains, respectively). It was found that their ionization affected the chemical shifts of the surrounding protons through a maximum of seven consecutive covalent bonds, but scarcely through non-covalent bonds. Furthermore, it was revealed that the formation of two hydrogen bonds of Ser4L(NH)-Asp9H(β-CO 2H) and Lys19H(NH)-Asp32H(β-CO2H) influenced not only the chemical shifts of the amide protons of Ser4L and Lys19H but also those of the alpha protons of Asp9H and Asp32H.
Glutamine amidotransferases (GATases) hydrolyze glutamine and generate ammonia. The glutamine amide nitrogen is utilized for the biosynthesis of a variety of molecules such as amino acids, coenzymes, antibiotics, purine and pyrimidine nucleotides, and glucosamine. Here, we determined the crystal structure of a GATase (PH1346) from the hyperthermophilic archaeon Pyrococcus horikoshii OT3 at 1.89 Å resolution. Its overall structure and active site are the most similar to those of E. coli guanosine 5'-monophosphate (GMP) synthase and Sulfolobus solfataricus anthranilate synthase, respectively.
Using SELEX (systematic evolution of ligands by exponential environment) experiments, from a set of DNA fragments, ∼150bps, most of them originated in the genome of an archaeon, Pyrococcus furiosus, five fragments were selected as containing binding-sites of a transcription factor, FL10 (pot0377090, LrpA). The nucleotide sequences of these fragments were analyzed in the light of our previous finding that FFRPs in general recognize DNA sequences in the 5-3-5 arrangement: NANBNCNDNE[TTT/AAA]NENDNCNBNA, where, e.g. NA is the base complementary to NA. One of the seven 5-3-5 sequences, shared by the five fragments with the smallest numbers of mismatches, was TTCGA [TTT/AAA]TCGAA. In three of the five fragments selected, signal sequences were found immediately upstream of TATA boxes, suggesting possible activation of transcription by FL10 by recruiting the TATA-binding protein (TBP). In another fragment the signal sequence was positioned upstream of a TATA box, and at the same time downstream of another TATA box, thereby repressing transcription of another gene coded in the other direction. Some of the genes coded in these fragments are involved in active oxygen detoxification, suggesting the nature of regulation by FL10.
The metabolic syndrome represents an aggregation of cardiovascular risk factors including obesity, raised blood pressure, impaired glucose tolerance, and dyslipidemia that are associated with increased incidence of arteriosclerosis. Evidence accumulated indicates that the visceral fat accumulation is essential in the development of the syndrome. To investigate the prevalence of the metabolic syndrome in Japan, we analyzed cross-sectional data from 3574 middle aged Japanese (2947 men and 627 women, aged 40-59 years) in a large company, whose visceral fat accumulation was assessed by computed tomography. We employed receiver operation characteristic analysis to identify the optimal visceral fat area (VFA) value that has the sensitivity and the specificity to predict the presence of at least two components of the syndrome in an individual. The sensitivities and the specificities for men were 0.67 and 0.60 at VFA of 100 cm2, and for women, 0.73 and 0.70 at VFA of 65 cm2, respectively. Waist circumferences that corresponded to the VFA cutoff were 86.0 cm for men, and 77.0 cm for women. Using 100 cm2 in men and 65 cm2 in women as the criteria of visceral adiposity, the prevalence of the metabolic syndrome was 25.5% in men and 11.0% in women. Although obesity is less prevalent than in western countries, the metabolic syndrome is substantially widespread in Japan.