scholarly journals The mechanism of a one-substrate transketolase reaction

2020 ◽  
Vol 40 (8) ◽  
Author(s):  
Olga N. Solovjeva ◽  
Marina V. Kovina ◽  
Maria G. Zavialova ◽  
Victor G. Zgoda ◽  
Dmitrii S. Shcherbinin ◽  
...  

Abstract Transketolase catalyzes the transfer of a glycolaldehyde residue from ketose (the donor substrate) to aldose (the acceptor substrate). In the absence of aldose, transketolase catalyzes a one-substrate reaction that involves only ketose. The mechanism of this reaction is unknown. Here, we show that hydroxypyruvate serves as a substrate for the one-substrate reaction and, as well as with the xylulose-5-phosphate, the reaction product is erythrulose rather than glycolaldehyde. The amount of erythrulose released into the medium is equimolar to a double amount of the transformed substrate. This could only be the case if the glycol aldehyde formed by conversion of the first ketose molecule (the product of the first half reaction) remains bound to the enzyme, waiting for condensation with the second molecule of glycol aldehyde. Using mass spectrometry of catalytic intermediates and their subsequent fragmentation, we show here that interaction of the holotransketolase with hydroxypyruvate results in the equiprobable binding of the active glycolaldehyde to the thiazole ring of thiamine diphosphate and to the amino group of its aminopyrimidine ring. We also show that these two loci can accommodate simultaneously two glycolaldehyde molecules. It explains well their condensation without release into the medium, which we have shown earlier.

Molbank ◽  
10.3390/m1140 ◽  
2020 ◽  
Vol 2020 (2) ◽  
pp. M1140
Author(s):  
Jack Bennett ◽  
Paul Murphy

(2S,3R,6R)-2-[(R)-1-Hydroxyallyl]-4,4-dimethoxy-6-methyltetrahydro-2H-pyran-3-ol was isolated in 18% after treating the glucose derived (5R,6S,7R)-5,6,7-tris[(triethylsilyl)oxy]nona-1,8-dien-4-one with (1S)-(+)-10-camphorsulfonic acid (CSA). The one-pot formation of the title compound involved triethylsilyl (TES) removal, alkene isomerization, intramolecular conjugate addition and ketal formation. The compound was characterized by 1H and 13C NMR spectroscopy, ESI mass spectrometry and IR spectroscopy. NMR spectroscopy was used to establish the product structure, including the conformation of its tetrahydropyran ring.


2005 ◽  
Vol 11 (5) ◽  
pp. 535-546 ◽  
Author(s):  
Anna Kondakov ◽  
Buko Lindner

Bacterial glycolipids are complex amphiphilic molecules which are, on the one hand, of utmost importance for the organization and function of bacterial membranes and which, on the other hand, play a major role in the activation of cells of the innate and adaptive immune system of the host. Already small alterations to their chemical structure may influence the biological activity tremendously. Due to their intrinsic biological heterogeneity [number and type of fatty acids, saccharide structures and substitution with for example, phosphate ( P), 2-aminoethyl-(pyro)phosphate groups ( P-Etn) or 4-amino-4-deoxyarabinose (Ara4N)], separation of the different components are a prerequisite for unequivocal chemical and nuclear magnetic resonance structural analyses. In this contribution, the structural information which can be obtained from heterogenous samples of glycolipids by Fourier transform (FT) ion cyclotron resonance mass spectrometric methods is described. By means of recently analysed complex biological samples, the possibilities of high-resolution electrospray ionization FT-MS are demonstrated. Capillary skimmer dissociation, as well as tandem mass spectrometry (MS/MS) analysis utilizing collision-induced dissociation and infrared multiphoton dissociation, are compared and their advantages in providing structural information of diagnostic importance are discussed.


2004 ◽  
Vol 186 (11) ◽  
pp. 3415-3422 ◽  
Author(s):  
Véronique David ◽  
Bülent Bozdogan ◽  
Jean-Luc Mainardi ◽  
Raymond Legrand ◽  
Laurent Gutmann ◽  
...  

ABSTRACT We have studied the basis for intrinsic resistance to low levels of vancomycin in Clostridium innocuum NCIB 10674 (MIC = 8 μg/ml). Analysis by high-pressure liquid chromatography (HPLC) and mass spectrometry of peptidoglycan nucleotide precursors pools revealed the presence of two types of UDP-MurNac-pentapeptide precursors constitutively produced, an UDP-MurNAc-pentapeptide with a serine at the C terminus which represented 93% of the pool and an UDP-MurNAc-pentapeptide with an alanine at the C terminus which represented the rest of the pool. C. innocuum cell wall muropeptides containing pentapeptide[Ser], either dialanine substituted on the epsilon amino group of lysine or not, were identified and represented about 10% of the monomers while only 1% of pentapeptide[d-Ala] monomers were found. The sequence of a 2,465-bp chromosomal fragment from C. innocuum was determined and revealed the presence of ddlc. innocuum and C. innocuum racemase genes putatively encoding homologues of d-Ala:d-X ligases and amino acid racemases, respectively. Analysis of the pool of precursors of Enterococcus faecalis JH2-2, containing cloned ddlc. innocuum and C. innocuum racemase genes showed in addition to the UDP-MurNAc-pentapeptide[d-Ala], the presence of an UDP-MurNAc-pentapeptide[d-Ser] precursor. However, the expression of low-level resistance to vancomycin was observed only when both genes were cloned in E. faecalis JH2-2 together with the vanXYc gene from Enterococcus gallinarum BM4174 which encodes a d,d-peptidase which eliminates preferentially the high affinity vancomycin UDP-MurNAc-pentapeptide [d-Ala] precursors produced by the host. We conclude that resistance to vancomycin in C. innocuum NCIB 10674 was related to the presence of the two chromosomal ddlc. innocuum and C. innocuum racemase genes allowing the synthesis of a peptidoglycan precursor terminating in serine with low affinity for vancomycin.


Author(s):  
J M Matey ◽  
Adrián López-Fernández ◽  
Carmen García-Ruiz ◽  
Gemma Montalvo ◽  
M D Moreno ◽  
...  

Abstract The analysis of drugs of abuse in hair and other biological matrices of forensic interest requires great selectivity and sensitivity. This is done traditionally through target analysis, with one or more analytical methods, or with different and specific preanalytical phases, and complex procedures performed by the toxicological laboratories, and there is no exception with ketamine-like compounds, such as methoxetamine, a new psychoactive substance whose use has increased in the last decades, and continues to grow quickly year by year. More validated methods of analysis are needed to detect these substances in low concentrations selectively. Reanalyzing the samples of a former case of a polydrug consumer accused of a crime against public health in Spain, five metabolites of methoxetamine (normethoxetamine, O-desmethylmethoxetamine, dehydromethoxetamine, dihydronormethoxetamine and hydroxynormethoxetamine) were tentatively detected using a high-resolution technique, i.e., liquid chromatography coupled to high-resolution mass spectrometry (LC–HR-MS-MS). The highest analytical selectivity of LC–HR-MS-MS method together a universal and simpler pretreatment stages has demonstrated to allow faster analysis and more sensitivity than the one performed traditionally at the INTCF laboratories, which was gas chromatography coupled to mass spectrometry.


Author(s):  
Meng Wang ◽  
Lihua Jiang ◽  
Ruiqi Jian ◽  
Joanne Y Chan ◽  
Qing Liu ◽  
...  

Abstract Motivation Data normalization is an important step in processing proteomics data generated in mass spectrometry experiments, which aims to reduce sample-level variation and facilitate comparisons of samples. Previously published methods for normalization primarily depend on the assumption that the distribution of protein expression is similar across all samples. However, this assumption fails when the protein expression data is generated from heterogenous samples, such as from various tissue types. This led us to develop a novel data-driven method for improved normalization to correct the systematic bias meanwhile maintaining underlying biological heterogeneity. Results To robustly correct the systematic bias, we used the density-power-weight method to down-weigh outliers and extended the one-dimensional robust fitting method described in the previous work to our structured data. We then constructed a robustness criterion and developed a new normalization algorithm, called RobNorm. In simulation studies and analysis of real data from the genotype-tissue expression project, we compared and evaluated the performance of RobNorm against other normalization methods. We found that the RobNorm approach exhibits the greatest reduction in systematic bias while maintaining across-tissue variation, especially for datasets from highly heterogeneous samples. Availabilityand implementation https://github.com/mwgrassgreen/RobNorm. Supplementary information Supplementary data are available at Bioinformatics online.


1969 ◽  
Vol 47 (12) ◽  
pp. 1103-1107 ◽  
Author(s):  
W. M. Johnson ◽  
D. W. S. Westlake

Active cell-free extracts of Peptococcus aerogenes were prepared which metabolized glutamic acid to α-hydroxyglutaric acid. Factors affecting the formation of this intermediate were studied by following the conversion of glutamic acid labelled with 14C in the one or five positions. The results of these experiments revealed that the production of α-hydroxyglutaric acid from glutamic acid by cell-free extracts was NAD-dependent. The labelled α-hydroxyglutaric acid produced by NAD-supplemented extracts was purified by anion exchange chromatography and identified by several methods including paper and thin-layer chromatography, mass spectrometry, and infrared spectroscopy. A pathway has been proposed for the conversion of glutamic acid to α-hydroxyglutaric acid by cell-free extracts of P. aerogenes.


1993 ◽  
Vol 7 (8) ◽  
pp. 704-706 ◽  
Author(s):  
J.-L. Aubagnac ◽  
I. Gilles ◽  
G. Gosselin ◽  
C. Perigaud ◽  
P. Labataille ◽  
...  

Radiocarbon ◽  
2002 ◽  
Vol 44 (1) ◽  
pp. 45-52 ◽  
Author(s):  
D J Donahue ◽  
J S Olin ◽  
G Harbottle

The Vinland Map, drawn on a 27.8 × 41.0 cm parchment bifolium, is housed in the Beinecke Rare Book and Manuscript Library at Yale University. In the northwest Atlantic Ocean, it shows “the Island of Vinland, discovered by Bjarni and Leif in company.” Skelton, Marston, and Painter (Skelton et al. 1965, 1995) firmly argued the map's authenticity, associating it with the Council of Basle (AD 1431–1449), that is, half a century before Columbus's voyage. Nevertheless, vigorous scholarly questioning of the map's authenticity has persisted (Washburn 1966; McCrone 1974; Olin and Towe 1976; Cahill et al. 1987; McCrone 1988; Towe 1990). We have determined the precise radiocarbon age of the map's parchment by accelerator mass spectrometry (AMS). The one-sigma calibrated calendrical date range is AD 1434 ± 11 years: the 95% confidence level age range is AD 1411–1468.


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