Biosynthetic controls that determine the branching and microheterogeneity of protein-bound oligosaccharides

1986 ◽  
Vol 64 (3) ◽  
pp. 163-181 ◽  
Author(s):  
Harry Schachter
Keyword(s):  
Enzyme Activity ◽  
Substrate Specificity ◽  
Substrate Availability ◽  
Enzyme Substrate ◽  
General Rules ◽  
Branching Patterns ◽  
Common Substrate ◽  
Branch Specificity

Detailed studies on the enzyme machinery responsible for the biosynthesis of protein-bound oligosaccharides of the Asn-GlcNAc and Ser(Thr)-GalNAc linkage types have allowed the formulation of some general rules which explain, at least in part, the branching patterns and microheterogeneity of these structures. These rules are discussed under the following headings: (i) competition of two or more enzymes for a common substrate; (ii) controls at the level of enzyme substrate specificity (e.g., critical sugar residues which turn enzyme activity on or off, branch specificity, and the role of the polypeptide in the glycoprotein substrate); (iii) substrate availability.

scholarly journals Machine learning-based prediction of activity and substrate specificity for OleA enzymes in the thiolase superfamily

2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Serina L Robinson ◽  
Megan D Smith ◽  
Jack E Richman ◽  
Kelly G Aukema ◽  
Lawrence P Wackett
Keyword(s):  
Machine Learning ◽  
Enzyme Activity ◽  
Substrate Specificity ◽  
Xanthomonas Campestris ◽  
Membrane Lipids ◽  
Characteristic Curve ◽  
Structural Features ◽  
Activity Levels ◽  
Enzyme Substrate ◽  
Carbon Carbon Bond

Abstract Enzymes in the thiolase superfamily catalyze carbon–carbon bond formation for the biosynthesis of polyhydroxyalkanoate storage molecules, membrane lipids and bioactive secondary metabolites. Natural and engineered thiolases have applications in synthetic biology for the production of high-value compounds, including personal care products and therapeutics. A fundamental understanding of thiolase substrate specificity is lacking, particularly within the OleA protein family. The ability to predict substrates from sequence would advance (meta)genome mining efforts to identify active thiolases for the production of desired metabolites. To gain a deeper understanding of substrate scope within the OleA family, we measured the activity of 73 diverse bacterial thiolases with a library of 15 p-nitrophenyl ester substrates to build a training set of 1095 unique enzyme–substrate pairs. We then used machine learning to predict thiolase substrate specificity from physicochemical and structural features. The area under the receiver operating characteristic curve was 0.89 for random forest classification of enzyme activity, and our regression model had a test set root mean square error of 0.22 (R2 = 0.75) to quantitatively predict enzyme activity levels. Substrate aromaticity, oxygen content and molecular connectivity were the strongest predictors of enzyme–substrate pairing. Key amino acid residues A173, I284, V287, T292 and I316 in the Xanthomonas campestris OleA crystal structure lining the substrate binding pockets were important for thiolase substrate specificity and are attractive targets for future protein engineering studies. The predictive framework described here is generalizable and demonstrates how machine learning can be used to quantitatively understand and predict enzyme substrate specificity.

The role of secondary alcoholic groups of D-galacturonan in its degradation with exo-D-galacturonanase

1980 ◽  
Vol 45 (2) ◽  
pp. 427-434 ◽  
Author(s):  
Kveta Heinrichová ◽  
Rudolf Kohn
Keyword(s):  
Acetyl Derivative ◽  
Competitive Inhibitor ◽  
Hydroxyl Groups ◽  
Pectic Acid ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
The Individual ◽  
Degradation Degree ◽  
Derivatives Of

The effect of exo-D-galacturonanase from carrot on O-acetyl derivatives of pectic acid of variousacetylation degree was studied. Substitution of hydroxyl groups at C(2) and C(3) of D-galactopyranuronic acid units influences the initial rate of degradation, degree of degradation and its maximum rate, the differences being found also in the time of limit degradations of the individual O-acetyl derivatives. Value of the apparent Michaelis constant increases with increase of substitution and value of Vmax changes. O-Acetyl derivatives act as a competitive inhibitor of degradation of D-galacturonan. The extent of the inhibition effect depends on the degree of substitution. The only product of enzymic reaction is D-galactopyranuronic acid, what indicates that no degradation of the terminal substituted unit of O-acetyl derivative of pectic acid takes place. Substitution of hydroxyl groups influences the affinity of the enzyme towards the modified substrate. The results let us presume that hydroxyl groups at C(2) and C(3) of galacturonic unit of pectic acid are essential for formation of the enzyme-substrate complex.

scholarly journals System-wide identification and prioritization of enzyme substrates by thermal analysis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Amir Ata Saei ◽  
Christian M. Beusch ◽  
Pierre Sabatier ◽  
Juan Astorga Wells ◽  
Hassan Gharibi ◽  
...  
Keyword(s):  
Thermal Analysis ◽  
Thioredoxin Reductase ◽  
Structural Level ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Enzyme Substrate ◽  
Thioredoxin Reductase 1 ◽  
Enzyme Substrates ◽  
Substrate Proteins

AbstractDespite the immense importance of enzyme–substrate reactions, there is a lack of general and unbiased tools for identifying and prioritizing substrate proteins that are modified by the enzyme on the structural level. Here we describe a high-throughput unbiased proteomics method called System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis (SIESTA). The approach assumes that the enzymatic post-translational modification of substrate proteins is likely to change their thermal stability. In our proof-of-concept studies, SIESTA successfully identifies several known and novel substrate candidates for selenoprotein thioredoxin reductase 1, protein kinase B (AKT1) and poly-(ADP-ribose) polymerase-10 systems. Wider application of SIESTA can enhance our understanding of the role of enzymes in homeostasis and disease, opening opportunities to investigate the effect of post-translational modifications on signal transduction and facilitate drug discovery.

scholarly journals Organic substrate availability and enzyme activity affect microbial-controlled carbon dynamics in areas disturbed by a mining dam failure

2022 ◽  
Vol 169 ◽  
pp. 104169
Author(s):  
Éder Rodrigues Batista ◽  
Aline de Jesus Franco ◽  
Ana Paula Valadares da Silva ◽  
Jessyca Adriana Gomes Florêncio da Silva ◽  
Davi Santos Tavares ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Carbon Dynamics ◽  
Organic Substrate ◽  
Dam Failure ◽  
Substrate Availability ◽  
Mining Dam

A possible role of arginase in the regulation of polyamine biosynthesis in the rat thyroid

1981 ◽  
Vol 98 (1) ◽  
pp. 57-61 ◽  
Author(s):  
Shigeru Matsuzaki ◽  
Mitsuo Suzuki ◽  
Koei Hamana
Keyword(s):  
Amino Acids ◽  
Enzyme Activity ◽  
Arginase Activity ◽  
Polyamine Biosynthesis ◽  
Rat Thyroid ◽  
Arginine Concentration

Abstract. Effect of chronic methylthiouracil (MTU) treatment on the thyroid arginase activity and thyroidal concentration of arginine, ornithine and other amino acids was studied in the rat. The activity of thyroid arginase increased significantly at 15 days of MTU treatment and the elevated enzyme activity was reduced to normal by l-thyroxine (T4) injection. The thyroidal concentration of polyamines was increased by MTU and decreased by T4 with the exception of spermine. The thyroidal concentration of arginine and lysine, a substrate and an inhibitor for arginase respectively decreased significantly, while that of ornithine remained unchanged after MTU treatment. T4 injected to MTU-pretreated rats restored the decreased arginine concentration to normal. These results suggest that ornithine supply for polyamine biosynthesis is regulated by the level of both arginase and lysine in the thyroid.

Possible role of a histidine residue in the substrate specificity of yeast d-aspartate oxidase

2015 ◽  
pp. mvv108 ◽  
Author(s):  
Shouji Takahashi ◽  
Kozue Shimada ◽  
Shunsuke Nozawa ◽  
Masaru Goto ◽  
Katsumasa Abe ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Histidine Residue
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