Characterising Complex Enzyme Reaction Data

2016-2-3
Dönertaş, Handan Melike
Cuesta, Sergio Martínez
Rahman, Syed Asad
Thornton, Janet M.
Show full item record
Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
181
views
139
downloads
The relationship between enzyme-catalysed reactions and the Enzyme Commission (EC) number, the widely accepted classification scheme used to characterise enzyme activity, is complex and with the rapid increase in our knowledge of the reactions catalysed by enzymes needs revisiting. We present a manual and computational analysis to investigate this complexity and found that almost one-third of all known EC numbers are linked to more than one reaction in the secondary reaction databases (e.g., KEGG). Although this complexity is often resolved by defining generic, alternative and partial reactions, we have also found individual EC numbers with more than one reaction catalysing different types of bond changes. This analysis adds a new dimension to our understanding of enzyme function and might be useful for the accurate annotation of the function of enzymes and to study the changes in enzyme function during evolution.
General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine
https://hdl.handle.net/11511/51404
Department of Biology, Article

Suggestions

Ca2+ binding induced sequential allosteric activation of sortase A: An example for ion-triggered conformational selection
Ugur, Iike; Schatte, Martin; Marıon, Antoıne; Glaser, Manuel; Boenitz-Dulat, Mara; Antes, Iris (Public Library of Science (PLoS), 2018-10-15)
The allosteric activation of the intrinsically disordered enzyme Staphylococcus aureus sortase A is initiated via binding of a Ca2+ ion. Although Ca2+ binding was shown to initiate structural changes inducing disorder-to-order transitions, the details of the allosteric activation mechanism remain elusive. We performed long-term molecular dynamics simulations of sortase A without (3 simulations of 1.6 mu s) and with bound Ca2+ (simulations of 1.6 mu s, 1.8 mu s, and 2.5 mu s). Our results show that Ca2+ bind...
A Comparative Study for the Evaluation of Two Doses of Ellagic Acid on Hepatic Drug Metabolizing and Antioxidant Enzymes in the Rat
Celik, Gurbet; SEMİZ, ASLI; Karakurt, Serdar; ARSLAN, ŞEVKİ; Adalı, Orhan; ŞEN, ALAATTİN (Hindawi Limited, 2013-01-01)
The present study was designed to evaluate different doses of ellagic acid (EA) in vivo in rats for its potential to modulate hepatic phases I, II, and antioxidant enzymes. EA (10 or 30 mg/kg/day, intragastrically) was administered for 14 consecutive days, and activity, protein, and mRNA levels were determined. Although the cytochrome P450 (CYP) 2B and CYP2E enzyme activities were decreased significantly, the activities of all other enzymes were unchanged with the 10 mg/kg/day EA. In addition, western-blot ...
GOPred: GO Molecular Function Prediction by Combined Classifiers
Sarac, Oemer Sinan; Atalay, Mehmet Volkan; Atalay, Rengül (Public Library of Science (PLoS), 2010-08-31)
Functional protein annotation is an important matter for in vivo and in silico biology. Several computational methods have been proposed that make use of a wide range of features such as motifs, domains, homology, structure and physicochemical properties. There is no single method that performs best in all functional classification problems because information obtained using any of these features depends on the function to be assigned to the protein. In this study, we portray a novel approach that combines ...
Various applications of immobilized glucose oxidase and polyphenol oxidase in a conducting polymer matrix
Cil, M.; Boyukbayram, A. E.; Kiralp, S.; Toppare, Levent Kamil; Yagci, Y. (Elsevier BV, 2007-06-01)
In this study, glucose oxidase and polyphenol oxidase were immobilized in conducting polymer matrices; polypyrrole and poly(N-(4-(3-thienyl methylene)-oxycarbonyl phenyl) maleimide-co-pyrrole) via electrochemical method. Fourier transform infrared and scanning electron microscope were employed to characterize the copolymer of (N-(4-(3-thienyl methylene)-oxycarbonyl phenyl) maleimide) with pyrrole. Kinetic parameters, maximum reaction rate and Michealis-Menten constant, were determined. Effects of temperatur...
The effect of cysteine-43 mutation on thermostability and kinetic properties of citrate synthase from Thermoplasma acidophilum
Kocabıyık, Semra; Russel, RJM; Danson, MJ; Hough, DW (Elsevier BV, 1996-07-05)
In this study, we have substituted serine-43 by cysteine in the recombinant citrate synthase from a moderately thermophilic Archaeon Thermoplasma acidophilum, for site-specific attachment of labels and have investigated the effects of this mutation on the biochemical properties and thermal stability of the enzyme. Both wild-type and the mutant enzymes were purified to homogenity using affinity chromatography on Matrex Gel Red A. The mutant Thermoplasma citrate synthase is very similar to wild-type citrate s...
Citation Formats
H. M. Dönertaş, S. M. Cuesta, S. A. Rahman, and J. M. Thornton, “Characterising Complex Enzyme Reaction Data,” PLOS ONE, 2016, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/51404.
METU IIS - Integrated Information Service open@metu.edu.tr