Download or read book 2 Oxoglutarate Dependent Oxygenases written by Christopher J Schofield and published by Royal Society of Chemistry. This book was released on 2015-05-06 with total page 508 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the discovery of the first examples of 2-oxoglutarate-dependent oxygenase-catalysed reactions in the 1960s, a remarkably broad diversity of alternate reactions and substrates has been revealed, and extensive advances have been achieved in our understanding of the structures and catalytic mechanisms. These enzymes are important agrochemical targets and are being pursued as therapeutic targets for a wide range of diseases including cancer and anemia. This book provides a central source of information that summarizes the key features of the essential group of 2-oxoglutarate-dependent dioxygenases and related enzymes. Given the numerous recent advances and biomedical interest in the field, this book aims to unite the latest research for those already working in the field as well as to provide an introduction for those newly approaching the topic, and for those interested in translating the basic science into medicinal and agricultural benefits. The book begins with four broad chapters that highlight critical aspects, including an overview of possible catalytic reactions, structures and mechanisms. The following seventeen chapters focus on carefully selected topics, each written by leading experts in the area. Readers will find explanations of rapidly evolving research, from the chemistry of isopenicillin N synthase to the oxidation mechanism of 5-methylcytosine in DNA by ten-eleven-translocase oxygenases.
Download or read book Crystallographic Studies on 2 oxoglutarate Dependent Oxygenases written by Wei Shen Aik and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Functional and Inhibition Studies on 2 oxoglutarate dependent Oxygenases written by Armin Thalhammer and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Mechanistic Studies on 2 oxoglutarate Dependent Oxygenases written by Andrea Szollossi and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Kinetic and Mechanistic Studies of Oxygen Sensing Fe II 2 oxoglutarate Dependent Oxygenases written by Hanna Tarhonskaya and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Structural Basis for Alternative Reaction Outcome by the Iron and 2 oxoglutarate dependent Oxygenases written by Andrew Mitchell and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenases utilize a non-heme mononuclear Fe(II) cofactor to catalyze oxidative transformations of unreactive aliphatic carbon centers in a wide variety of biological substrates. The 2OG cosubstrate allows the enzyme to access the oxidizing potential of molecular oxygen to generate a highly reactive Fe(IV)-oxo (ferryl) intermediate. This species is able to abstract an H-atom from the substrate and, in the most common outcome hydroxylation the enzyme subsequently couples the resulting OH group to a carbon-centered radical on the substrate. Excitingly, the biosynthetic capacity of this platform has expanded to include desaturation, C-O/C bond formation, halogenation, endoperoxidation, epoxidation, stereo-inversion, and even the formation of ethylene. The Fe/2OG oxygenases are considered ideal candidates for biotechnology applications owing to their catalytic diversity, simple and readily available cofactors/cosubstrates, and ability to activate inert C-H bonds. To capitalize on this promise and successfully harness this enzyme scaffold for biotechnology purposes, it is necessary to obtain detailed mechanistic and structural information, particularly for non-hydroxylation systems. The mechanism of OH installation by the Fe/2OG oxygenases is largely understood. In the non-hydroxylases reactivity likely diverges after the substrate hydrogen-atom transfer (HAT) step, resulting in alternate transformation of the carbon-centered radical. It is likely that tight spatial control of the substrate HAT target and the oxygen-derived ligands via interaction with specific active site residues and other components of the Fe coordination sphere are crucial for controlling reaction outcome. Although many Fe/2OG hydroxylases are well-characterized via x-ray crystallography, comprehensive high-resolution structural data for complete enzyme-substrate reactant complexes is lacking for non-hydroxylation systems. Here, we will explore the structural properties of non-canonical Fe/2OG oxygenases, in particular the features that dictate reactivity. A novel set of halogenase crystal structures revealed important active site features for selective catalysis. These findings subsequently allowed for the first successful demonstration of novel halogenation activity from a hydroxylating scaffold. Furthermore, crystallographic snapshots of a hydroxylating system allowed for the visualization of a previously unobserved intermediate and new structural probe for the elusive ferryl species. This work has enabled development of universal hypotheses for control of reaction outcome in these enzymes.
Download or read book Studies on the 2 oxoglutarate Dependent Oxygenases of Flavonoid Biosynthesis written by Jonathan J. Turnbull and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book 2 Oxoglutarate Dependent Oxygenases written by Christopher Schofield and published by Royal Society of Chemistry. This book was released on 2015-04-23 with total page 508 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the discovery of the first examples of 2-oxoglutarate-dependent oxygenase-catalysed reactions in the 1960s, a remarkably broad diversity of alternate reactions and substrates has been revealed, and extensive advances have been achieved in our understanding of the structures and catalytic mechanisms. These enzymes are important agrochemical targets and are being pursued as therapeutic targets for a wide range of diseases including cancer and anemia. This book provides a central source of information that summarizes the key features of the essential group of 2-oxoglutarate-dependent dioxygenases and related enzymes. Given the numerous recent advances and biomedical interest in the field, this book aims to unite the latest research for those already working in the field as well as to provide an introduction for those newly approaching the topic, and for those interested in translating the basic science into medicinal and agricultural benefits. The book begins with four broad chapters that highlight critical aspects, including an overview of possible catalytic reactions, structures and mechanisms. The following seventeen chapters focus on carefully selected topics, each written by leading experts in the area. Readers will find explanations of rapidly evolving research, from the chemistry of isopenicillin N synthase to the oxidation mechanism of 5-methylcytosine in DNA by ten-eleven-translocase oxygenases.
Download or read book Molecular and Cellular Studies on the 2 oxoglutarate dependent Oxygenase MINA53 written by Eline Hendrix and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Lasso Peptides written by Yanyan Li and published by Springer. This book was released on 2014-10-21 with total page 113 pages. Available in PDF, EPUB and Kindle. Book excerpt: Lasso peptides form a growing family of fascinating ribosomally-synthesized and post-translationally modified peptides produced by bacteria. They contain 15 to 24 residues and share a unique interlocked topology that involves an N-terminal 7 to 9-residue macrolactam ring where the C-terminal tail is threaded and irreversibly trapped. The ring results from the condensation of the N-terminal amino group with a side-chain carboxylate of a glutamate at position 8 or 9, or an aspartate at position 7, 8 or 9. The trapping of the tail involves bulky amino acids located in the tail below and above the ring and/or disulfide bridges connecting the ring and the tail. Lasso peptides are subdivided into three subtypes depending on the absence (class II) or presence of one (class III) or two (class I) disulfide bridges. The lasso topology results in highly compact structures that give to lasso peptides an extraordinary stability towards both protease degradation and denaturing conditions. Lasso peptides are generally receptor antagonists, enzyme inhibitors and/or antibacterial or antiviral (anti-HIV) agents. The lasso scaffold and the associated biological activities shown by lasso peptides on different key targets make them promising molecules with high therapeutic potential. Their application in drug design has been exemplified by the development of an integrin antagonist based on a lasso peptide scaffold. The biosynthesis machinery of lasso peptides is therefore of high biotechnological interest, especially since such highly compact and stable structures have to date revealed inaccessible by peptide synthesis. Lasso peptides are produced from a linear precursor LasA, which undergoes a maturation process involving several steps, in particular cleavage of the leader peptide and cyclization. The post-translational modifications are ensured by a dedicated enzymatic machinery, which is composed of an ATP-dependent cysteine protease (LasB) and a lactam synthetase (LasC) that form an enzymatic complex called lasso synthetase. Microcin J25, produced by Escherichia coli AY25, is the archetype of lasso peptides and the most extensively studied. To date only around forty lasso peptides have been isolated, but genome mining approaches have revealed that they are widely distributed among Proteobacteria and Actinobacteria, particularly in Streptomyces, making available a rich resource of novel lasso peptides and enzyme machineries towards lasso topologies.
Download or read book Characterisation of 2 oxoglutarate and Fe II dependent Oxygenases Targeting the Protein Synthesis Apparatus written by Tianshu Feng and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Oxygen Sensing written by and published by Elsevier. This book was released on 2004-05-10 with total page 867 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ability of cells to sense and respond to changes in oxygenation underlies a multitude of developmental, physiological, and pathological processes. This volume provides a comprehensive compendium of experimental approaches to the study of oxygen sensing in 48 chapters that are written by leaders in their fields.
Download or read book Identification of Inhibitors for a Family of Human Oxoglutarate dependent Oxygenases written by Radosław Piotr Nowak and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Mechanistic Study of Halogenation by Iron II and 2 Oxoglutarate Dependent Oxygenases written by Bryce Katch and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Enzymes are responsible for catalyzing chemical reactions in living systems, making life as we know it possible. Many of the most challenging chemical reactions - reactions that involve breaking very stable bonds - are performed by enzymes that contain transition metals. The aliphatic carbon-hydrogen bond is an example of a bond that is typically considered inert; however, many enzymes in nature can make use of iron cofactors to activate this unreactive bond. One class of iron-dependent enzymes achieves C-H activation by coupling its chemistry to the oxidative decarboxylation of the small molecule 2-oxo-glutarate. This class of enzymes is known as the iron(II) and 2-oxo-glutarate-dependent (Fe/2OG) oxygenase superfamily. Here, we detail the study of two Fe/2OG enzymes- SadA and BesD- that perform halogenation of unactivated carbon-hydrogen bonds. SadA is a hydroxylase enzyme that we engineered to install a halide on an amino-acid derivative substrate, while BesD is natively a halogenase of a lysine substrate. Our work demonstrates that the reactivity of these enzymes can be expanded beyond their primary activity through mutagenesis or reaction with alternative substrates. We also show that these enzymes display creative strategies to favor the halogenation reaction over the canonical hydroxylation reaction. This work furthers our understanding of enzymatic C-H activation and showcases the potential biocatalytic value of this enzyme superfamily.
Download or read book A Spectroelectrochemical Investigation of the Thermodynamic and Structural Properties of the 2 oxoglutarate dependent Oxygenase Taud written by Christopher Wayne John and published by . This book was released on 2019 with total page 143 pages. Available in PDF, EPUB and Kindle. Book excerpt: 2-Oxoglutarate (2OG)-dependent dioxygenases catalyze C-H activation while performing a wide range of chemical transformations making their method of action and thermodynamic properties of great interest to industrial synthesis. In contrast to their heme analogues, non-heme iron centers afford greater structural flexibility with important implications for their diverse catalytic mechanisms. Unfortunately, the non-heme and less accessible active sites of these enzymes makes it a challenge to study them. To counteract this issue, we develop a method that uses electrochemical mediators and combines normal pulse spectrovoltammetry (NPSV) with Fourier transform infrared (FTIR) for detection and subsequent global spectral regression analysis to resolve the structural and thermodynamic properties simultaneously. We develop comprehensive semiemipirical kinetic simulation models to investigate the thermodynamic and kinetic limitations of mediators/analyte interactions. These methods are first validated using methylene green and thionine acetate as mediators and myoglobin (Mb) as the analyte. Both the E1⁄2 and unbiased redox difference FTIR spectra of the Fe(II)/Fe(III) redox couple of Mb in reduction and oxidation NPSV modes were in good agreement with those reported earlier by independent techniques. The modeling effort yielded a flexible computational tool capable of quantitatively predicting the redox response in mediated electrochemical studies and defining its limitations. These methods are used to characterize an in situ structural model of the putative transient ferric intermediate of 2OG:taurine dioxygenase (TauD), demonstrating that the FeIII/II transition involves a substantial, fully reversible, redox-linked conformational change at the active site. This rearrangement changes the apparent redox potential of the active site between -272 mV for reduction of the ferric state and 196 mV for oxidation of the ferrous state of the 2OG-Fe-TauD complex resulting in a maximal observed redox hysteresis in the wild type enzyme of 468 mV. Quantitative modeling of the transient redox response using two alternative reaction schemes across a variety of experimental conditions strongly supports the proposal for intrinsic protein reorganization as the origin of the experimental observations. We use H99A, D101Q, H255Q, and Y73I variants of TauD to investigate the structural origin of the redox-linked reorganization and the relative contributions of the active site residues to the dynamic tuning of the redox potential of TauD. Extended time-dependent redox titrations show that, in all cases, reorganization occurs as a multi-step process, with individual phases exhibiting different sensitivities to ligand substitutions. The H99A variant shows the largest net redox change relative to the wild type protein, suggesting that redox-coupled protonation of H99 is required for TauD to support highly positive potentials. The effect of the D101Q substitution suggests that changes in the metal coordination of the carboxylate group may be secondary to changes involving H99 and are required for the ensuing reorganization steps. The H255Q substitution inhibits the conformational change, providing evidence for its involvement in the structural rearrangement. An investigation of the pD sensitivity of wild type TauD exposes a protonation event at the active site of TauD most likely attributable to H99 or H255. Ultimately, we propose H99 is protonated in the ferrous form of TauD and forms a hydrogen bond with the protein backbone. Oxidation of the enzyme results in the loss of this hydrogen bond allowing movement in the H99-T100-D101 chain so that D101 can form a bidentate ligand with the ferric iron center.
Download or read book Plant Functional Genomics written by Erich Grotewold and published by Springer Science & Business Media. This book was released on 2008-02-03 with total page 443 pages. Available in PDF, EPUB and Kindle. Book excerpt: Functional genomics is a young discipline whose origin can be traced back to the late 1980s and early 1990s, when molecular tools became available to determine the cellular functions of genes. Today, functional genomics is p- ceived as the analysis, often large-scale, that bridges the structure and organi- tion of genomes and the assessment of gene function. The completion in 2000 of the genome sequence of Arabidopsis thaliana has created a number of new and exciting challenges in plant functional genomics. The immediate task for the plant biology community is to establish the functions of the approximately 25,000 genes present in this model plant. One major issue that will remain even after this formidable task is c- pleted is establishing to what degree our understanding of the genome of one model organism, such as the dicot Arabidopsis, provides insight into the or- nization and function of genes in other plants. The genome sequence of rice, completed in 2002 as a result of the synergistic interaction of the private and public sectors, promises to significantly enrich our knowledge of the general organization of plant genomes. However, the tools available to investigate gene function in rice are lagging behind those offered by other model plant systems. Approaches available to investigate gene function become even more limited for plants other than the model systems of Arabidopsis, rice, and maize.
Download or read book Natural Product Biosynthesis written by Christopher T. Walsh and published by Royal Society of Chemistry. This book was released on 2017-04-28 with total page 787 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook describes the types of natural products, the biosynthetic pathways that enable the production of these molecules, and an update on the discovery of novel products in the post-genomic era.
