Structural Investigations of Class la Ribonucleotide Reductases by Electron Microscopy PDF Download
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Author: Gyunghoon Kang
Publisher:
ISBN:
Category :
Languages : en
Pages : 178
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Book Description
Ribonucleotide reductase (RNR) catalyzes the reduction of nucleotides to their 2'-deoxynucleotide counterparts. The class la RNR from Escherichia coli is composed of two homodimeric subunits [alpha]2 and [beta]2 that form an [alpha]2[beta]2 complex to perform nucleotide reduction. Chemistry is initiated by a thiyl-radical (C439·) in the active site of [beta]2 that is reversibly generated by a diferric-tyrosyl radical cofactor (Y122·) in [beta]2 by a series of proton-coupled electron transfer steps: Y122[beta] - [W48[beta]] - Y356[beta] - Y731[alpha] - Y730[alpha] - C439[alpha]. A high-resolution structure of the active [alpha]2[beta]2 complex has long eluded the field due to the weak and transient nature of the a2-P2 interaction. Previous studies revealed that perturbing radical transfer by incorporating unnatural amino acids along the transfer pathway, or by using mechanistic inhibitors that trap the radical in the active site, can extend the lifetime of the [alpha]2[beta]2 complex, allowing for structural studies. Here, we present our efforts to study the E. coli class la RNR [alpha]2[beta]2 complex, trapped using these different perturbation methods, using cryo-electron microscopy. The two [alpha]2[beta]2 structures presented here provide deeper insight into the structural dynamics of nucleotide reduction. We end with a brief discussion of class la RNR from T4 bacteriophage, which despite sharing high sequence identity to its host E. coli class la RNR, employs a very different mode of oligomeric regulation.
Author: Gyunghoon Kang
Publisher:
ISBN:
Category :
Languages : en
Pages : 178
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Book Description
Ribonucleotide reductase (RNR) catalyzes the reduction of nucleotides to their 2'-deoxynucleotide counterparts. The class la RNR from Escherichia coli is composed of two homodimeric subunits [alpha]2 and [beta]2 that form an [alpha]2[beta]2 complex to perform nucleotide reduction. Chemistry is initiated by a thiyl-radical (C439·) in the active site of [beta]2 that is reversibly generated by a diferric-tyrosyl radical cofactor (Y122·) in [beta]2 by a series of proton-coupled electron transfer steps: Y122[beta] - [W48[beta]] - Y356[beta] - Y731[alpha] - Y730[alpha] - C439[alpha]. A high-resolution structure of the active [alpha]2[beta]2 complex has long eluded the field due to the weak and transient nature of the a2-P2 interaction. Previous studies revealed that perturbing radical transfer by incorporating unnatural amino acids along the transfer pathway, or by using mechanistic inhibitors that trap the radical in the active site, can extend the lifetime of the [alpha]2[beta]2 complex, allowing for structural studies. Here, we present our efforts to study the E. coli class la RNR [alpha]2[beta]2 complex, trapped using these different perturbation methods, using cryo-electron microscopy. The two [alpha]2[beta]2 structures presented here provide deeper insight into the structural dynamics of nucleotide reduction. We end with a brief discussion of class la RNR from T4 bacteriophage, which despite sharing high sequence identity to its host E. coli class la RNR, employs a very different mode of oligomeric regulation.
Author: Christina Marie Zimanyi
Publisher:
ISBN:
Category :
Languages : en
Pages : 274
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Book Description
Ribonucleotide reductase (RNR) converts ribonucleotides to deoxyribonucleotides, the building blocks for DNA replication and repair. The E. coli class Ia enzyme requires two subunits to catalyze the radical-based reduction reaction. [beta]2 houses a diferric-tyrosyl radical cofactor and [alpha]2 contains the active site and two allosteric effector binding sites. Allosteric control of RNR fine-tunes both the relative ratios (via substrate specificity regulation) and the total amount (via activity regulation) of deoxyribonucleotides (dNTPs) in the cell. The molecular basis of this regulation has been enigmatic, largely due to a lack of structural information about how the [alpha]2 and [beta]2 subunits interact. Here, we present the structure of a complex between the [alpha]2 and [beta]2 subunits in the presence of negative activity effector dATP, revealing an [alpha]4[beta]4 ring-like structure. Using electron microscopy (EM), small-angle X-ray scattering (SAXS), and analytical ultracentrifugation (AUC) we show how activity regulation is achieved by modulating the distributions of active [alpha]2[beta]2 and inhibited [alpha]4[beta]4, an interconversion that requires dramatic subunit rearrangements. The X-ray crystal structure of the dATP-inhibited RNR and a second structure obtained using a mechanism based inhibitor reveal that [alpha]4[beta]4 rings can interlock to form an ([alpha]4[beta]4)2 megacomplex. We use SAXS to understand the solution conditions that contribute to the observed concatenation and present a mechanism for the formation of these unusual structures. We also present the first X-ray crystal structures of [alpha]2 with ATP or dATP bound at both allosteric sites, and discuss how observed differences in their binding influence the modulation between [alpha]2[beta]2 and [alpha]4[beta]4. Finally, we present structures that comprise a full set of cognate substrate/specificity effector pairs bound to the E. coli class Ia RNR. These structures allow us to describe how binding of dNTP effectors at the specificity site promotes binding of a preferred substrate. With these structural data, we describe in molecular detail, how the binding of allosteric effectors influences RNR activity and substrate specificity.
Author:
Publisher: Elsevier
ISBN: 0081026919
Category : Science
Languages : en
Pages : 4266
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Book Description
Comprehensive Natural Products III, Third Edition, Seven Volume Set updates and complements the previous two editions, including recent advances in cofactor chemistry, structural diversity of natural products and secondary metabolites, enzymes and enzyme mechanisms and new bioinformatics tools. Natural products research is a dynamic discipline at the intersection of chemistry and biology concerned with isolation, identification, structure elucidation, and chemical characteristics of naturally occurring compounds such as pheromones, carbohydrates, nucleic acids and enzymes. This book reviews the accumulated efforts of chemical and biological research to understand living organisms and their distinctive effects on health and medicine and to stimulate new ideas among the established natural products community. Provides readers with an in-depth review of current natural products research and a critical insight into the future direction of the field Bridges the gap in knowledge by covering developments in the field since the second edition published in 2010 Split into 7 sections on key topics to allow students, researchers and professionals to find relevant information quickly and easily Ensures that the knowledge within is easily understood by and applicable to a large audience
Author: William F. Martin
Publisher: Walter de Gruyter GmbH & Co KG
ISBN: 3110612410
Category : Science
Languages : en
Pages : 269
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Book Description
Mitochondria are sometimes called the powerhouses of eukaryotic cells, because mitochondria are the site of ATP synthesis in the cell. ATP is the universal energy currency, it provides the power that runs all other life processes. Humans need oxygen to survive because of ATP synthesis in mitochondria. The sugars from our diet are converted to carbon dioxide in mitochondria in a process that requires oxygen. Just like a fire needs oxygen to burn, our mitochondria need oxygen to make ATP. From textbooks and popular literature one can easily get the impression that all mitochondria require oxygen. But that is not the case. There are many groups of organismsm known that make ATP in mitochondria without the help of oxygen. They have preserved biochemical relicts from the early evolution of eukaryotic cells, which took place during times in Earth history when there was hardly any oxygen avaiable, certainly not enough to breathe. How the anaerobic forms of mitochondria work, in which organisms they occur, and how the eukaryotic anaerobes that possess them fit into the larger picture of rising atmospheric oxygen during Earth history are the topic of this book.
Author:
Publisher:
ISBN:
Category : Medicine
Languages : en
Pages : 1148
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Author: Judith P. Klinman
Publisher: Gulf Professional Publishing
ISBN: 9780120342587
Category : Medical
Languages : en
Pages : 502
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Book Description
A cofactor is a component part of many enzymes and functions by uniting with another molecule in order to become active. The use of cofactors to supplement the native amino acids of a protein is essential to maintain the chemical capabilities necessary for organisms to survive. This volume focuses on the significant advances of the past decade in identifying and describing new cofactors--either small molecules or those derived posttranslationally.
Author:
Publisher:
ISBN:
Category : Biochemistry
Languages : en
Pages : 700
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Author: Jose M. Arguello
Publisher: Academic Press
ISBN: 0123943906
Category : Science
Languages : en
Pages : 478
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Book Description
This volume of Current Topics in Membranes focuses on metal transmembrane transporters and pumps, a recently discovered family of membrane proteins with many important roles in the physiology of living organisms. The book summarizes the most recent advances in the field of metal ion transport and provides a broad overview of the major classes of transporters involved in homeostasis of heavy metals. Various families of the transporters and metal specificities are discussed with the focus on the structural and mechanistic aspects of their function and regulation. The reader will access information obtained through a variety of approaches ranging from X-ray crystallography to cell biology and bioinformatics, which have been applied to transporters identified in diverse biological systems, such as pathogenic bacteria, plants, humans and others. Field is cutting-edge and a lot of the information is new to research community Wide breadth of topic coverage Contributors of high renown and expertise
Author:
Publisher:
ISBN:
Category : Agriculture
Languages : en
Pages : 3036
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Author: Shmuel Razin
Publisher: Springer Science & Business Media
ISBN: 0306476061
Category : Science
Languages : en
Pages : 574
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Book Description
was the result of the efforts of Robert Cleverdon. The rapidly developing discipline of molecular biology and the rapidly expanding knowledge of the PPLO were brought together at this meeting. In addition to the PPLO specialists, the conference invited Julius Marmur to compare PPLO DNA to DNA of other organisms; David Garfinkel, who was one of the first to develop computer models of metabolism; Cyrus Levinthal to talk about coding; and Henry Quastler to discuss information theory constraints on very small cells. The conference was an announcement of the role of PPLO in the fundamental understanding of molecular biology. Looking back 40-some years to the Connecticut meeting, it was a rather bold enterprise. The meeting was international and inter-disciplinary and began a series of important collaborations with influences resonating down to the present. If I may be allowed a personal remark, it was where I first met Shmuel Razin, who has been a leading figure in the emerging mycoplasma research and a good friend. This present volume is in some ways the fulfillment of the promise of that early meeting. It is an example of the collaborative work of scientists in building an understanding of fundamental aspects of biology.
