Coenzyme B12 Enzymes Part B

Coenzyme B12 Enzymes Part B

1st Edition - May 27, 2022

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  • Editor: Neil Marsh
  • Hardcover ISBN: 9780323955577
  • eBook ISBN: 9780323955584

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Description

Coenzyme B12 Enzymes, Part B, Volume 169 in the Methods in Enzymology series, highlights new advances in the field,  with this new volume presenting interesting chapters on Structural characterization of cobalamin-dependent radical SAM methylases, Purification and characterization of sequential cobalamin-dependent radical SAM methylases ThnK and TokK in -lactam antibiotic biosynthesis, Characterization of the cobalamin-dependent radical S-adenosyl-L-methionine enzyme C-methyltransferase Fom3 in fosfomycin biosynthesis, Studies of OxsB and GenK, two B12-dependent radical SAM enzymes involved in natural product biosynthesis, Purification and structural elucidation of the cobalamin-dependent radical SAM enzyme OxsB, and more. Other chapters discuss Methods for studying the mechanisms of B12 enzymes, Computational investigations of B12 dependent enzymatic reactions, Using kinetic isotope effects to probe the mechanisms of adenosylcobalamin-dependent enzymes, Steady-state and pre-steady state kinetic analysis of ornithine 4,5-aminomutase, and more.

Key Features

  • Provides the authority and expertise of leading contributors from an international board of authors
  • Presents the latest release in Methods in Enzymology series
  • Includes the latest information on B12 Enzymes

Readership

Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists

Table of Contents

  • Cover image
  • Title Page
  • Table of Contents
  • Copyright
  • Contributors
  • Preface
  • Section III: B12-dependent radical SAM enzymes
  • Chapter One: Structural characterization of cobalamin-dependent radical S-adenosylmethionine methylases
  • Abstract
  • 1: Introduction
  • 2: Overproduction and purification of cobalamin-dependent radical SAM methylases
  • 3: Protocols for crystallization and structure determination
  • 4: Structure analysis
  • 5: Conclusions
  • Acknowledgments
  • References
  • Chapter Two: Purification and characterization of sequential cobalamin-dependent radical SAM methylases ThnK and TokK in carbapenem β-lactam antibiotic biosynthesis
  • Abstract
  • 1: Introduction
  • 2: Heterologous expression and purification of ThnK and TokK
  • 3: Time-course assays of ThnK and TokK
  • 4: Conclusion
  • References
  • Chapter Three: Characterization of the cobalamin-dependent radical S-adenosyl-l-methionine enzyme C-methyltransferase Fom3 in fosfomycin biosynthesis
  • Abstract
  • 1: Introduction
  • 2: Heterologous expression and purification of Fom3
  • 3: Enzymatic synthesis of HEP-CMP and HPP-CMP using the cytidylyltransferase domain of Fom1
  • 4: Elucidation of the true substrate and product of Fom3
  • 5: Enzyme reaction of Fom3 using deuterium-labeled substrates
  • 6: Perspective
  • Acknowledgments
  • References
  • Chapter Four: Studies of GenK and OxsB, two B12-dependent radical SAM enzymes involved in natural product biosynthesis
  • Abstract
  • 1: Introduction
  • 2: GenK catalyzes 6′-C methylation in gentamicin biosynthesis
  • 3: OxsB and OxsA catalyzes ring contraction in oxetanocin A biosynthesis
  • 4: Conclusion
  • Acknowledgment
  • References
  • Chapter Five: Purification and structural elucidation of a cobalamin-dependent radical SAM enzyme
  • Abstract
  • 1: Introduction
  • 2: Expression and purification of apo-OxsB
  • 3: Crystallization of apo- and selenomethionine (SeMet)-labeled OxsB
  • 4: Reconstitution of OxsB and crystallization of different cofactor-bound states
  • 5: Lessons applicable to crystallography of other Cbl-dependent radical SAM enzymes
  • 6: Conclusions
  • Acknowledgments
  • References
  • Section IV: Methods for studying the mechanisms of B12 enzymes
  • Chapter Six: Computational investigations of B12-dependent enzymatic reactions
  • Abstract
  • 1: Introduction
  • 2: Computational approach
  • 3: Model systems
  • 4: Conclusions
  • References
  • Chapter Seven: Using kinetic isotope effects to probe the mechanism of adenosylcobalamin-dependent enzymes
  • Abstract
  • 1: Introduction
  • 2: Methods
  • 3: Using isotope effects to probe the mechanism of glutamate mutase
  • 4: Conclusion
  • Acknowledgments
  • References
  • Chapter Eight: Steady-state and pre-steady state kinetic analysis of ornithine 4,5-aminomutase
  • Abstract
  • 1: Introduction
  • 2: Steady state kinetic analysis of 4,5-OAM
  • 3: Pre-steady-state kinetic analysis of 4,5-OAM
  • 4: Conclusions
  • Acknowledgment
  • References
  • Chapter Nine: Exploring the mechanism of action of lysine 5,6-aminomutase using EPR and ENDOR spectroscopies
  • Abstract
  • 1: Introduction
  • 2: Protocol for the preparation of protein samples for EPR and ENDOR measurements
  • 3: Typical spectrometer settings for measurements of EPR and ENDOR spectra
  • 4: Simulation protocol of EPR and ENDOR spectra
  • 5: Tracking conformational movement
  • 6: Identification and characterization of relevant radical intermediates
  • 7: Conclusions
  • Acknowledgments
  • References
  • Chapter Ten: Resolution and characterization of contributions of select protein and coupled solvent configurational fluctuations to radical rearrangement catalysis in coenzyme B12-dependent ethanolamine ammonia-lyase
  • Abstract
  • 1: Introduction
  • 2: Protein dynamics and contributions to enzyme catalysis: Definitions and concepts
  • 3: Revealing contributions of select protein configurational dynamics to enzyme catalysis under ensemble conditions
  • 4: Sample preparation and measurement of reaction kinetics
  • 5: Temperature-dependence of substrate radical decay reaction in ethanolamine ammonia-lyase
  • 6: Interpretation: Contributions of select protein configurational dynamics to EAL enzyme catalysis
  • 7: Role of solvent coupling in select protein configurational dynamics
  • 8: Conclusions
  • Acknowledgments
  • References
  • Chapter Eleven: Investigating radical pair reaction dynamics of B12 coenzymes 1: Transient absorption spectroscopy and magnetic field effects
  • Abstract
  • 1: Introduction
  • 2: Materials, equipment and reagents
  • 3: Method details: Instrumental setup and sample preparation
  • 4: Step-by-step protocol: Measuring MFEs on the ultrafast photochemical dynamics of AdoCbl
  • 5: Data analysis
  • 6: Advantages and limitations
  • 7: Summary
  • Acknowledgments
  • References
  • Chapter Twelve: Investigating radical pair reaction dynamics of B12 coenzymes 2: Time-resolved electron paramagnetic resonance spectroscopy
  • Abstract
  • 1: Introduction
  • 2: Equipment, materials and reagents
  • 3: Method details: Instrumental setup and sample preparation
  • 4: Step-by-step protocol: Measuring MeCbl RP dynamics using TREPR
  • 5: Assembly and analysis of the TREPR spectra
  • 6: Advantages and limitations
  • 7: Optimization and troubleshooting
  • 8: Summary
  • Acknowledgments
  • References
  • Chapter Thirteen: Time-resolved spectroscopy: Advances in understanding the electronic structure and dynamics of cobalamins
  • Abstract
  • 1: Introduction
  • 2: Sample delivery
  • 3: Polarization dependence
  • 4: Power
  • 5: Kinetics description of photoexcited cobalamins
  • 6: Comparison of theory and experiment
  • Acknowledgments
  • References
  • Chapter Fourteen: Electronic structure studies of free and enzyme-bound B12 species by magnetic circular dichroism and complementary spectroscopic techniques
  • Abstract
  • 1: Overview
  • 2: Spectroscopic studies of free B12 species
  • 3: Application of MCD spectroscopy to the study of enzyme-bound B12 species
  • 4: Reductive dehalogenases
  • Acknowledgments
  • References

Product details

  • No. of pages: 384
  • Language: English
  • Copyright: © Academic Press 2022
  • Published: May 27, 2022
  • Imprint: Academic Press
  • Hardcover ISBN: 9780323955577
  • eBook ISBN: 9780323955584

About the Serial Volume Editor

Neil Marsh

I am currently Professor of Chemistry and Biological Chemistry at the University of Michigan in Ann Arbor. My research interests center on enzyme mechanisms and protein structure and design. We are currently working on a variety of research projects. In particular, we have a long-standing interest in enzymes that use free radicals to catalyze a variety of unusual chemical transformations. More recently, we have become interested in enzymes involved in hydrocarbon biosynthesis, many of which have novel mechanisms and are of practical interest for the biosynthesis of next-generation biofuels. We are also interested in understanding in molecular detail how enzymes interact with abiological surfaces as this is key to many industrial and biomedical applications where enzymes are immobilized on solid supports. More information about my research can be found here:http://www.lsa.umich.edu/chem/people/faculty/ci.marsheneilg_ci.detail

Affiliations and Expertise

Dow Distinguished Faculty Fellow in Sustainability, Professor of Chemistry and Biological Chemistry, Department of Chemistry, University of Michigan, USA

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