ACS Publications. Most Trusted. Most Cited. Most Read
Interaction of the Substrate Radical and the 5‘-Deoxyadenosine-5‘-Methyl Group in Vitamin B12 Coenzyme-Dependent Ethanolamine Deaminase

OR SEARCH CITATIONS

My Activity
Publications

Figure 1Loading Img
Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Am. Chem. Soc. 2001, 123, 35, 8564-8572
    Article

    Interaction of the Substrate Radical and the 5‘-Deoxyadenosine-5‘-Methyl Group in Vitamin B12 Coenzyme-Dependent Ethanolamine Deaminase
    Click to copy article linkArticle link copied!

    View Author Information
    Contribution from the Department of Physics, Emory University, Atlanta, Georgia 30322
    Other Access Options

    Journal of the American Chemical Society

    Cite this: J. Am. Chem. Soc. 2001, 123, 35, 8564–8572
    Click to copy citationCitation copied!
    https://doi.org/10.1021/ja003658l
    Published August 10, 2001
    Copyright © 2001 American Chemical Society
    Request reuse permissions

    Abstract

    Click to copy section linkSection link copied!

    The distance and relative orientation of the C5‘ methyl group of 5‘-deoxyadenosine and the substrate radical in vitamin B12 coenzyme-dependent ethanolamine deaminase from Salmonella typhimurium have been characterized by using X-band two-pulse electron spin−echo envelope modulation (ESEEM) spectroscopy in the disordered solid state. The (S)-2-aminopropanol-generated substrate radical catalytic intermediate was prepared by cryotrapping steady-state mixtures of enzyme in which catalytically exchangeable hydrogen sites in the active site had been labeled by previous turnover on 2H4-ethanolamine. Simulation of the time- and frequency-domain ESEEM requires two types of coupled 2H. The strongly coupled 2H has an effective dipole distance (reff) of 2.2 Å, and isotropic coupling constant (Aiso) of −0.35 MHz. The weakly coupled 2H has reff = 3.8 Å and Aiso = 0 MHz. The best 2H ESEEM time- and frequency-domain simulations are achieved with a model in which the hyperfine couplings arise from one strongly coupled hydrogen site and two equivalent weakly coupled hydrogen sites located on the C5‘ methyl group of 5‘-deoxyadenosine. This model indicates that the unpaired electron on C1 of the substrate radical and C5‘ are separated by 3.2 Å and are thus at closest contact. The close proximity of C1 and C5‘ indicates that C5‘ of the 5‘-deoxyadenosyl moiety directly mediates radical migration between cobalt in cobalamin and the substrate/product site over a distance of 5−7 Å in the active site of ethanolamine deaminase.

    Copyright © 2001 American Chemical Society

    Subjects

    what are subjects

    Read this article

    To access this article, please review the available access options below.

    Get instant access

    Purchase Access

    Read this article for 48 hours. Check out below using your ACS ID or as a guest.

    Recommended

    Access through Your Institution

    You may have access to this article through your institution.

    Your institution does not have access to this content. Add or change your institution or let them know you’d like them to include access.

    *

     Corresponding author. Department of Physics, 1001 Rollins Research Center, 1510 Clifton Road, Emory University, Atlanta, GA 30322, Telephone:  404-727-2975. Fax:  404-727-0873. E-mail:  kwarncke@physics. emory.edu.

    Cited By

    Click to copy section linkSection link copied!
    Citation Statements
    Explore this article's citation statements on scite.ai
    powered by  Scite

    This article is cited by 48 publications.

    1. Laura D. Elmendorf, Ryan L. Hall, Flavia G. Costa, Jorge C. Escalante-Semerena, Thomas C. Brunold. Spectroscopic and Computational Insights into the Mechanism of Cofactor Cobalt–Carbon Bond Homolysis by the Adenosylcobalamin-Dependent Enzyme Ethanolamine Ammonia-Lyase. Journal of the American Chemical Society 2025, 147 (3) , 2380-2392. https://doi.org/10.1021/jacs.4c11488
    2. Hao Yang, Madeline B. Ho, Maike N. Lundahl, Martín A. Mosquera, William E. Broderick, Joan B. Broderick, Brian M. Hoffman. ENDOR Spectroscopy Reveals the “Free” 5′-Deoxyadenosyl Radical in a Radical SAM Enzyme Active Site Actually is Chaperoned by Close Interaction with the Methionine-Bound [4Fe–4S]2+ Cluster. Journal of the American Chemical Society 2024, 146 (6) , 3710-3720. https://doi.org/10.1021/jacs.3c09428
    3. Wei Li, Meghan Kohne, Kurt Warncke. Reactivity Tracking of an Enzyme Progress Coordinate. The Journal of Physical Chemistry Letters 2023, 14 (32) , 7157-7164. https://doi.org/10.1021/acs.jpclett.3c01464
    4. Jun-Ru Chen, Ting-Xi Ke, Perry A. Frey, Shyue-Chu Ke. Electron Spin Echo Envelope Modulation Spectroscopy Reveals How Adenosylcobalamin-Dependent Lysine 5,6-Aminomutase Positions the Radical Pair Intermediates and Modulates Their Stabilities for Efficient Catalysis. ACS Catalysis 2021, 11 (23) , 14352-14368. https://doi.org/10.1021/acscatal.1c03182
    5. Meghan Kohne, Wei Li, Chen Zhu, Kurt Warncke. Deuterium Kinetic Isotope Effects Resolve Low-Temperature Substrate Radical Reaction Pathways and Steps in B12-Dependent Ethanolamine Ammonia-Lyase. Biochemistry 2019, 58 (35) , 3683-3690. https://doi.org/10.1021/acs.biochem.9b00588
    6. Abdullah Al Mamun, Megan J. Toda, Piotr Lodowski, Maria Jaworska, Pawel M. Kozlowski. Mechanism of Light Induced Radical Pair Formation in Coenzyme B12-Dependent Ethanolamine Ammonia-Lyase. ACS Catalysis 2018, 8 (8) , 7164-7178. https://doi.org/10.1021/acscatal.8b00120
    7. Masaki Horitani, Amanda S. Byer, Krista A. Shisler, Tilak Chandra, Joan B. Broderick, and Brian M. Hoffman . Why Nature Uses Radical SAM Enzymes so Widely: Electron Nuclear Double Resonance Studies of Lysine 2,3-Aminomutase Show the 5′-dAdo• “Free Radical” Is Never Free. Journal of the American Chemical Society 2015, 137 (22) , 7111-7121. https://doi.org/10.1021/jacs.5b00498
    8. Adonis Miguel Bovell and Kurt Warncke . The Structural Model of Salmonella typhimurium Ethanolamine Ammonia-Lyase Directs a Rational Approach to the Assembly of the Functional [(EutB–EutC)2]3 Oligomer from Isolated Subunits. Biochemistry 2013, 52 (8) , 1419-1428. https://doi.org/10.1021/bi301651n
    9. Caitlyn Makins, Alex V. Pickering, Chloe Mariani, and Kirsten R. Wolthers . Mutagenesis of a Conserved Glutamate Reveals the Contribution of Electrostatic Energy to Adenosylcobalamin Co–C Bond Homolysis in Ornithine 4,5-Aminomutase and Methylmalonyl-CoA Mutase. Biochemistry 2013, 52 (5) , 878-888. https://doi.org/10.1021/bi3012719
    10. Wesley D. Robertson, Miao Wang, and Kurt Warncke . Characterization of Protein Contributions to Cobalt−Carbon Bond Cleavage Catalysis in Adenosylcobalamin-Dependent Ethanolamine Ammonia-Lyase by using Photolysis in the Ternary Complex. Journal of the American Chemical Society 2011, 133 (18) , 6968-6977. https://doi.org/10.1021/ja107052p
    11. Naoki Shibata, Yoshiki Higuchi, and Tetsuo Toraya . How Coenzyme B12-Dependent Ethanolamine Ammonia-Lyase Deals with Both Enantiomers of 2-Amino-1-propanol as Substrates: Structure-Based Rationalization,,. Biochemistry 2011, 50 (4) , 591-598. https://doi.org/10.1021/bi101696h
    12. Israel Fernández, Fernando P. Cossío and Miguel A. Sierra. Dyotropic Reactions: Mechanisms and Synthetic Applications. Chemical Reviews 2009, 109 (12) , 6687-6711. https://doi.org/10.1021/cr900209c
    13. Stefan Mebs, Julian Henn, Birger Dittrich, Carsten Paulmann and Peter Luger . Electron Densities of Three B12 Vitamins. The Journal of Physical Chemistry A 2009, 113 (29) , 8366-8378. https://doi.org/10.1021/jp902433x
    14. Li Sun, Olivia A. Groover, Jeffrey M. Canfield and Kurt Warncke. Critical Role of Arginine 160 of the EutB Protein Subunit for Active Site Structure and Radical Catalysis in Coenzyme B12-Dependent Ethanolamine Ammonia-lyase. Biochemistry 2008, 47 (20) , 5523-5535. https://doi.org/10.1021/bi702366e
    15. Miao Wang and, Kurt Warncke. Kinetic and Thermodynamic Characterization of CoII−Substrate Radical Pair Formation in Coenzyme B12-Dependent Ethanolamine Ammonia-Lyase in a Cryosolvent System by Using Time-Resolved, Full-Spectrum Continuous-Wave Electron Paramagnetic Resonance Spectroscopy. Journal of the American Chemical Society 2008, 130 (14) , 4846-4858. https://doi.org/10.1021/ja710069y
    16. Alex R. Jones,, Sam Hay,, Jonathan R. Woodward, and, Nigel S. Scrutton. Magnetic Field Effect Studies Indicate Reduced Geminate Recombination of the Radical Pair in Substrate-Bound Adenosylcobalamin-Dependent Ethanolamine Ammonia Lyase. Journal of the American Chemical Society 2007, 129 (50) , 15718-15727. https://doi.org/10.1021/ja077124x
    17. Nicholas S. Lees,, Dawei Chen,, Charles J. Walsby,, Elham Behshad,, Perry A. Frey, and, Brian M. Hoffman. How an Enzyme Tames Reactive Intermediates:  Positioning of the Active-Site Components of Lysine 2,3-Aminomutase during Enzymatic Turnover As Determined by ENDOR Spectroscopy. Journal of the American Chemical Society 2006, 128 (31) , 10145-10154. https://doi.org/10.1021/ja061282r
    18. Gregory M. Sandala,, David M. Smith, and, Leo Radom. Divergent Mechanisms of Suicide Inactivation for Ethanolamine Ammonia-Lyase. Journal of the American Chemical Society 2005, 127 (24) , 8856-8864. https://doi.org/10.1021/ja051527k
    19. Kurt Warncke. Characterization of the Product Radical Structure in the CoII-Product Radical Pair State of Coenzyme B12-Dependent Ethanolamine Deaminase by Using Three-Pulse 2H ESEEM Spectroscopy. Biochemistry 2005, 44 (9) , 3184-3193. https://doi.org/10.1021/bi048196t
    20. Mamoru Yamanishi,, Hirofumi Ide,, Yoshitake Murakami, and, Tetsuo Toraya. Identification of the 1,2-Propanediol-1-yl Radical as an Intermediate in Adenosylcobalamin-Dependent Diol Dehydratase Reaction. Biochemistry 2005, 44 (6) , 2113-2118. https://doi.org/10.1021/bi0481850
    21. Jeffrey M. Canfield and, Kurt Warncke. Active Site Reactant Center Geometry in the CoII−Product Radical Pair State of Coenzyme B12-Dependent Ethanolamine Deaminase Determined by Using Orientation-Selection Electron Spin−Echo Envelope Modulation Spectroscopy. The Journal of Physical Chemistry B 2005, 109 (7) , 3053-3064. https://doi.org/10.1021/jp046167m
    22. Kurt Warncke and, Jeffrey M. Canfield. Direct Determination of Product Radical Structure Reveals the Radical Rearrangement Pathway in a Coenzyme B12-Dependent Enzyme. Journal of the American Chemical Society 2004, 126 (19) , 5930-5931. https://doi.org/10.1021/ja031569d
    23. Tetsuo Toraya. Radical Catalysis in Coenzyme B12-Dependent Isomerization (Eliminating) Reactions. Chemical Reviews 2003, 103 (6) , 2095-2128. https://doi.org/10.1021/cr020428b
    24. Dmitry V. Khoroshun,, Kurt Warncke,, Shyue-Chu Ke,, Djamaladdin G. Musaev, and, Keiji Morokuma. Internal Degrees of Freedom, Structural Motifs, and Conformational Energetics of the 5‘-Deoxyadenosyl Radical:  Implications for Function in Adenosylcobalamin-Dependent Enzymes. A Computational Study. Journal of the American Chemical Society 2003, 125 (2) , 570-579. https://doi.org/10.1021/ja028393k
    25. Stacey D. Wetmore,, David M. Smith,, Justine T. Bennett, and, Leo Radom. Understanding the Mechanism of Action of B12-Dependent Ethanolamine Ammonia-Lyase:  Synergistic Interactions at Play. Journal of the American Chemical Society 2002, 124 (47) , 14054-14065. https://doi.org/10.1021/ja027579g
    26. Jeffrey M. Canfield and, Kurt Warncke. Geometry of Reactant Centers in the CoII-Substrate Radical Pair State of Coenzyme B12-Dependent Ethanolamine Deaminase Determined by Using Orientation-Selection-ESEEM Spectroscopy. The Journal of Physical Chemistry B 2002, 106 (34) , 8831-8841. https://doi.org/10.1021/jp0207634
    27. Vahe Bandarian and, George H. Reed. Analysis of the Electron Paramagnetic Resonance Spectrum of a Radical Intermediate in the Coenzyme B12-Dependent Ethanolamine Ammonia-Lyase Catalyzed Reaction of S-2-Aminopropanol. Biochemistry 2002, 41 (27) , 8580-8588. https://doi.org/10.1021/bi0201217
    28. Laura D. Elmendorf, Thomas C. Brunold. Electronic structure studies of free and enzyme-bound B12 species by magnetic circular dichroism and complementary spectroscopic techniques. 2022, 333-365. https://doi.org/10.1016/bs.mie.2022.02.002
    29. Arghya Pratim Ghosh, Megan J. Toda, Pawel M. Kozlowski. Photolytic properties of B12-dependent enzymes: A theoretical perspective. 2022, 185-220. https://doi.org/10.1016/bs.vh.2022.01.012
    30. Abdullah Al Mamun, Megan J. Toda, Pawel M. Kozlowski. Can photolysis of the Co C bond in coenzyme B12-dependent enzymes be used to mimic the native reaction?. Journal of Photochemistry and Photobiology B: Biology 2019, 191 , 175-184. https://doi.org/10.1016/j.jphotobiol.2018.12.018
    31. Neslihan Ucuncuoglu, Kurt Warncke. Protein Configurational States Guide Radical Rearrangement Catalysis in Ethanolamine Ammonia-Lyase. Biophysical Journal 2018, 114 (12) , 2775-2786. https://doi.org/10.1016/j.bpj.2018.03.039
    32. Masaki HORITANI. Trapping of the Reaction Intermediates and Analysis of Enzymatic Catalytic Reaction on Radical SAM Enzymes. Seibutsu Butsuri 2017, 57 (4) , 202-204. https://doi.org/10.2142/biophys.57.202
    33. Binuraj R. K. Menon, Navya Menon, Karl Fisher, Stephen E. J. Rigby, David Leys, Nigel S. Scrutton. Glutamate 338 is an electrostatic facilitator of C–Co bond breakage in a dynamic/electrostatic model of catalysis by ornithine aminomutase. The FEBS Journal 2015, 282 (7) , 1242-1255. https://doi.org/10.1111/febs.13215
    34. Miao Wang, Chen Zhu, Meghan Kohne, Kurt Warncke. Resolution and Characterization of Chemical Steps in Enzyme Catalytic Sequences by Using Low-Temperature and Time-Resolved, Full-Spectrum EPR Spectroscopy in Fluid Cryosolvent and Frozen Solution Systems. 2015, 59-94. https://doi.org/10.1016/bs.mie.2015.08.015
    35. Tetsuo Toraya. Cobalamin-dependent dehydratases and a deaminase: Radical catalysis and reactivating chaperones. Archives of Biochemistry and Biophysics 2014, 544 , 40-57. https://doi.org/10.1016/j.abb.2013.11.002
    36. Li Sun, Joshua J. Savory, Kurt Warncke. Design and implementation of an FPGA‐based timing pulse programmer for pulsed‐electron paramagnetic resonance applications. Concepts in Magnetic Resonance Part B: Magnetic Resonance Engineering 2013, 43 (3) , 100-109. https://doi.org/10.1002/cmr.b.21240
    37. Jenner N. Bonanata, Santiago Signorelli, E. Laura Coitiño. Increasing complexity models for describing the generation of substrate radicals at the active site of ethanolamine ammonia-lyase/B12. Computational and Theoretical Chemistry 2011, 975 (1-3) , 52-60. https://doi.org/10.1016/j.comptc.2011.07.029
    38. Hava Ozay, Yakup Baran, Hiroshi Miyamae. The stabilities and formation kinetics of some macrocycles with copper(II): crystal structures of some pendant arm macrocycles. Journal of Coordination Chemistry 2011, 64 (8) , 1469-1480. https://doi.org/10.1080/00958972.2011.574128
    39. Naoki Shibata, Hiroko Tamagaki, Naoki Hieda, Keita Akita, Hirofumi Komori, Yasuhito Shomura, Shin-ichi Terawaki, Koichi Mori, Noritake Yasuoka, Yoshiki Higuchi, Tetsuo Toraya. Crystal Structures of Ethanolamine Ammonia-lyase Complexed with Coenzyme B12 Analogs and Substrates. Journal of Biological Chemistry 2010, 285 (34) , 26484-26493. https://doi.org/10.1074/jbc.M110.125112
    40. Perry Allen Frey. Cobalamin Coenzymes in Enzymology. 2010, 501-546. https://doi.org/10.1016/B978-008045382-8.00145-3
    41. Rowena G. Matthews. Cobalamin- and Corrinoid-Dependent Enzymes. 2009, 53-114. https://doi.org/10.1039/9781847559333-00053
    42. Dominique Padovani, Ruma Banerjee. Coenzyme B12-Catalyzed Radical Isomerizations. 2009, 330-342. https://doi.org/10.1007/978-0-387-78518-9_21
    43. Iwao Omae. Three characteristic reactions of organocobalt compounds in organic synthesis. Applied Organometallic Chemistry 2007, 21 (5) , 318-344. https://doi.org/10.1002/aoc.1213
    44. Sabine Van Doorslaer, Evi Vinck. The strength of EPR and ENDOR techniques in revealing structure–function relationships in metalloproteins. Physical Chemistry Chemical Physics 2007, 9 (33) , 4620. https://doi.org/10.1039/b701568b
    45. Li Sun, Kurt Warncke. Comparative model of EutB from coenzyme B 12 ‐dependent ethanolamine ammonia‐lyase reveals a β 8 α 8 , TIM‐barrel fold and radical catalytic site structural features. Proteins: Structure, Function, and Bioinformatics 2006, 64 (2) , 308-319. https://doi.org/10.1002/prot.20997
    46. Marija Semialjac, Helmut Schwarz. Computational Investigation of Hydrogen Abstraction from 2‐Aminoethanol by the 1,5‐Dideoxyribose‐5‐yl Radical: A Model Study of a Reaction Occurring in the Active Site of Ethanolamine Ammonia Lyase. Chemistry – A European Journal 2004, 10 (11) , 2781-2788. https://doi.org/10.1002/chem.200305773
    47. Ruma Banerjee, Stephen W. Ragsdale. The Many Faces of Vitamin B 12 : Catalysis by Cobalamin-Dependent Enzymes. Annual Review of Biochemistry 2003, 72 (1) , 209-247. https://doi.org/10.1146/annurev.biochem.72.121801.161828
    48. J. McMaster. 29  Bioinorganic chemistry. Annu. Rep. Prog. Chem., Sect. A: Inorg. Chem. 2002, 98 , 593-614. https://doi.org/10.1039/B109735K
    Download PDF
    Go to Journal of the American Chemical Society
    Get e-Alerts
    Get e-Alerts

    Journal of the American Chemical Society

    Cite this: J. Am. Chem. Soc. 2001, 123, 35, 8564–8572
    Click to copy citationCitation copied!
    https://doi.org/10.1021/ja003658l
    Published August 10, 2001
    Copyright © 2001 American Chemical Society
    Request reuse permissions

    Article Views

    306

    Altmetric

    -

    Citations

    48
    Learn about these metrics

    Article Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.

    Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.

    The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated.