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Interaction of the Substrate Radical and the 5‘-Deoxyadenosine-5‘-Methyl Group in Vitamin B12 Coenzyme-Dependent Ethanolamine Deaminase

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    Interaction of the Substrate Radical and the 5‘-Deoxyadenosine-5‘-Methyl Group in Vitamin B12 Coenzyme-Dependent Ethanolamine Deaminase
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    Contribution from the Department of Physics, Emory University, Atlanta, Georgia 30322
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    Journal of the American Chemical Society

    Cite this: J. Am. Chem. Soc. 2001, 123, 35, 8564–8572
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    https://doi.org/10.1021/ja003658l
    Published August 10, 2001
    Copyright © 2001 American Chemical Society
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    Abstract

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    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

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     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.

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    8. 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
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    11. 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
    12. 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
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    34. 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
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    36. 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
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    39. Perry Allen Frey. Cobalamin Coenzymes in Enzymology. 2010, 501-546. https://doi.org/10.1016/B978-008045382-8.00145-3
    40. Rowena G. Matthews. Cobalamin- and Corrinoid-Dependent Enzymes. 2009, 53-114. https://doi.org/10.1039/9781847559333-00053
    41. Dominique Padovani, Ruma Banerjee. Coenzyme B12-Catalyzed Radical Isomerizations. 2009, 330-342. https://doi.org/10.1007/978-0-387-78518-9_21
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    47. J. McMaster. 29  Bioinorganic chemistry. Annu. Rep. Prog. Chem., Sect. A: Inorg. Chem. 2002, 98 , 593-614. https://doi.org/10.1039/B109735K
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    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

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