Computational study on mechanistic details of the aminoethanol rearrangement catalyzed by the vitamin B12-dependent ethanolamine ammonia lyase: His and Asp/Glu acting simultaneously as catalytic auxiliaries.
The rearrangement of aminoethanol catalyzed by ethanolamine ammonia lyase is investigated by computational means employing DFT (B3LYP/6-31G) and ab initio molecular orbital theory (QCISD/cc-pVDZ). The study aims at providing a detailed account on various crucial aspects, in particular a distinction between a direct intramolecular migration of the partially protonated NH(2) group vs elimination of NH(4)(+). Three mechanistic scenarios were explored: (i) According to the calculations, irrespective of the nature of the protonating species, intramolecular migration of the NH(3) group is energetically less demanding than elimination of NH(4)(+). However, all computed activation enthalpies exceed the experimentally derived activation enthalpy (15 kcal/mol) associated with the rate-determining step, i.e., the hydrogen abstraction from the 5'-deoxyadenosine by the product radical. For example, when imidazole is used as a model system for His interacting with the NH(3) group of the substrate, the activation enthalpy for the migration process amounts to 27.4 kcal/mol. If acetic acid is employed to mimic Asp or Glu, the activation enthalpy is somewhat lower, being equal to 24.2 kcal/mol. (ii) For a partial deprotonation of the substrate 2 at the OH group, the rearrangement mechanism consists of the dissociation of an NH(2) radical from C(2) and its association at C(1) atom. For all investigated proton acceptors (i.e., OH(-), HCOO(-), CH(3)COO(-), CH(2)NH, imidazole), the activation enthalpy for the dissociation step also exceeds 15 kcal/mol. Typical data are 20.2 kcal/mol for Ac(-) and 23.8 kcal/mol for imidazole. (iii) However, in a synergistic action of partial protonation of the NH(2) group and partial deprotonation of the OH group by the two conceivable catalytic auxiliaries Asp/Glu and His, the activation enthalpy computed is compatible with the experimental data. For imidazole and acetate as model systems, the activation enthalpy is equal to 13.7 kcal/mol. This synergistic action of the two catalytic groups is expected to take place in a physiologically realistic pH range of 6-9.5, and the present computational findings may help to further characterize the yet unknown structural details of the ethanolamine ammonia lyase's active site.
Semialjac
Marija
M
Institut für Chemie der Technischen Universität Berlin, D-10623 Berlin, Germany.
Schwarz
Helmut
H
D001224:Aspartic Acid / Q000737:chemistry; D001665:Binding Sites; D002384:Catalysis; D019295:Computational Biology; D004981:Ethanolamine Ammonia-Lyase / Q000737:chemistry*; D004983:Ethanolamines / Q000737:chemistry*; D018698:Glutamic Acid / Q000737:chemistry; D006639:Histidine / Q000737:chemistry; D007202:Indicators and Reagents; D008968:Molecular Conformation; D013816:Thermodynamics; D014805:Vitamin B 12 / Q000737:chemistry*
D004983:Ethanolamines; D007202:Indicators and Reagents; D001224:Aspartic Acid; D018698:Glutamic Acid; D006639:Histidine; D004981:Ethanolamine Ammonia-Lyase; D014805:Vitamin B 12