EC Number   |
General Information |
Reference |
|---|
    5.4.3.5 | evolution |
the enzyme belongs to the class III dAdoCbl-dependent isomerase family |
727644 |
| 5.4.3.5 | malfunction |
conservative substitutions of the residues that form salt bridges to the alpha-carboxylate (R297) or the alpha-amine (E81) of D-ornithine results in a 300-600fold reduction in catalytic turnover and a more pronounced 1000 to 14000fold decrease in catalytic efficiency compared to wild-type. Mutating residues that solely interact with the pyridoxal 5'-phosphate cofactor leads to more modest decreases (10-60fold) in kcat and kcat/Km. All but one variant (S162A) elicite an increase in the kinetic isotope effect on kcat and kcat/Km with D,L-ornithine-3,3,4,4,5,5-d6 as the substrate, which indicates that hydrogen atom abstraction is more rate determining. The substitutions decrease the extent of CoeC bond homolysis, they do not affect the structural integrity of the active site |
-, 747193 |
| 5.4.3.5 | malfunction |
substrate-induced C-Co bond homolysis is compromised in Glu388 variant forms of OAM, although photolysis of the C-Co bond is not affected by the identity of residue 338. Electrostatic interactions of Glu338 with the 5'-deoxyadenosyl group of B12 potentiate C-Co bond homolysis in closed conformations only. These conformations are unlocked by substrate binding. Conformational sampling of the mobile cobalamin-binding domain occurs in the Glu388 variants, but that, in adopting the closed conformation, C-Co bond homolysis is compromised. The population of the closed conformation has an associated lifetime. Each time the closed conformation is populated, there is a higher probability of bond homolysis in wild-type OAM relative to the variant forms because of the electrostatic interactions formed between Glu338 and the cobalamin cofactor that facilitate bond homolysis |
747738 |
| 5.4.3.5 | metabolism |
catalyzes step 2 in the ornithine fermentation pathway |
-, 704292 |
| 5.4.3.5 | metabolism |
the enzyme catalyzes the second step in the oxidative breakdown of the amino acid, converting D-ornithine to 2,4-diaminopentanoic acid |
-, 727131 |
| 5.4.3.5 | more |
computational study on the experimentally elusive cyclisation step in the cofactor pyridoxal 5'-phosphate-dependent D-ornithine 4,5-aminomutase-catalysed reaction, quantum mechanics/molecular mechanics (QM/MM) studies on the mechanism of action of cofactor pyridoxal 5-phosphate in ornithine 4,5-aminomutase, modeling, overview. Calculations using both model systems and a combined QM/MM approach suggest that regulation of the cyclic radical intermediate is achieved through the synergy of the intrinsic catalytic power of cofactor pyridoxal 5'-phosphate and enzyme active site. The captodative effect of pyridoxal 5'-phosphate is balanced by an enzyme active site that controls the deprotonation of both the pyridine nitrogen atom (N1) and the Schiff-base nitrogen atom (N2). Electrostatic interactions between the terminal carboxylate and amino groups of the substrate and Arg297 and Glu81 impose substantial strain energy on the orientation of the cyclic intermediate to control its trajectory. In addition the strain energy, which appears to be sensitive to both the number of carbon atoms in the substrate/analogue and the position of the radical intermediates, may play a key role in controlling the transition of the enzyme from the closed to the open state |
747565 |
| 5.4.3.5 | more |
for the pyridoxal 5'-phosphate and cobalamin-dependent enzyme ornithine 4,5-aminomutase, large-scale re-orientation of the cobalamin-binding domain linked to C-Co bond breakage is proposed. In the model, substrate binding triggers dynamic sampling of the B12-binding Rossmann domain to achieve a catalytically competent closed conformational state. In closed conformations of the enzyme, Glu338 is thought to facilitate C-Co bond breakage by close association with the cobalamin adenosyl group. Large-scale motion is required to pre-organize the active site by enabling transient formation of closed conformations of OAM. In closed conformations, Glu338 interacts with the 5'-deoxyadenosyl group of cobalamin. This interaction is required to potentiate C-Co homolysis, and is a crucial component of the approximately 1012 rate enhancement achieved by cobalamin-dependent enzymes for C-Co bond homolysis. Three-dimensional enzyme structure and active site structure analysis, spectral analysis of substrate-bound wild-type and beta-subunit mutant enzymes, overview |
747738 |
| 5.4.3.5 | more |
going from the open, catalytically inactive form to the closed, catalytically active form, the Rossmann domain of the enzyme effectively approaches the active site as a rigid body. It undergoes a combination of a about 52° rotation and a 14 A translation to bring AdoCbl, initially positioned about 25 A away, into the active site cavity. This process is coupled to repositioning of the Ado moiety of adenosylcobalamin from the eastern conformation to the northern conformation. Combined quantum mechanics and molecular mechanics calculations further indicate that in the open form, the protein environment does not impact significantly on the Co-C bond homolytic rupture, rendering it unusually stable, and thus catalytically inactive |
727677 |
| 5.4.3.5 | more |
important role in catalysis of enzyme residue tyrosine 187, which lies planar to the pyridoxal 5'-phosphate pyridine ring. The level of protein-substrate interactions in aminomutases not only influences substrate specificity, but also controls radical chemistry. Substrate molecular docking simulations |
747073 |
| 5.4.3.5 | more |
modeling of the closed conformation of the enzyme, domain motions, overview |
727644 |
