A Second Allosteric Site in <i>Escherichia coli</i> Aspartate Transcarbamoylase

<i>Escherichia coli</i> aspartate transcarbamoylase is feedback inhibited by CTP and UTP in the presence of CTP. Here, we show by X-ray crystallography that UTP binds to a unique site on each regulatory chain of the enzyme that is near but not overlapping with the known CTP site. These results bring into question all of the previously proposed mechanisms of allosteric regulation in aspartate transcarbamoylase

Selectivity of the Highly Preorganized Tetradentate Ligand 2,9-Di(pyrid-2-yl)-1,10-phenanthroline for Metal Ions in Aqueous Solution, Including Lanthanide(III) Ions and the Uranyl(VI) Cation

Some metal ion complexing properties of DPP (2,9-Di­(pyrid-2-yl)-1,10-phenanthroline) are reported with a variety of Ln­(III) (Lanthanide­(III)) ions and alkali earth metal ions, as well as the uranyl­(VI) cation. The intense π–π* transitions in the absorption spectra of aqueous solutions of 10^–5 M DPP were monitored as a function of pH and metal ion concentration to determine formation constants of the alkali-earth metal ions and Ln­(III) (Ln = lanthanide) ions. It was found that log <i>K</i>₁(DPP) for the Ln­(III) ions has a peak at Ln­(III) = Sm­(III) in a plot of log <i>K</i>₁ versus 1/<i>r</i>⁺ (<i>r</i>⁺ = ionic radius for 8-coordination). For Ln­(III) ions larger than Sm­(III), there is a steady rise in log <i>K</i>₁ from La­(III) to Sm­(III), while for Ln­(III) ions smaller than Sm­(III), log <i>K</i>₁ decreases slightly to the smallest Ln­(III) ion, Lu­(III). This pattern of variation of log <i>K</i>₁ with varying size of Ln­(III) ion was analyzed using MM (molecular mechanics) and DFT (density functional theory) calculations. Values of strain energy (∑U) were calculated for the [Ln­(DPP)­(H₂O)₅]³⁺ and [Ln­(qpy)­(H₂O)₅]³⁺ (qpy = quaterpyrdine) complexes of all the Ln­(III) ions. The ideal M–N bond lengths used for the Ln­(III) ions were the average of those found in the CSD (Cambridge Structural Database) for the complexes of each of the Ln­(III) ions with polypyridyl ligands. Similarly, the ideal M–O bond lengths were those for complexes of the Ln­(III) ions with coordinated aqua ligands in the CSD. The MM calculations suggested that in a plot of ∑U versus ideal M–N length, a minimum in ∑U occurred at Pm­(III), adjacent in the series to Sm­(III). The significance of this result is that (1) MM calculations suggest that a similar metal ion size preference will occur for all polypyridyl-type ligands, including those containing triazine groups, that are being developed as solvent extractants in the separation of Am­(III) and Ln­(III) ions in the treatment of nuclear waste, and (2) Am­(III) is very close in M–N bond lengths to Pm­(III), so that an important aspect of the selectivity of polypyridyl type ligands for Am­(III) will depend on the above metal ion size-based selectivity. The selectivity patterns of DPP with the alkali-earth metal ions shows a similar preference for Ca­(II), which has the most appropriate M–N lengths. The structures of DPP complexes of Zn­(II) and Bi­(III), as representative of a small and of a large metal ion respectively, are reported. [Zn­(DPP)₂]­(ClO₄)₂ (triclinic, <i>P</i>1, <i>R</i> = 0.0507) has a six-coordinate Zn­(II), with each of the two DPP ligands having one noncoordinated pyridyl group appearing to be π-stacked on the central aromatic ring of the other DPP ligand. [Bi­(DPP)­(H₂O)₂(ClO₄)₂]­(ClO₄) (triclinic, <i>P</i>1, <i>R</i> = 0.0709) has an eight-coordinate Bi, with the coordination sphere composed of the four N donors of the DPP ligand, two coordinated water molecules, and the O donors of two unidentate perchlorates. As is usually the case with Bi­(III), there is a gap in the coordination sphere that appears to be the position of a lone pair of electrons on the other side of the Bi from the DPP ligand. The Bi-L bonds become relatively longer as one moves from the side of the Bi containg the DPP to the side where the lone pair is thought to be situated. A DFT analysis of [Ln­(tpy)­(H₂O)_<i>n</i>]³⁺ and [Ln­(DPP)­(H₂O)₅]³⁺ complexes is reported. The structures predicted by DFT are shown to match very well with the literature crystal structures for the [Ln­(tpy)­(H₂O)_<i>n</i>]³⁺ with Ln = La and <i>n</i> = 6, and Ln = Lu with <i>n</i> = 5. This then gives one confidence that the structures for the DPP complexes generated by DFT are accurate. The structures generated by DFT for the [Ln­(DPP)­(H₂O)₅]³⁺ complexes are shown to agree very well with those generated by MM, giving one confidence in the accuracy of the latter. An analysis of the DFT and MM structures shows the decreasing O--O nonbonded distances as one progresses from La to Lu, with these distances being much less than the sum of the van der Waals radii for the smaller Ln­(III) ions. The effect that such short O--O nonbonded distances has on thermodynamic complex stability and coordination number is then discussed