In our paper, using a hybrid version of the enzyme in which only one of six catalytic chains can bind PALA, we show that the enzyme undergoes a quaternary conformational change to a structure similar to that of the wild type R state. For this hybrid enzyme, the binding of PALA to one and only one site is sufficient to induce a complete transition from the T to the R quaternary structure. The comment of Fetler and Vachette addresses the issue of whether this hybrid is a good model for the wild type enzyme. Obviously, no mutant or hybrid can be a perfect substitute for the wild type enzyme. However, in order to assure that the mutant ATCase (R105A) was a good model for the wild type enzyme, the X-ray structure was determined and was shown to be identical to the T state of wild type enzyme except at the site of the amino acid replacement.
As Fetler and Vachette point out, the SAXS patterns of the hybrid enzyme are slightly different from that of the wild type enzyme. There are a number of possible explanations for these differences. Fetler and Vachette only mention one: the hybrid exists as a mixture of T and R states. However, their fit of the data to a T and R state mixture is not exact as required, but has significant deviations. Moreover, the R state SAXS pattern of the hybrid is also different from the corresponding pattern of the wild type enzyme. Two other possibilities are that the enzyme is in a new quaternary structure different from the wild type T or R states or, that the enzyme preparation may contain an impurity that contributes to the scattering pattern of both the T and R states. As reported, the structure of the R105A enzyme in the T state is virtually identical to that of the wild type enzyme arguing against the enzyme being in a new quaternary conformation.
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