Narayanan Ramasubbu wrote:
> Dear all:
> I have a single residue mutant whose enzyme activity is about 50% of
> the wild type. Interestingly, the mutation
> is in a region that involves a secondary site but not the active site.
> The two structures with or without ligands
> fit well (0.18 A) and the metal binding and cofactor binding sites are
> all preserved in the mutant. The one difference
> noticed is that the ligand does not fill the active site (partially
> occupied subsites) unlike the wild type where all the
> subsites are occupied. Water structure around the actives site
> residues are "identical".
>
> I looked at the electrostatics and both surfaces look similar (not an
> expert).
>
> There are some residues whose sides chains show some positional
> disorder and these residues are at the edges of the
> active site.
>
> The resolution of the both data sets are 1.5A.
> The mutant enzyme was derived by MR.
>
> One another possibility that I want to look at is to compare the
> compactness of the two enzyme structures.
> What is the best way to compare that? I am wondering whether the
> "breathing" that was mentioned for some enzymes
> might be playing a role in the mutant enzyme.
>
> Also, I would appreciate comments on other possible explanations for
> this unusual (?) behavior.
>
>
> Thanks a lot
>
> Subbu
>
If your rmsd is 0.18 you might not see a breathing. I assume you did SSM
superposition, try superpositioning specific residues which e.g. belong
to a helix and then see if there are major differences in the rest of
the structure. You'll have to find the right site/area to superposition
perhaps to see the difference at all.
Juergen
--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch
|