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
