There are theories that the NAD carboxamide group in an enzyme active
site should be out of the nicotine plane by 20-30 degrees, to help
develop a partial positive charge on the C4 atom. This also helps
distorting the planarity of the nicotine ring to ease the catalytic
transformation of NAD to NADH. A while ago we published a paper on a
related topic, the enzymatic activation of NADH: Meijers et al
https://www.ncbi.nlm.nih.gov/pubmed/11134046
Victor Lamzin
On 19/05/2017 00:44, Dale Tronrud wrote:
I have looked over a number of high resolution models with NAD+ and
NADH in the PDB as well as small molecule structures. I also have some
familiarity with similar chemistry in the decorations on the edge of
bacteriochlorophyll-a molecules. The CONH2 group does flip over when
the hydrogen bonding environment calls for it. It is very hard to tell
the difference between the oxygen atom and the nitrogen atom from the
appearance of the electron density so you always have to check the
hydrogen bonding environment when building an NAD? model.
I have seen one case where a Ser -> Ala mutation in the protein
caused the group to flip with interesting consequences on the far side
of the co-factor. My go-to QM person tells me that flipping this group
will change the energies of the molecular orbitals and therefor the
redox potential of the NAD? molecule so this conformational change may
be important to the action of your catalysis.
I have also seen a number of NAD? models in the PDB where this group
is clearly misorientated.
As you note, the torsion angle should be close to zero or 180.
However it is unlikely to have exactly those values because there are
non-bonded clashes when everything is in one plane. Some restraint
libraries inappropriately restrain this group to be co-planar with the
six-membered ring. As always, check you CIF!
Dale Tronrud
On 5/17/2017 12:46 PM, Jorge Iulek wrote:
Dear all,
I came across some difficulty to refine a NAD molecule in a
structure, specially its amide of the nicotinamide moiety.
A (very) brief search in deposited structures seems to point that
not so ever the C2N-C3N-C7N-N7N dihedral is close to either 0 or 180
degrees, but in most cases it is to one of these, with a preference
towards 0 degrees. Another search in the literature, and I could not
find any study on either NAD or even the nicotinamide alone to calculate
the energy barrier to rotate around this bond (in vacuum, eg).
My data quality and resolution do not put much confidence on
B-factor differences, but they seem to indicate that the cited dihedral
angle should be close to 180 degrees, id est, O7N is "closer" to C2N
(and, consequently, to N1N) than N7N is. In fact, I have a glutamine
nearby whose terminal amide is interacting with the nicotinamide amide,
so my idea is to make one's nitrogen to interact with other's oxygen.
Concerning b-factor differences for this glutamine, they favor its NE2
to point to nicotinamide amide, what would imply that the
C2N-C3N-C7N-N7N dihedral to would be close to 180 degrees rather than 0
degree.
Is there any wide study on NAD nicotinamide amide conformation?
Specially, bound to protein structures?
Thanks,
Jorge
