Sajid,
It is not clear what you are asking. Are you asking whether there are
common structural features in domains that bind nucleotide di/tri
phosphates and dinucleotides? Or are there clear structural rules to
consider when designing a (di)nucleotide binding site. If it is the
former, then yes there are a whole class of enzymes/proteins that use
a common motif design for binding (di)nucleotides. However, that
being said, exceptions to these "rules" are also found. If you are
asking about the latter, there are no clear rules, but structural
considerations (how the nucleotide base is bound, the stereochemistry
of the base to the ribose ring - syn or anti, how to ligand the
ribose, etc.) that must be dealt with. But again, there are
exceptions to these "rules." Michael's seminal Nature paper did get
everyone thinking about the issue of structure-function relationships
(and yes we did structural superpositions back in 1970's on our trusty
CDC 6600 with 60-bit words), proposing even the existence of a half
Rossmann fold to bind nucleotides. However, even today, observing a
Rossmann fold in a structure does not mean that the domain binds a
dinucleotide, and a protein with no Rossmann fold can bind
(di)nucleotides quite nicely. The latter situation is illustrated by
these papers:
Jin, Y. et al. Crystal structure of human type III 3alpha-
hydroxysteroid dehydrogenase/bile acid binding protein complexed with
NADP(+) and ursodeoxycholate. (2001) Biochemistry 40: 10161-10168
Putnam, C.D. et al. Active and inhibited human catalase structures:
ligand and NADPH binding and catalytic mechanism. (2000) J.Mol.Biol.
296: 295-309
As suggested I would query Michael's papers from the 70's and 80's on
the dehydrogenases:
Eventoff and Rossmann. (1975) The evolution of Dehydrogenase and
Kinases. CRC Crit. Rev. Biochem. 3, 111-140.
Rossmann and Argos (1978) The Taxonomy of Binding Sites in Proteins.
Molec. Cell. Biochem. 3(21), 161-182.
These papers should give the information, from a historical and
structural perspective, you need, from a historical and structural
perspective, to begin your analysis.
Regards,
Michael
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R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology
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On Oct 20, 2009, at 7:42 AM, Mark Brooks wrote:
This is a good start for Rossmann folds, I find. (I'm not sure if this
is what you want though.)
"Chemical and biological evolution of a nucleotide-binding protein."
Michael G. Rossmann, Dino Moras & Kenneth W. Olsen. Nature Vol. 250
July 19 1974, p194.
(Structural alignments in 1974 - wow!)
If anyone has votes for other favourite papers of this ilk, I'm all
ears!
Mark
2009/10/20 Vellieux Frederic <frederic.velli...@ibs.fr>:
Michael Rossmann and colleagues did some work on the binding of
fragments of
cofactors to dogfish lactate dehydrogenase. In the 70's I think.
Can be
found on google scholar. Perhaps that's what you are after? Can't
find the
reference right now (it's in one of my drawers but I don't know which
one...). I passed the reference on to Nicolas Coquelle @ualberta
(coque...@ualberta.ca) a few days ago but that was from my home e-
mail
address so I don't have it here in the office.
Fred.
sajid akthar wrote:
Dear All
Can any one mention some reference regarding the binding of NADPH
or ADP
in the surface of the protein. Is there any rules that dominate
these two
cofactors to select the surface istead of typical Rossmann fold.
Thank you
Sajid
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