All-D World

From: Miri Hirshberg
Date: 15 February 2012 22:28


Weds., Feb. 15th 2012
EBI

Good evening,

PDB entries with spg P 1- or I -4 C 2 are

3al1 3boi 2gpm 1krl 2gq7 2gq6 2gq5 2gq4 2g32 1pup 3e7r 1vtu 3odv 3trw
3try

you can get information on each from pdbe

pdbe.org/entry
i.e.
pdbe.org/3al1
etc.

Miri, PDBe

On Wed, 15 Feb 2012, Jacob Keller wrote:

So who out there wants to start an all-D microbial culture by total
synthesis, a la the bacterium with the synthetic genome a while back?
Could it work, I wonder? I guess that would be a certain benchmark for
Man's conquest of nature.

JPK

ps maybe if there is a broadly-acting amino-acid isomerase or set of
isomerases of appropriate properties, this could be helpful for
getting the culture started--or even for preying on the L world?



On Wed, Feb 15, 2012 at 12:17 PM, David Schuller  wrote:

On 02/15/12 12:41, Jacob Keller wrote:

Are there any all-D proteins out there, of known structure or
otherwise? If so, do enantiomer-specific catalyses become inverted?

JPK

What do you mean by "Out There"? If you mean in the PDB, then yes.  As of
two weeks ago, there are ~ 14 racemic structures deposited; most in space
group P -1, with one outlier in space group I -4  C 2. This includes RNA,
DNA, and PNA, but 6 entries are actually protein. The longest is over 80
residues.

Theoretically, enantiomer-specific catalysis ought to be inverted, but most
of the structures solved are not enzymes. kaliotoxin, plectasin, antifreeze
protein, monellin, villin, and a designed peptide.

On the other hand, if by "out there" you meant in nature outside of
biochemistry and organic chemistry labs; then no, I am not aware of any
all-D proteins. There are a few protein/peptides which include a small
number of D-residues, which is marked up to nonribosomal synthesis.

The first paper I managed to Google:
http://jb.asm.org/content/185/24/7036.full
Learning from Nature's Drug Factories: Nonribosomal Synthesis of Macrocyclic
Peptides
doi: 10.1128/JB.185.24.7036-7043.2003 J. Bacteriol. December 2003 vol. 185
no. 24 7036-7043

If racemic crystallization isn't exciting enough for you, look into
quasi-racemic crystallization.


On Wed, Feb 15, 2012 at 8:05 AM, David Schuller  wrote:

Wukovitz & Yeates (1995) Nature Struc. Biol. 2(12): 1062-1067
predicts that the most probable space group for macromolecular
crystallization is P -1 (P 1-bar). All you have to do to try it out is
synthesize the all-D enantiomer of your protein and get it to fold properly.


On 02/14/12 18:36, Prem Kaushal wrote:


Hi

We have a protein that crystallized in P21212 space group. We are looking
for some different crystal forms. We tried few things did not work. Now we
are thinking to mutate surface residues. Anybody aware of any software which
can predict the mutations that might help in crystallizing protein in
different space group, please inform me.

Thanks in advance

Prem


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All Things Serve the Beam
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                              David J. Schuller
                             

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Jacob Pearson Keller
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Weds. Feb. 15th, 2012
EBI