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dirigent proteins

Smith, Roger rsmith at tigr.org
Wed Jul 3 05:32:29 PDT 2002


Thanks for all of your replies!  The definition from PMID:8994027 is, in my
opinion, the most accurate, and I too agree that dirigent proteins are not
acting as enzymes specifically.  They are more involved in enzyme
regulation? (it seems).  

I'm glad that this has sparked some discussion as some of the same questions
that I initially had are surfacing here too.  Thanks again, and I look
forward to this gene product being added to the ontology.
-Roger

-------------------------------------- 
  Roger K. Smith Jr., Ph.D. 
  The Institute for Genomic Research 
  9712 Medical Center Dr. 
  Rockville, MD  20850 
  (301) 838-5893 
  e-mail: rsmith at tigr.org
  

-----Original Message-----
From: Pankaj Jaiswal
To: Michael Ashburner (Genetics)
Cc: geneontology-term-request at lists.sourceforge.net; rsmith at tigr.org;
lhannick at tigr.org; midori
Sent: 7/2/02 10:30 AM
Subject: Re: dirigent proteins

Hi,

What i figured out about this enzyme is 

"Dirigent protein in the presence of an oxidase or one electron oxidant,
effects
stereoselective bimolecular phenoxy radical coupling in vitro. Itself
lacking a
catalytically active (oxidative) center, its mechanism of action is
presumed to
involve capture of E-coniferyl alcohol-derived free-radical
intermediates, with
consequent stereoselective coupling to give (+)-pinoresinol." PMID:
8994027

definition: Lacking catalytic active site, the protein in the presence
of an
oxidase or one electron oxidant, effects stereoselective bimolecular
phenoxy
radical coupling, thus becoming a part of holozyme. Best characterised
as a
function during lignan biosynthesis.
term name: stereoselective coupling (as function) 
synonym:dirigent protein



instance of "enzyme regulator" (GO:0030234) as Michael suggested

First I thought about it as a isomerase/racemase, but since its not
responsible
for this kind of an activity it can go as an enzyme regulator. Though
its
clearly a part of oxidase carrying out the reaction converting
E-coniferyl
alcohol to a(+)-pinoresinol


"Michael Ashburner (Genetics)" wrote:
> 
> Sorry to be so long in replying to this:
> 
> I think that we need a new function term for dirigent proteins.  I
have done
> some reading and suggest this new term:
> 
> guiding stereospecific synthesis ; GO:??????? ; synonym:dirigent
protein
> 
> definition: The orientation of free radical substrates in such a way
that
> only a particular stereoisomer is synthesised by an enzyme. Best
characterised
> as a function during lignan biosynthesis.
> 
> It is not clear where this should go, but I suggest that it could be a
> direct child of "enzyme regulator" (GO:0030234) whose definition is
> "Modulates the activity of an enzyme."
> 
> Feedback please.
> 
> Michael
> 
> > From owner-gofriends at genome.stanford.edu Thu Jun 13 18:51:43 2002
> > Envelope-to: ma11 at gen.cam.ac.uk
> > Delivery-date: Thu, 13 Jun 2002 18:51:43 +0100
> > X-Authentication-Warning: alberich.Stanford.EDU: majordom set sender
to owner-gofriends at genome-mail.stanford.edu using -f
> > From: "Hannick, Linda" <lhannick at tigr.org>
> > To: geneontology-term-request at lists.sourceforge.net,
> >         "Smith, Roger"
> >        <rsmith at tigr.org>
> > Cc: Midori A Harris <midori at genome.Stanford.EDU>,
gofriend at genome.Stanford.EDU
> > Date: Thu, 13 Jun 2002 13:50:08 -0400
> > MIME-Version: 1.0
> > X-Mailer: Internet Mail Service (5.5.2653.19)
> > Content-Type: multipart/alternative;
boundary="----_=_NextPart_001_01C21302.C1E0C230"
> > Sender: owner-gofriends at genome.stanford.edu
> > Content-Length: 12447
> >
> > We are currently looking at dirigent proteins, and are not experts
in lignan
> > biosynthesis.  Maybe someone with more expertise in this field can
help us
> > come up with a GO term to accurately describe the function of this
protein
> > and where it fits in the DAG (GO:0009807 accurately describes the
process
> > that it is involved in).
> >
> > Dirigent proteins, in the presence of an oxidase or one electron
oxidant,
> > affect stereoselective biomolecular phenoxy radical coupling (See
Gang et
> > al. (1999) Chem Biol 6, 143-151).  They do not have a catalytically
active
> > (oxidative) center, but they orient free radical substrates in such
a way
> > that random coupling cannot occur, and only the 8-8'-coupled
intermediate
> > (+)-pinoresinol is formed.  Any suggestions on where this should be
added?
> >
> > Thanks
> > Roger Smith
> > The Institute for Genomic Research
> > Bioinformatics Analyst
> > rsmith at tigr.org
> >
> >
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > Linda I. Hannick, Ph.D.
> > The Institute for Genomic Research
> > Bioinformatics Analyst
> > 9712 Medical Center Drive
> > Rockville  MD  20850
> > ~~~~~~~~~~~~~~~~~~~~
> >
> > 301-838-5857 voice
> > 301-838-0208 fax
> > lhannick at tigr.org
> >
> 
> --
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-- 

******************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   
******************************************

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