[Annotation] compartment annotation of a protein complex

[D'Eustachio, Peter]

The authors describe two experiments supporting the assertion that the complex is a heterotrimer: if one polypeptide is His-tagged, the whole complex associates with nickel resin; the activity migrates on gel filtration with mobility appropriate for a heterotrimer. If those are believable results, they are hard to explain unless all three polypeptides are stuck together (although the results say nothing about which specific intersubunit contacts are responsible for the sticking).

As to location, the closest the authors come to data is this sentence in the discussion: "The YagT protein contains a 49 amino acid Tat leader peptide that allows the export of the active heterotrimer to the periplasm (data not shown)." That sounds NASish.

-----Original Message-----
From: annotation-bounces at genome.stanford.edu [mailto:annotation-bounces at genome.stanford.edu] On Behalf Of Harold Drabkin
Sent: Wednesday, June 24, 2009 4:11 PM
To: keseler at ai.sri.com
Cc: amackie at ics.mq.edu.au; GO Annotation list
Subject: Re: [Annotation] compartment annotation of a protein complex

Ingrid Keseler wrote:
> Hi,
>
> I have a question regarding how to annotate the localization of the
> components of a protein complex.  PMID 19368556 describes the YagTSR
> complex of E. coli.  Looks like they did size exclusion chromatography
> to show that it is a heterotrimer.  It also turns out that one of the
> components, YagT, normally contains a Tat signal sequence and has been
> experimentally shown to be transported to the periplasm.  So the
> question is, how would you annotate the presumably (and stated by the
> authors) periplasmic localization of the other two components of the
> complex?  Using NAS?  Using IC?  But "with" what?  Or IPI?  Something
> I'd be tempted to do, but pairwise interactions between YagS/R and
> YagT weren't shown.
>
> I'm hoping that the answer is obvious to somebody... :-)
>
> Thanks,
> Ingrid
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always with the experiment; the other two are hearsay for this paper; If
they don't give a reference to look at, then how do they know?

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