Comments on: How overrated is phosphorylation? – an opinion

By: Kay at Suicyte

Kay at Suicyte — Mon, 19 May 2008 10:08:01 +0000

@Bill: Most people cite the review “The Protein Kinase Complement of the Human Genome” by G. Manning et al, in Science 298:1912-1934 (2002). A useful resource for the kinase figures can be found at http://kinase.com/human/kinome/
The ubiquitin figures are unpublished work from my group.

By: bill

bill — Mon, 19 May 2008 07:22:18 +0000

@Kay: huh. Now I want to find the review I (thought I) remembered those numbers from, and see whether the review or my memory was at fault. (The latter is more likely!)

By: Kay at Suicyte

Kay at Suicyte — Sun, 18 May 2008 23:14:00 +0000

I cannot leave this uncommented

First, I do not think that the importance of phosphorylation is (too much) overrated. I would not build so much on this ‘1/3′ number, though, but rather on the number of genes/proteins dedicated to effecting, removing or recognizing phosphorylation. It is possible that the number of targets is both real and meaningful, but I am always wary that the number of targets (of anything) might include a high proportion of meaningless accidental modifications. I have talked about this concept of ‘not everything observed has to be meaningful’ in many of my own blog entries, e.g. with regard to alternative splicing and intragenic transcription. The same reasoning also applies to phosphorylation or, my favourite topic, ubiquitination.

@Bill: I think a current estimate for the human kinase complement is 517 active kinases, plus some 100 putative pseudogenes. As for ubiquitin E3s, my latest figure is 604 substrate recognition components (there are several E3 complexes consisting of some constitutive subunits plus one specificity factor). Both numbers are not carved into stone, I would expect them to increase slightly over the next decade. Nevertheless, we are in the same ballpark region for both modification types.

By: bill

bill — Fri, 16 May 2008 14:15:37 +0000

I read recently that there are hundreds of kinases (about 300?), but at least a thousand E3 ubiquitin ligases in a typical mammalian cell. That suggests that ubiquitination, for one, may be more important than phosphorylation. My guess is that this will turn out to be true, once we have the tools to study ubiquitination in detail (better probes for Ub-proteins, mutant Ub, etc etc).

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By: Neil

Neil — Fri, 16 May 2008 06:09:25 +0000

Everyone cites that 1/3 of all proteins figure; I've done it myself and I don't know the original source! Try these from PubMed: How do protein kinases recognize their substrates? Kinomics: methods for deciphering the kinome.