interaction type: sumoylation

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Sumoylated lysine is a PTM term, but no corresponding sumoylation interaction type term exists. In general, should the interaction type tree mirror the PTM tree completely?

Reported by: gbader

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isn't it just a covalent interaction between a protein and SUMO ? same situation as ubiquitination ?

lukasz

Original comment by: lukasz99

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Yes, but sumoylation seems to be missing from interaction type, while ubiquitination is there.

Original comment by: gbader

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I wouldn't mind ubiquitination going away.. just for the consistency sake. otherwise every covalent bond between two protein chains should have a corresponding postranslational modification term...

lukasz

Original comment by: lukasz99

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I wouldn't mind ubiquitination going away.. just for the consistency sake. otherwise every covalent bond between two protein chains should have a corresponding postranslational modification term...

lukasz

Original comment by: lukasz99

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I would agree with you for peptide bonds, but ubiquitination and sumoylation are not peptide bonds - they are knwon post-translational modifications e.g. on lysine, with their own host of specific modifying enzymes. So in that sense, they are very similar to other PTMs.

Original comment by: gbader

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well.. it looks like you're trying to sneak through semantics ;o) otherwise, why is sumo/ubiquitin a modifying group and the other protein a postranslationally modified one ? why should be sumo/ubiquitin treated in a different manner than the protein it is attached to ?

in general - just imagine two proteins covalently bound to each other through a covalent, but non-peptide bond. which chain is 'protein' and which one 'modifying group' ?

lukasz

Original comment by: lukasz99

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You do have a point there - maybe the definition of what a PTM is should be clearer. I would say a good start is a modification of an amino acid side chain by a specific enzyme. Then we can think of counter examples and refine the definition. Are the following PTMs? prolyl-isomerase, disulphide bond formation by Dsb proteins, cleavage by protease, N or C terminal modification, etc.

The other thing is to check if RESID DB or other similar DBs consider it a PTM.

Original comment by: gbader

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>You do have a point there - maybe the definition of what a >PTM is should be clearer. I would say a good start is a >modification of an amino acid side chain by a specific enzyme.

did anyone know about a specfic enzyme when the first protein-Ub complex was described ? assuming the definition above once a specific enzyme is discovered a wave of reanotation follows ?

>Are the following PTMs? prolyl-isomerase, disulphide bond formation > by Dsb proteins, cleavage by protease, N or C terminal modification, etc.

i guess it depends... - as long as they are constrained to the same polypeptide chain - yes. otherwise - no. so intra-molecular disulfide bond is a PTM, inter-molecular is not.

l

Original comment by: lukasz99

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I should had add sumoylation as interaction type, as Gary is right we have tryed to keep the ptm and interaction tree consistent. I am keen on adding it.

Is that a problem to consider SUMO NEDD as PTMs? There are signalling small proteins to me functionally quite equivalent to 'phospho-residues' and phosphorylation. This is not be the case for any covalent bound among given proteins.

luisa

Original comment by: luisa_montecchi

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Addition of terms approved in Munich see MI:0565 to MI:0569

Original comment by: luisa_montecchi

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done see MI:0566 also added de-sumolylation and similarly added all set of terms for neddylation

Original comment by: luisa_montecchi

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• status: open --> closed

Original comment by: luisa_montecchi