MP:peptidyl-diphthamide biosynthetic process from peptidyl-h

[gocentral]

GO:0017183 peptidyl-diphthamide biosynthetic process from peptidyl-histidine is defined The posttranslational modification of peptidyl-histidine to 2'-(3-carboxamido-3-(trimethylammonio)propyl)-L-histidine, known as diphthamide, found in translation elongation factor eEF-2.

but does not have a post-translational modification parent.

I also wondered why "peptidyl-histidine" was part of the term name?

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/6034":https://sourceforge.net/p/geneontology/ontology-requests/6034

[gocentral]

possibly also these: GO:0010731 protein amino acid glutathionylation GO:0006486 protein amino acid glycosylation GO:0002084 protein depalmitoylation GO:0043543 protein amino acid acylation IGO:0006517 protein deglycosylation GO:0032446 protein modification by small protein conjugation

Original comment by: ValWood

[gocentral]

We got the term name for GO:0017183 from RESID/John G ... I guess we don't absolutely need the "from peptidyl-histidine" if peptidyl-diphthamide isn't formed any other way, but it's not wrong.

Modification of peptidyl-whatever doesn't rule out the possibility that the modification could be co-translational (and of course I have no idea ...). I'll ask John to take a look at this; I know he said some modifications can be either co- or post-translational, but at the moment I don't remember which ones.

m

Original comment by: mah11

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• labels: --> Other term-related request
• milestone: --> 224410

Original comment by: mah11

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For this one (0017183), the def staes the "post-translational modification"

Original comment by: ValWood

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yeah, but some of the others don't (haven't checked all yet); I figured if any others needed fixing I could do all at once

Original comment by: mah11

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A few years ago, not much was known about the first step of diphthamide biosynthesis except that it was only possible with the one particular histidine in eEF2. The EC usually names the protein modification enzymes that act only on particular amino acids within a peptide chain as "peptidyl-aa" so that is what I suggested they call this. The first step is now known to be the unusual SAM cleavage (eEF2) peptidyl-histine + S-adenosyl-methionine = peptidyl-[2'-(3-amino-3-carboxypropyl)histidine] + adenosyl-methylsulfide This is followed by 3 methyl transfers from SAM to make peptidyl-diphthine, and a final amidation to make peptidyl-diphthamide. All these reactions are posttranslational.

The point I have made in the past about distinguishing posttranslational and co-translational processes is that it is usually not very meaningful or useful. Some glycosylation processes are known to occur before a protein has been released from the ribosome. But the same type of glycosylation may occur in the same organism for other proteins only after they have left the ribosome. I think for most GO purposes this distinction is too fine-grained, being organism and possibly even tissue specific. N-terminal glycine myristoylation is usually co-translational, as is cysteine S-myristoylation when those cysteines are near the N-terminal, but posttranslational when they are near tranwsmembrane regions or near C-terminal prenylation sites. Do you really want to go around shoe-horning every organism/tissue/protein into the same GO category based on enzyme reactions that are only well-charaterized in yeast? I usually urge people to avoid saying PTM and "posttranslational modification"; simplify your lives and just say "protein modification".

Original comment by: jsgaravelli

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In addition to the usual assortment on typos, ie for "histine" read "histidine", I said "cysteine S-myristoylation" when I meant to say "cysteine S-palmitoylation". Sorry --- but the argument is the same.

Original comment by: jsgaravelli

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So, why don;t we get rid of the term "post-translational modification" from GO (and merge into protein modification), we wouldn't lose anything process wise if we did this. Val

Original comment by: ValWood

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Might be something to consider in the long run, but for now I think we have a reasonable compromise. Anyone who cares to capture that a particular gp is involved in co- or post-translational modification can co-annotate to one of those two terms as well as one for the type of modification. Those who aren't bothered, don't have to co-annotate.

m

Original comment by: mah11

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closing for now

Original comment by: mah11

[gocentral]

• status: open --> closed-works-for-me

Original comment by: mah11

[gocentral]

• milestone: 224410 --> PomBase

Original comment by: mah11