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Term issue: canonical isoform for UniProtKB:P05480 has changed #285

Closed nataled closed 1 year ago

nataled commented 2 years ago

Hi Harold, It seems that the canonical isoform for the UniProtKB entry P05480 has changed, so that the residues indicated below no longer match. Tyr-424 in isoform 1 (the previous canonical) is Tyr-418 in isoform 2 (the new canonical) and Tyr-527 in isoform 1 is now Tyr-521. Looks like the new canonical lacks 6 residues in the former (probably to align the isoforms between species, but I haven't checked).

Please advise as to whether the residues should be changed in the stanzas below, or if the specific isoform should be indicated. Based on your usual modus operandi (specifying the precise isoform when known), I'm guessing the residues should be changed, but wanted to double check.

[Term] id: PR:000037500 name: proto-oncogene tyrosine-protein kinase Src phosphorylated 1 (mouse) def: "A proto-oncogene tyrosine-protein kinase Src (mouse) that has been phosphorylated on a Tyr residue as in UniProtKB:P05480, Tyr-527, MOD:00048. UniProtKB:P05480, Tyr-527, MOD:00048." [PRO:HJD, PMID:23526378, PMID:2480346] comment: Category=organism-modification. Kinase=("CSK"; PR:P41241). synonym: "mSRC/Phos:1" EXACT PRO-short-label [PRO:DNx] synonym: "UniProtKB:P05480, Tyr-527, MOD:00048" EXACT PRO-proteoform-std [PRO:DNx] synonym: "pp60c-src phosphorylated (mouse)" RELATED [] is_a: PR:P05480 ! proto-oncogene tyrosine-protein kinase Src (mouse) relationship: has_part MOD:00048 ! O4'-phospho-L-tyrosine relationship: only_in_taxon NCBITaxon:10090 ! Mus musculus

[Term] id: PR:000037501 name: proto-oncogene tyrosine-protein kinase Src phosphorylated 2 (mouse) def: "A proto-oncogene tyrosine-protein kinase Src (mouse) that has been phosphorylated on a Tyr residue as in UniProtKB:P05480, Tyr-424, MOD:00048. UniProtKB:P05480, Tyr-424, MOD:00048." [PRO:HJD, PMID:23526378, PMID:2480346] comment: Category=organism-modification. Note: Tyr-416 Src residue number in cited article is based on the chicken Src protein. This corresponds to Tyr-424 in mouse. synonym: "mSRC/Phos:2" EXACT PRO-short-label [PRO:DNx] synonym: "UniProtKB:P05480, Tyr-424, MOD:00048" EXACT PRO-proteoform-std [PRO:DNx] synonym: "pp60c-src phosphorylated (mouse)" RELATED [] is_a: PR:P05480 ! proto-oncogene tyrosine-protein kinase Src (mouse) relationship: has_part MOD:00048 ! O4'-phospho-L-tyrosine relationship: only_in_taxon NCBITaxon:10090 ! Mus musculus

[Term] id: PR:000037502 name: proto-oncogene tyrosine-protein kinase Src phosphorylated 3 (mouse) def: "A proto-oncogene tyrosine-protein kinase Src (mouse) that has been phosphorylated on two residues at positions corresponding to Tyr-424 and Tyr-527 in UniProtKB:P05480. UniProtKB:P05480, Tyr-424/Tyr-527, MOD:00048." [PRO:HJD, PMID:23526378, PMID:2480346] comment: Category=organism-modification. Kinase=("CSK"; PR:P41241; Tyr-527). Kinase=("SRC"; PR:P05480; Tyr-424). Note: Tyr-416 Src residue number in cited article is based on the chicken Src protein. This corresponds to Tyr-424 in mouse. synonym: "mSRC/Phos:3" EXACT PRO-short-label [PRO:DNx] synonym: "UniProtKB:P05480, Tyr-424/Tyr-527, MOD:00048" EXACT PRO-proteoform-std [PRO:DNx] synonym: "pp60c-src phosphorylated (mouse)" RELATED [] is_a: PR:P05480 ! proto-oncogene tyrosine-protein kinase Src (mouse) relationship: has_part MOD:00048 ! O4'-phospho-L-tyrosine relationship: only_in_taxon NCBITaxon:10090 ! Mus musculus

[Term] id: PR:000049780 name: proto-oncogene tyrosine-protein kinase Src unphosphorylated 2 (mouse) def: "A proto-oncogene tyrosine-protein kinase Src (mouse) that lacks phosphorylation at the position equivalent to Tyr-424 of the amino acid sequence represented by UniProtKB:P05480. UniProtKB:P05480, Tyr-424, PR:000026291." [PRO:HJD, PMID:26764350] synonym: "mSRC/UnPhos:2" EXACT PRO-short-label [PRO:DNx] synonym: "UniProtKB:P05480, Tyr-424, PR:000026291" EXACT PRO-proteoform-std [PRO:DNx]

[Term] id: PR:000049781 name: proto-oncogene tyrosine-protein kinase Src unphosphorylated 1 (mouse) def: "A proto-oncogene tyrosine-protein kinase Src (mouse) that is unphosphorylated at the position equivalent to Tyr-527 of the amino acid sequence represented by UniProtKB:P05480. UniProtKB:P05480, Tyr-527, PR:000026291." [PRO:HJD, PMID:26764350] synonym: "mSRC/UnPhos:1" EXACT PRO-short-label [PRO:DNx] synonym: "UniProtKB:P05480, Tyr-527, PR:000026291" EXACT PRO-proteoform-std [PRO:DNx]

hdrabkin commented 2 years ago

I have a vague remembrance of these because as I recall the numbering system many people use for Src is actually based on the chicken Src. This might get complicated.

hdrabkin commented 2 years ago

PR:000037500 tyr 527 of Mouse src isoform 2 AALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFTSTEPQYQPGEN

positon 521 to 530 (521) QAFLEDYFTS(530) This is position 527 for isoform 1; (note isoform 2 is canonical at UniProt).

Canonical isoform 2 the postion would be Y521 (511)FEYLQAFLEDYFTSTEPQYQ(530)

I took this from the current public UniProt site. Is this different from what you are loooking at now?

hdrabkin commented 2 years ago

I find this odd that I did not specify isoform 1 since it has the correct position, even if the sequence is still in isoform 2

hdrabkin commented 2 years ago

So I think specifiying isoform 1 would make everything ok.

nataled commented 2 years ago

What has me wondering is that it is difficult to tell whether or not the positions given in the paper were based on actual knowledge of isoforms, or simply because they looked up the sequence in some database and just used the numbering given there. I note that, at the time the paper was published, UniProtKB only had isoform 1. That being said, when I looked up information about isoforms, it seems that isoform 1 is neuronal (see PMID:2440106), and it is unlikely that this was the isoform tested in the paper (they used material of placental origin). I think this means we should change the positions, and probably also specify isoform 2. Let me know if you agree.

hdrabkin commented 2 years ago

In PMID:23526378, they are mostly analyzing osteoclasts. and is from 2013, However the paper you cite is older (1987) so I just wonder why the authors of the 2013 paper did not consider this. But I think they maybe just applied the chick Src number.; I see no gc-ms data to suggest what they analyzed. And certainly adding 6 residues to isoform 2 brings the numbering to 527.

nataled commented 2 years ago

Sorry, I'm not understanding something. Are you agreeinging that we should specify isoform 2 and renumber?

hdrabkin commented 2 years ago

Thanks Darren I’ll look into this this morning.

H

From: "Darren A. Natale" @.> Reply-To: PROconsortium/PRoteinOntology @.> Date: Thursday, September 29, 2022 at 7:10 PM To: PROconsortium/PRoteinOntology @.> Cc: me @.>, Assign @.***> Subject: [EXTERNAL][PROconsortium/PRoteinOntology] Term issue: (Issue #285)

Hi Harold, It seems that the canonical isoform for the UniProtKB entry P05480 has changed, so that the residues indicated below no longer match. Tyr-424 in isoform 1 (the previous canonical) is Tyr-418 in isoform 2 (the new canonical) and Tyr-527 in isoform 1 is now Tyr-521. Looks like the new canonical lacks 6 residues in the former (probably to align the isoforms between species, but I haven't checked).

Please advise as to whether the residues should be changed in the stanzas below, or if the specific isoform should be indicated. Based on your usual modus operandi (specifying the precise isoform when known), I'm guessing the residues should be changed, but wanted to double check.

[Term] id: PR:000037500 name: proto-oncogene tyrosine-protein kinase Src phosphorylated 1 (mouse) def: "A proto-oncogene tyrosine-protein kinase Src (mouse) that has been phosphorylated on a Tyr residue as in UniProtKB:P05480, Tyr-527, MOD:00048. UniProtKB:P05480, Tyr-527, MOD:00048." [PRO:HJD, PMID:23526378, PMID:2480346] comment: Category=organism-modification. Kinase=("CSK"; PR:P41241). synonym: "mSRC/Phos:1" EXACT PRO-short-label [PRO:DNx] synonym: "UniProtKB:P05480, Tyr-527, MOD:00048" EXACT PRO-proteoform-std [PRO:DNx] synonym: "pp60c-src phosphorylated (mouse)" RELATED [] is_a: PR:P05480 ! proto-oncogene tyrosine-protein kinase Src (mouse) relationship: has_part MOD:00048 ! O4'-phospho-L-tyrosine relationship: only_in_taxon NCBITaxon:10090 ! Mus musculus

[Term] id: PR:000037501 name: proto-oncogene tyrosine-protein kinase Src phosphorylated 2 (mouse) def: "A proto-oncogene tyrosine-protein kinase Src (mouse) that has been phosphorylated on a Tyr residue as in UniProtKB:P05480, Tyr-424, MOD:00048. UniProtKB:P05480, Tyr-424, MOD:00048." [PRO:HJD, PMID:23526378, PMID:2480346] comment: Category=organism-modification. Note: Tyr-416 Src residue number in cited article is based on the chicken Src protein. This corresponds to Tyr-424 in mouse. synonym: "mSRC/Phos:2" EXACT PRO-short-label [PRO:DNx] synonym: "UniProtKB:P05480, Tyr-424, MOD:00048" EXACT PRO-proteoform-std [PRO:DNx] synonym: "pp60c-src phosphorylated (mouse)" RELATED [] is_a: PR:P05480 ! proto-oncogene tyrosine-protein kinase Src (mouse) relationship: has_part MOD:00048 ! O4'-phospho-L-tyrosine relationship: only_in_taxon NCBITaxon:10090 ! Mus musculus

[Term] id: PR:000037502 name: proto-oncogene tyrosine-protein kinase Src phosphorylated 3 (mouse) def: "A proto-oncogene tyrosine-protein kinase Src (mouse) that has been phosphorylated on two residues at positions corresponding to Tyr-424 and Tyr-527 in UniProtKB:P05480. UniProtKB:P05480, Tyr-424/Tyr-527, MOD:00048." [PRO:HJD, PMID:23526378, PMID:2480346] comment: Category=organism-modification. Kinase=("CSK"; PR:P41241; Tyr-527). Kinase=("SRC"; PR:P05480; Tyr-424). Note: Tyr-416 Src residue number in cited article is based on the chicken Src protein. This corresponds to Tyr-424 in mouse. synonym: "mSRC/Phos:3" EXACT PRO-short-label [PRO:DNx] synonym: "UniProtKB:P05480, Tyr-424/Tyr-527, MOD:00048" EXACT PRO-proteoform-std [PRO:DNx] synonym: "pp60c-src phosphorylated (mouse)" RELATED [] is_a: PR:P05480 ! proto-oncogene tyrosine-protein kinase Src (mouse) relationship: has_part MOD:00048 ! O4'-phospho-L-tyrosine relationship: only_in_taxon NCBITaxon:10090 ! Mus musculus

[Term] id: PR:000049780 name: proto-oncogene tyrosine-protein kinase Src unphosphorylated 2 (mouse) def: "A proto-oncogene tyrosine-protein kinase Src (mouse) that lacks phosphorylation at the position equivalent to Tyr-424 of the amino acid sequence represented by UniProtKB:P05480. UniProtKB:P05480, Tyr-424, PR:000026291." [PRO:HJD, PMID:26764350] synonym: "mSRC/UnPhos:2" EXACT PRO-short-label [PRO:DNx] synonym: "UniProtKB:P05480, Tyr-424, PR:000026291" EXACT PRO-proteoform-std [PRO:DNx]

[Term] id: PR:000049781 name: proto-oncogene tyrosine-protein kinase Src unphosphorylated 1 (mouse) def: "A proto-oncogene tyrosine-protein kinase Src (mouse) that is unphosphorylated at the position equivalent to Tyr-527 of the amino acid sequence represented by UniProtKB:P05480. UniProtKB:P05480, Tyr-527, PR:000026291." [PRO:HJD, PMID:26764350] synonym: "mSRC/UnPhos:1" EXACT PRO-short-label [PRO:DNx] synonym: "UniProtKB:P05480, Tyr-527, PR:000026291" EXACT PRO-proteoform-std [PRO:DNx]

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nataled commented 1 year ago

Hi Harold, What is your final recommendation for this?

(a) Leave numbering and indicate isoform 1 (b) Change numbering to match current canonical, but don't specify isoform (c) Change numbering and indicate isoform 2 (current canonical)

hdrabkin commented 1 year ago

I think c is best.