Obsoletion request: GO:1990189 peptide-serine-alpha-N-acetyltransferase activity

[ValWood]

Please provide as much information as you can:

• GO term ID and Label

GO:1990189 peptide-serine-alpha-N-acetyltransferase activity

• Reason for deprecation Put an x in the appropriate box:

• The reason for obsoletion is that this term was added in error.

• "Replace by" term (ID and label)
  If all annotations can safely be moved to that term

GO:0004596 peptide alpha-N-acetyltransferase activity

• Are there annotations to this term?

• How many EXP: 7

EcoCyc 2
PomBase 4
UniProt 1

• Are there mappings and cross references to this term? (InterPro, Keywords; check QuickGO cross-references section)

• Any other information

This term doesn't really make sense.

The
Catalysis of the reaction: acetyl-CoA + N-terminal L-seryl-[protein] = CoA + H+ + N-terminal Nalpha-acetyl-L-seryl-[protein].

specifies a specific residue, but it isn't the residue side chain that is N-acetylated is the amino group?

I think these terms were probably created for proteins where the Methionine is removed, so the N-term residue is no longer a methionine, but this is problematic because we only specify the specific residues for histones and RNA polymerase II CTD residues to disambiguate the codes.

There are also sibling terms so the same applies to these?

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Checklist for ontology editor

Check term usage and metadata in Protégé

• check term usage in the ontology
• check internal mappings: RHEA, EC, MetaCyc
• check subset usage
• check taxon constraints

Check annotations

• create Annotation Review spreadsheet
• • Annotation Review template: https://docs.google.com/spreadsheets/d/1izV3q1jnq_Ybg5MJ53O_b5BCTkGtjl_Fi-cOg3-7eBE/edit#gid=0
• • Instructions: https://wiki.geneontology.org/Annotation_Review_Request
• create annotation review ticket: https://github.com/geneontology/go-annotation/issues/new?assignees=&labels=annotation+review&template=annotation-review-for-obsoletion.md&title=Review+annotations+to+%5BINSERT+GO+TERM%5D
• find external mappings (via IEAS), include in obsoletion notice
• tag curators in Annotation Review ticket. Responsible annotator for each group: https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv

Notification

• create obsoletion announcement
• announce to GO friends ([email protected])
• paste the text in the ontology ticket

[ValWood]

To illustrate the problem:

These are annotations to NAA10

describing the same activity. This is an additional axis of classification (but it doesn't really make sense )

[ValWood]

I would need instead
NTR histone H4 alpha-N acetyltransferase
as a descendant of
GO:0004596 peptide alpha-N-acetyltransferase activity
and
GO:0010485 histone H4 acetyltransferase activity

[raymond91125]

GO:1990189 peptide-serine-alpha-N-acetyltransferase activity has a definition reference to PMID:23912279, which is about NatA. "NatA, which is composed of the catalytic NAA10 subunit and the auxiliary NAA15 subunit, is the most promiscuous of all NAT enzymes; it will traditionally acetylate an α-amino group on nascent peptide chains with an amino-terminal alanine, cysteine, glycine, serine, threonine, or valine residue". It should be XREFed EC:2.3.1.255. Its other definition reference RHE:50504 is only part of what it can do.
Strangely, GO:1990189 is not XREFed to EC:2.3.1.255 (its parent term GO:0004596 is), but has a narrow match to EC:2.3.1.257, which is N-terminal L-serine N(alpha)-acetyltransferase NatD.
@sjm41 any insights? Per #27532

[raymond91125]

These annotations look to be for NAA40, which is a NatD, and of EC:2.3.1.257. Perhaps we should follow the EC scheme: MF of Nat(LETTER).

To illustrate the problem:

These are annotations to NAA10

describing the same activity. This is an additional axis of classification (but it doesn't really make sense )