Obsoletion request: GO:0002094 polyprenyltransferase activity

[sjm41]

• GO term ID and Label
  id: GO:0002094
  name: polyprenyltransferase activity
  namespace: molecular_function
  def: "Catalysis of the transfer of multiple prenyl groups from one compound (donor) to another (acceptor)." [GOC:hjd]
  is_a: GO:0004659 ! prenyltransferase activity

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

• The reason for obsoletion is that the term is not clearly defined and usage has been inconsistent.
• The reason for obsoletion is that more specific terms were created.
• The reason for obsoletion is that this term was an unnecessary grouping term.
• The reason for obsoletion is that the meaning of the term is ambiguous.

This term currently has 3 prenyltransferase children, though from its current def, most/all prenyltransferase terms could go under this orthogonal grouping - I don't think it's useful.

• I will move the 3 current children to be direct children of GO:0004659 ! prenyltransferase activity
  GO:0047295 geranylgeranylglycerol-phosphate geranylgeranyltransferase activity
  GO:0046428 1,4-dihydroxy-2-naphthoate polyprenyltransferase activity
  GO:0008412 4-hydroxybenzoate polyprenyltransferase activity

• "Replace by" term (ID and label)
  GO:0004659 ! prenyltransferase activity

• "Consider" term(s) (ID and label)
  See below

• Are there annotations to this term?

• How many EXP: 7

4 from PMID:21761520 by UniProt:
UniProtKB:O34790 pcrB = Heptaprenylglyceryl phosphate synthase
UniProtKB:Q53726 pcrB = Heptaprenylglyceryl phosphate synthase
UniProtKB:Q5L3C1 pcrB = Heptaprenylglyceryl phosphate synthase
UniProtKB:Q8Y6C8 pcrB = Heptaprenylglyceryl phosphate synthase
=> Reannotate to newly created 'heptaprenylglyceryl phosphate synthase activity GO:0120536 (=EC:2.5.1.n9) term

1 from PMID:25066056 by MGI:
UniProtKB:Q86SQ9 DHDDS = Dehydrodolichyl diphosphate synthase complex subunit
=> UP annotates to EC:2.5.1.87 from same paper, which is correct
=> so, reannotate to = GO:0045547 ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] activity (=EC:2.5.1.87)

1 from PMID:28655749 by TAIR:
UniProtKB:Q56Y11 At5g58770 = Dehydrodolichyl diphosphate synthase 2
=> paper says "the enzyme synthesizes polyprenols of ∼55 carbons in length using geranylgeranyl diphosphate (GGPP) and isopentenyl diphosphate as substrates"
=> re-annotate to 'GO:0120531 prenyl diphosphate synthase activity'

1 from PMID:22883514 by TAIR:
UniProtKB:Q8RX73 At5g58780 = Dehydrodolichyl diphosphate synthase 3
=> characterized as "a novel cis,trans-mixed heptaprenyl diphosphate synthase"
=> re-annotate to 'GO:0120531 prenyl diphosphate synthase activity'

• Are there mappings and cross references to this term? (InterPro, Keywords; check QuickGO cross-references section)
  One:
  InterPro IPR026438 Geranylgeranylglyceryl phosphate synthase, archaea
  This can be remapped to:
  id: GO:0047294
  name: phosphoglycerol geranylgeranyltransferase activity
  def: "Catalysis of the reaction: (2E,6E,10E)-geranylgeranyl diphosphate + sn-glycerol 1-phosphate = diphosphate + sn-3-O-(geranylgeranyl)glycerol 1-phosphate." [PMID:12801917, PMID:17253090, PMID:8408023, RHEA:23404]
  xref: EC:2.5.1.41 {source="skos:exactMatch"}

• Is this term in a subset? (check the AmiGO page for that term)
  No

• Any other information
  This obsoletion was originally discussed in Prenyltransferase term relations #20661

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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

[raymond91125]

@LiNiMGI @tberardini @Antonialock Please review your annotations per @sjm41 suggestions above.
@sarach06 Please check InterPro IPR026438 per @sjm41 suggestion above.
Thanks.

[sarach06]

Hi,
Thank you bery much for this. I have replaced the term as suggested. The changes will be visible in InterPro 104.0.

Best,
Sara

[tberardini]

I've reannotated the Arabidopsis genes. Thanks for the help in mapping forward @sjm41.

[Antonialock]

uniprot done.

[LiNiMGI]

MGI done!