GO:0071972 ! peptidoglycan L,D-transpeptidase activity

[gocentral]

GO:0071972 ! peptidoglycan L,D-transpeptidase activity is the only peptidoglycan transpeptidase activity I can find in GO, and defined based on a MetaCyc reaction making the crosslinks between a Lysine and a modified Lysine as found in Enterococcus faecium. This is only one of several kinds of peptidoglycan transpeptidase activities and is not the major one common to most bacteria.

I am looking for how to propose to restructure peptidoglycan-related activity terms, but I wanted to post a ticket in case someone else can weigh in. It's more complicated than the textbook view. See

http://mmbr.asm.org/content/36/4/407.full.pdf

and

http://www.jbc.org/content/282/18/13151.long

Cursory look at ChEBI is not finding anything helpful

Reported by: jimhu

Original Ticket: geneontology/ontology-requests/10445

[gocentral]

I've been reviewing the literature and here's what I'm thinking so far.

Umbrella term:

NTR: peptidoglycan transpeptidase activity: catalyzes a transpeptidation reaction transferring a oligopeptide group from a donor peptidoglycan oligopeptide to an acceptor amino group . <-is_a: NTR D,D peptidoglycan transpeptidase activity: D-Ala(4)-mDAP(3) D,D peptidoglycan transpeptidase ... donor is a linkage between D amino acids and the acceptor is a D amino acid . . <-is_a: |-NTR 4-3 D,D peptidoglycan transpeptidase activity: ... where the donor is cleaved at the peptide bond between the 4th and 5th residue of a peptidoglycan pentapeptide and the acceptor is a side chain from the residue at the 3 position of another peptide . . . <-is_a: |-NTR D-Ala(4)->mDAP(3) D,D peptidoglycan transpeptidase activity . . . <-is_a:|-NTR D-Ala(4)->(N epsilon D-Asx)-L-Lys(3) transpedtidase activity . <-is_a: NTR: L, D peptidoglycan transpeptidase . . <-is_a:NTR (N epsilon D-Asx)-L-Lys(3)->(N epsilon D-Asx)-L-Lys(3) L,D transpedtidase activity. This is what GO:0071972 is for, but see below . . . <- NTR m-DAP(3)-> m-DAP(3) L,D transpedtidase activity . . . <- NTR m-DAP(3)-> protein L,D transpedtidase activity . . . . <-NTR m-DAP(3)-> lipoprotein L,D transpedtidase activity

GO:0071972 peptidoglycan L,D-transpeptidase activity should be obsoleted because the definition has an incorrect reaction, based on figure 1 of http://www.jbc.org/content/277/39/35801.long

The D-Asx-L-Lys acceptor is in a pentapeptide (I don't know if it also works from a tetrapeptide). It doesn't release 4 D-Ala residues, it releases one if the acceptor is a tetrapeptide. If it works with a pentapeptide donor, then the leaving group would be a dipeptide. I believe there is an additional activity that may or may not trim the pentapeptides to tetrapeptides. More notes on my blog

http://jimhu.org/peptidoglycan-transpeptidase-diversity-and-nomenclature/

Markdown is annoying!!

Original comment by: jimhu

[gocentral]

• labels: --> mini-project

Original comment by: dosumis

[pgaudet]

@jimhu-tamu Would the proteins currently annotated to http://amigo.geneontology.org/amigo/term/GO:0071972 be OK under the "new" parent term term you proposed ? (peptidoglycan transpeptidase activity) In this case I could just rename it ? (and all other children as requested)

Thanks, Pascale

[jimhu-tamu]

I think the umbrella term covers it, but they aren't EXACT, so not sure what you mean by "rename it"

[pgaudet]

I was proposing to change label of 'GO:0071972 ! peptidoglycan L,D-transpeptidase activity' to the new umbrella term you propose: NTR: peptidoglycan transpeptidase activity

and yes, 'peptidoglycan L,D-transpeptidase activity' would be a 'NARROW synonym'.

---

In fact my question was, out of the list of terms you have above, to which should have the proteins already annotated have been annotated to ? (which would avoid reannotation).

Or perhaps the annotations are not correct, in which case obsoletion would be better.

Thanks, Pascale

[pgaudet]

Out of date - if needed we'll open a new ticket.