query about peptide synthase terms.

[gocentral]

Hello,

We were looking for a MF terms to use for as peptide synthase. Our ferrichrome synthase currently has ligase activity, forming carbon-nitrogen bonds which did not seem specific enough.

This unearthed a couple of things

1. GO:0019184 nonribosomal peptide biosynthetic process has the child GO:0043042 amino acid adenylylation by nonribosomal peptide synthase

any idea why this isn't a MF (it sounds single step if it is performed by the synthase?)

2. Could we have a MF term amino acid ligation activity by nonribosomal peptide synthase

which would be a child of MF GO:0016881 acid-amino acid ligase activity

and BP GO:0019184 nonribosomal peptide biosynthetic process

Does that sound right?

Val

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/9798

[gocentral]

Hi Val,

In response to question 1: GO:0043042 amino acid adenylylation by nonribosomal peptide synthase is defined as 'Activation of an amino acid for incorporation into a peptide by a nonribosomal process, catalyzed by subunits of nonribosomal peptide synthase. The amino acid is adenylated at its carboxylate group (ATP-dependent) then transferred to the thiol group of an enzyme-bound phosphopantetheine cofactor.' This sounds like two steps to me, regardless of whether they're both performed by the synthase. Our current 'policy' for multi-step reactions performed by the same enzyme is as follows: 'if the enzyme catalyzed all steps, and if all steps always occurred together, then we'd add GO terms for the separate steps as HAS_PART children of the overall reaction.' (see http://wiki.geneontology.org/index.php?title=Curator\_Guide:\_Enzymes\_and\_Reactions\#Multi-Step\_Enzyme\_Reactions) As you'll read in the wiki, this isn't always straightforward to implement. In your specific case, I'm afraid I don't know enough about nonribosomal peptide synthases, and I can't find much on KEGG, Rhea or EC. Would you have a reference (possibly with graph/figure)? I might ask Harold and/or Peter to take a look.

As for your requested MF term in point 2, the term sounds good to me and I don't see any match in EC or Rhea (see e.g. http://www.chem.qmul.ac.uk/iubmb/enzyme/EC6/3/2/). I'd add it in but would again welcome Harold's or Peter's feedback on this, to get things right.

So if you could please suggest a reference showing details of nonribosomal peptide synthases' mechanism of action, I'll take it from there.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

• assigned_to: nobody --> paolaroncaglia

Original comment by: paolaroncaglia

[gocentral]

Hi Paola,

I think it should be possible to break these into single steps as children of the process term?

GO:0043042 term name is adenylylation which could, presumably, be described by the single steps, adenylation with another term for thiolation? (they appear to be performed by different domains if I have understood correctly) so maybe this could be obsoleted and redefined (it has no annotations at present)

The sibling of GO:0043042 also looks like a MF in BP.... GO:0043040 Name tRNA aminoacylation for nonribosomal peptide biosynthetic process Ontology Biological Process Definition The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in nonribosomal peptide synthesis.

I couldn't easily find a good reference or review, but the wikepedia page appears to describe the individual steps http://en.wikipedia.org/wiki/Nonribosomal\_peptide

I am winging it a bit here, so would be good to have input from Harold or Peter.

val

Original comment by: ValWood

[gocentral]

Just emailed Harold and Peter.

Original comment by: paolaroncaglia

[gocentral]

I don't know anything about this process, but I guess that's because it is something that does not happen in large vertebrates. Here is an Annual Reviews of Microbiology article that looks authoritative: http://www.ncbi.nlm.nih.gov/pubmed/15487945, and its abstract:

Bacteria and fungi use large multifunctional enzymes, the so-called nonribosomal peptide synthetases (NRPSs), to produce peptides of broad structural and biological activity. Biochemical studies have contributed substantially to the understanding of the key principles of these modular enzymes that can draw on a much larger number of catalytic tools for the incorporation of unusual features compared with the ribosomal system. Several crystal structures of NRPS-domains have yielded deep insight into the catalytic mechanisms involved and have led to a better prediction of the products assembled and to the construction of hybrid enzymes. In addition to the structure-function relationship of the core- and tailoring-domains of NRPSs, which is the main focus of this review, different biosynthetic strategies and essential enzymes for posttranslational modification and editing are discussed.

From the abstract the idea of a process term with has_part children as discussed in this thread sounds right. It also seems prudent because, at a guess over the evolutionary diversity of bacteria and fungi and specific peptides made in this way, there have probably been gene fusions and fragmentations, as well as modifications of the process to accommodate synthesis of non-standard peptide bonds, so a broad parent process term will let you generate a comprehensive menu of has part children to capture all of these combinations and permutations (and per standard GO practice, you now only create the children needed for Val's pombe(?) process, not the whole hypothetical menu).

Original comment by: deustp01

[gocentral]

Just jumping in here This amino acid adenylation thing sounds like an intermediate process required or activation Parallels: when making amino-acyl tRNA, even though done by a single enzyme, it is a two step reaction. aa +ATP-> aminoacid-adenlylate aminoacid-adenylate + tRNA -> aminoacyl-tRNA + AMP

This type of intermediate is seen in many "ligase" reactions (which is also why aminoacyl-TRNA synthetases area also called "ligases".

We have not broken the aminoacyl-tRNA reactions into two steps.

Is this were the GO:0043042 amino acid adenylylation by nonribosomal peptide synthase came from I wonder. If there are instances where each step is done by a different enzyme, then I see the value of two activities; But if not.... ? when would you use one but not the other for the normal gene product (I say that because one can make aminoacyl-tRNA synthetase mutants that just do the first step, but this is not normal).

Original comment by: hdrabkin

[gocentral]

Thanks Peter and Harold for your comments. Summing up, I'm not sure if the current knowledge on the subject would allow us to get all the has_part links right, so my suggestion would be to leave the existing structure under GO:0019184 nonribosomal peptide biosynthetic process as it is now, and add a new term: GO:NEW amino acid ligation activity by nonribosomal peptide synthase is_a GO:0016881 acid-amino acid ligase activity part_of GO:0019184 nonribosomal peptide biosynthetic process Def: Catalysis of the ligation of an amino acid to another amino acid via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate, carried out by a nonribosomal peptide synthase. Dbxref: GOC:vw

I'll implement that unless I hear to the contrary. Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

Hi again, just to mention that I discussed this with the other editors as well and they also agree with my suggestions. Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

It sounds a good solution to me

val

Original comment by: ValWood

[gocentral]

This is done:

+id: GO:0097429 +name: amino acid ligation activity by nonribosomal peptide synthase +namespace: molecular_function +def: "Catalysis of the ligation of an amino acid to another amino acid via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate, carried out by a nonribosomal peptide synthase." [GOC:vw] +is_a: GO:0016881 ! acid-amino acid ligase activity +relationship: part_of GO:0019184 ! nonribosomal peptide biosynthetic process

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

• status: open --> closed-accepted

Original comment by: paolaroncaglia