gocentral
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18 years ago Logged In: YES user_id=546388
The term of ligase for the aminoacyl-tRNA synthetases dates back quite a while; a ligase refers to an enzyme requiring ATP that has generates an intermediate of AMP-x, where X can be an amino acid (as in the case of the aminoacyl-tRNA synthetase (amino-acid adenylate), or, as in a (DNA/RNA) ligase , AMP-P-5'-Nucleic acid. Some definitions of a ligase actually say that they also called synthetase, but I have only seen the term "syntheteae" used in reference ot the aminoacyl-tRNA synthetase. GO:0004812 doesn't even have synthetase as a synonym. EC uses aminoacid-tRNA ligase as an official name, so I would definitely suggest that the main name be changed to aminoacyl-tRNA ligase activity, with aminoacyl-tRNA sythetase as a synonym. While I'm on it, I notice that glutamate -trNA (Gln) ligase (GO:0050561), as defined should be a child of 4812, not a sib. also GO:0050562, as defined is also a child. also GO:0050560, as defined is also a chiid, not a sib.
Original comment by: hdrabkin
Hi,
This item has been taken out of another sourceforge entry 'TAIR function terms-nov 2005'. I have included all the discussion on this subject from the previous entry.
Requested by Suparna:
6(Better name) tRNA ligase activity involved in
tRNA splicing ISA tRNA ligase activity GO:0004812 Def: three intrinsic activities: an N-terminal adenylyltransferase domain that resembles T4 RNA ligase 1, a central domain that resembles T4 polynucleotide kinase (without 30-phosphatase activity) and a C-terminal cyclic phosphodiesterase (CPDase) domain that is reminiscent of the 2H phosphotransferase enzyme superfamily (13–15). The multifunctional yeast tRNA ligase performs a series of reactions: (i) the 20,30-cyclic phosphate at the end of the 50 tRNA half is hydrolysed by the CPDase activity to generate a 20-phosphate and 30-OH; (ii) the 50-OH group at the end of the 30 tRNA half is phosphorylated by the GTP-dependent kinase activity and (iii) the ligase protein is adenylylated and the AMP is transferred to the 50-phosphate of the 30 tRNA half followed by the formation of the 20- phosphomonoester–30,50-phosphodiester bond and the release of AMP Ref: PMID: 15653639
Date: 2005-11-30 13:39 Sender: kchris Logged In: YES user_id=473890
Hi Suparna,
For your #6, the term you're talking about "tRNA ligase activity ; GO:0004812" is NOT the enzyme that is involved in splicing the introns that occur in tRNAs (and occasionally in other RNA types). This term refers to the class of activities that charge a tRNA by adding an amino acid to the tRNA. Currently this term has two roots to parent:
molecular_function .catalytic activity ..ligase activity ...ligase activity, forming phosphoric ester bonds ....RNA ligase activity .....tRNA ligase activity ...ligase activity, forming carbon-oxygen bonds ....ligase activity, forming aminoacyl-tRNA and related compounds .....tRNA ligase activity
It might be worth checking whether this type of tRNA ligase should really have parentage under "RNA ligase activity" and thus under "ligase activity, forming phosphoric ester bonds". I kind of wonder if it should really have parentage under both that term AND "ligase activity, forming carbon-oxygen bonds", but the review I'm looking at is only on the splicing of introns from tRNAs, not the charging reaction, so I'll leave that for the moment, and hopefully someone else to check out. It might also be worth investigating if there is another name that could be used for this term that is less ambiguous and the "tRNA ligase" name could be made a synonym.
Going back to the subject of splicing introns from tRNA, the tRNA ligase that performs this in S. cerevisiae is a multifunctional enzyme with three distinct activities: a phosphodiesterase activity, a polynucleotide kinase activity, and RNA ligase activity. It may be worth noting that metazoans seem to have two different redundant mechanisms for religating the two halfs of a cleaved pre- tRNA, one of which is mechanistically the same as that of cerevisiae and one which is not. The mechanism is not yet known in Archaea.
in SGD currently, the TRL1 gene, which encodes the tRNA ligase that is involved in splicing is annotated to only one function term: "RNA ligase (ATP) activity ; GO:0003972". Clearly, it should be annotated to additional function terms. I am not yet sure what terms should be used, or whether appropriate terms already exist. I'll look into that in the next week or so because SGD should really have this enzyme fully annotated.
-Karen
Date: 2005-11-23 04:27 Sender: gomidori Logged In: YES user_id=436423
> 6. (Better name) tRNA ligase activity involved in > tRNA splicing
I agree that this needs a different name - it's not consistent with our function term guidelines to make distinctions, or name terms, in the function ontology based on which process an activity or gene product is involved in. Also, it sounds like the protein you want to annotate has several activities -- but presumably Karen will find out what's going on.
Reported by: smundodi
Original Ticket: "geneontology/ontology-requests/3047":https://sourceforge.net/p/geneontology/ontology-requests/3047