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geneontology
NTR: CCA tRNA nucleotidyltransferase
Hello:
Two enzymes from Dictyostelium described in PMID: 32717856 are characterized as "CCA-adding enzyme". Currently in the GO, this activity is associated with GO:0004810 tRNA adenylyltransferase activity (EC 2.7.7.25). However, a comment in this entry says "This term represents a deleted EC activity and is scheduled for obsoletion".
A new enzymatic activity (EC 2.7.7.72), combining former EC 2.7.7.21 and EC 2.7.7.25 has been described by ExPASy described at:
https://enzyme.expasy.org/EC/2.7.7.72
Could you please create a new GO term according to the guidelines suggested by ExPASy?
Name: CCA tRNA nucleotidyltransferase Ontology: function Synonyms: Definition: A tRNA precursor + 2 CTP + ATP <=> a tRNA with a 3' CCA end + 3 diphosphate
Reference: PMID: 32717856 Unusual Occurrence of Two Bona-Fide CCA-Adding Enzymes in Dictyostelium discoideum
Update on my request. I think this activity is already in the GO as:
GO:0052929 ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity.
However, to avoid confusion, that GO entry should have the synonyms: CCA tRNA nucleotidyltransferase CCA-adding enzyme activity
I think I would modify the existing term with the corrected EC. And add RHEA while I'm at it.
NO: use strikeout ~I think I need to merge all of these terms into one; Tere is so far only one organism that uses two separate enzymes (one to add the CC, and another to add the A), otherwise, all others mentioned in #17855 refer to the same 'reaction" which is RHEA:14433. ~
GO:0052929 ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity. is actually the reaction that adds an A to the 3' CC of a tRNA As it turns out, organisms with TWO separate enzymes to perform the addition of CC, and then the addition of just A to the 3' end of a tRNA are quite numerous, and not just restricted to certain bacteria; Pombe needs two enzymes. This just adds the A The majority of eukaryotic organisms carry only a single gene for a CCA-adding enzyme that acts on both the cytosolic and mitochondrial tRNA pool. Most bacteria only have one enzyme.
At the moment, I don't see an activity in GO do describe adequate the entire CCA (in steps of course.). BUT a RHEA for it is associated with GO:0004810
Personal experience (I've purified the bacterial enzyme). The "CCA" enzyme can be used to 'swap' out the terminal A with radiolabeled ATP; so in that instance one is looking at just A addition, but that enzyme actually can do all three).
GO:0004810 tRNA adenylyltransferase activity: ATP + tRNA(n) = diphosphate + tRNA(n+1).
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[x] wrong definition based on RHEA and EC. the definition should be: "Catalysis of the reaction: a tRNA precursor + ATP + 2 CTP = a tRNA with a 3' CCA end + 3 diphosphate The RHEA:14433 IS the CCA transerase, EC:2.7.7.72
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[x] wrong label: tRNA adenylyltransferase activity -> should be 'CCA tRNA nucleotidyltransferase'
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[x] add synonyms: tRNA CCA transferase activity (all synonyms mentioned in EC:2.7.7.72 kept. synonym xref in all cases is EC:2.7.7.72; Where appropriate, EC:2.7.7.25 changed to EC:2.7.7.72)
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[x] add PMID Deutcher review article: PMID:2247609 (1990 reiview)
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[x] review annotations GO:0004810 to make sure this have been used correctly EC:2.7.7.72 is used for many terms:
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[x] CHANGE parent from 'RNA adenylyltransferase activity' to 'nucleotidyltransferase activity'
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[x] 'ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity' http://purl.obolibrary.org/obo/GO_0052929 Since the CC adding activities are not children of the CCA enzyme (GO:0004810), I moved this to a child of 'nucleotidyltransferase activity .
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[x] 'CTP:3'-cytidine-tRNA cytidylyltransferase activity' http://purl.obolibrary.org/obo/GO_0052928 Merged into GO:0052927 Add RHEA:60008 to this ; The two KEGGS become narrowMatch Xrefs
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[x] 'CTP:tRNA cytidylyltransferase activity' http://purl.obolibrary.org/obo/GO_0052927 Keep name
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[x] 'tRNA 3'-terminal CCA addition' http://purl.obolibrary.org/obo/GO_0001680 Process term. ok; BUT the 'activity' terms used as synonyms should be removed. Add the 3 activity terms as 'has part'
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[x] 'tRNA cytidylyltransferase activity' http://purl.obolibrary.org/obo/GO_0016437 This term was made based on EC:2.7.7.21, which was merged into EC:2.7.7.72; WIl thus merge into GO:0004810; this is consistent with IEAs annotaton using this term as well as the single IDA (for E.coli) based on the PMID uses. Removed all synonyms based on 2.7.7.21
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[x] GO:0009022 is currently called tRNA nucleotidyltransferase, but the EC:2.7.7.56 entry acknowledges that this enzyme is actually a phosphate-dependent exonuclease. Therefore, to avoid confusion with the CCA tRNA nucleotidyltransferase activity, we have renamed this term phosphate-dependent exonuclease activity, and referenced the Deutcher article PMID:2455297
(more tasks to come! )
Annotations to GO:0004810 have been checked-
- [x] Human PMID:11504732 was changed
- [x] Dicty PMID:32717856 was disputed in P2GO and fixed.
@hdrabkin There are also some related parentage inconsistencies to clean up here - see #17855
