search

geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
Creative Commons Attribution 4.0 International
221 stars 40 forks source link

GO:0004528 phosphodiesterase I activity #21569

Closed ValWood closed 1 year ago

ValWood commented 3 years ago

Is defined: Catalysis of the sequential hydrolytic removal of 5'-nucleotides from the 3'-hydroxy termini of 3'-hydroxy-terminated oligonucleotides.

but has synonyms

5'-nucleotide phosphodiesterase activity | related 5'-phosphodiesterase activity | related

these seem a bit confusing, because isn't it a 3'-phosphodiesterase?

If so could this (3'-phosphodiesterase) synonym be added as exact? Could the name be swapped to describe the activity rather than a gene product?

ValWood commented 3 years ago

I was checking annotations to this review abstract PMID:34083046

mah11 commented 3 years ago

isn't it a 3'-phosphodiesterase?

No. Perhaps the def could be changed to make it clearer, but the "5'-" in the synonyms is correct, and refers to the fact that one of the products is a nucleoside 5'-monophosphate (the other is the rest of the double-stranded oligonucleotide).

In other words, it's named for which position on the released NMP product is phosphorylated, not which end of the substrate oligo it acts on.

Could the name be swapped to describe the activity rather than a gene product?

This is a good idea.

ValWood commented 3 years ago

OK, also Pombase and TAIR annotate apn1 to "GO:0004528 phosphodiesterase I activity " and this has been transferred by PAINT. I will open an annotation tracker ticket for that, but I can't find a term describing a "3'-phosphodiesterase". Apn1 is a 3'phosphodiesterase

https://www.pombase.org/reference/PMID:24559510 & PMID:34083046

I will update the annotation once the term exists.

mah11 commented 3 years ago

The only things that come up easily when I search for "3'-phosphodiesterase" is 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity - which is GO:0004113 - and APE2 and its orthologs. I don't think APE2 has the GO:0004113 activity, but I also don't know what they mean by 3'-phosphodiesterase in the APE2 papers.

EricaBakker commented 3 years ago

What does TAIR need to do? Any specific genes that need updating?

EricaBakker commented 3 years ago

To confirm I update those GO terms only for this gene in TAIR: AT4G36050.1 (aka APE2:APURINIC/APYRIMIDINIC ENDONUCLEASE2

EricaBakker commented 3 years ago

The discussion above is not clear to me, can someone tell me which GO terms need to be changed to what?

ValWood commented 3 years ago

I am not sure either. The reviews and manuscripts refer to a "3'-phosphodiesterase" and the GO term used is a 5'-phosphodiesterase. I am hoping @hdrabkin will be able to help...either the publications are incorrect, or the GO term we used is incorrect but there is not a term for the 3'-phosphodiesterase.

hdrabkin commented 3 years ago

Does this help?

Catalysis of the sequential hydrolytic removal of 5'-nucleotides from the 3'-hydroxy termini of 3'-hydroxy-terminated oligonucleotides.

removes 5'pNMP, (ie, what is removed)

but has synonyms

5'-nucleotide phosphodiesterase activity | related (what is removed) 5'-phosphodiesterase activity | related (what is removed)

these seem a bit confusing, because isn't it a 3'-phosphodiesterase?

ValWood commented 3 years ago

OK, does that mean that this is a 5'phosphodiesterase, and the papers describing apn1 as 3' phosphodiesterase are incorrect? Is that right?

hdrabkin commented 3 years ago

If the reaction removes nucleotides from the 3 end it is a 3- phosphodiesterase. It generates 5'-NMPs in doing to

ValWood commented 3 years ago

OK, so back to the first question, do these synonyms need removing?

and could the term be renamed to describe the activity rather than the gene product name?

ValWood commented 3 years ago

pinging @hdrabkin

hdrabkin commented 3 years ago

So the term name is more of an enzyme name, but the def still remains that it removed 5'NMPs from the 3' terminaus of nucleic acids ending with a 3'OH group. I could add the ' 3'-phosphodiesterase' as a synonym.

hdrabkin commented 3 years ago

I can't seem to come up with any literature removing NTs sequentially from the 5' end (searching for 5'-phosphodiesterase', but it is a Monday. I've also reached out to my expert contact at MIT (UL RajBhandary) for nomenclature conventions here.

hdrabkin commented 3 years ago

AND, my expert reminded me about Spleen Phosphodiesterase, which works from the 5'-end, as well as a phosphodiesterase that works after CAP removal which degrades from 5'end . So I will change the term in question here from phosphodiesterase I to 3'-phosphodiesterase activity and make the old term name a synonym THEN make 5'activity .

hdrabkin commented 3 years ago

I think phosphodiesterase 1 is meant for the removal from the 3' end, although it's syonoyms ( Speen phosphodiesterase has a synonym of 3'-exonuclease.(EC) even though def is "Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 3'-phosphates" PDE 1 has 5' phosphodiesterase synonym to confuse things. (5'-exonuclease; 5'-phosphodiesterase; 5'-nucleotide phosphodiesterase, which are referring to WHAT gets removed (a 5'NMP) rather than the direction.

I think the best thing might be to keep the original name and make a comment as to what this does.

There is a Phosphodiesterase II ithat cleave of cGMP or cAMPs.

ValWood commented 1 year ago

Tracing from the mouse rat annotations phosphdiesterase I appears to be https://iubmb.qmul.ac.uk/enzyme/EC3/1/4/1.html oligonucleotide 5'-nucleotidohydrolase

ValWood commented 1 year ago

Will close this. I'm not sure what the outcome was but the term is essentially correct. Any issue here should eventually be fixed by Rhea alignment.