OTR: children of GO:0003906_!_DNA-(apurinic_or_apyrimidinic_site)_lyase_activity

[jimhu-tamu]

The flip side of #10725

GO:0003906 has these direct children Is a GO:0000703 oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity Is a GO:0000704 pyrimidine dimer DNA N-glycosylase activity Is a GO:0008534 oxidized purine nucleobase lesion DNA N-glycosylase activity

These are all incorrect. First, a DNA N-glycosylase is not the same as the endonuclease that cleaves the backbone. Second, the damaged bases are not abasic. These activities create the substrate for the APE, but they are not APEs themselves.

[pgaudet]

Hi @jimhu-tamu ,

I removed the parent 'GO:0003906_!_DNA-(apurinic_or_apyrimidinic_site)_lyase_activity'. The remaining parent is " GO:0000702 oxidized base lesion DNA N-glycosylase activity".

Thanks, Pascale

[pgaudet]

Hi @jimhu-tamu

One other question about this: do you know if it's OK that GO:0003906 DNA-(apurinic or apyrimidinic site) lyase activity is a child of both

• GO:0016835 carbon-oxygen lyase activity
• and indirectly ot GO:0016788 hydrolase activity, acting on ester bonds (via nuclease activity)?

Either these two reactions are synonymous, or the enzyme catalyzes two reactions - or one of the reactions is wrong.

Thanks, Pascale

[jimhu-tamu]

@pgaudet per wikipedia, there are four classes that use different chemistry and that cleave in different places.

https://en.wikipedia.org/wiki/AP_endonuclease

There are four types of AP endonucleases that have been classified according to their mechanism and site of incision. Class I AP endonucleases cleave 3' to AP sites by a β-lyase mechanism, leaving an unsaturated aldehyde, termed a 3'-(4-hydroxy-5-phospho-2-pentenal) residue, and a 5'-phosphate. Class II AP endonucleases incise DNA 5' to AP sites by a hydrolytic mechanism, leaving a 3'-hydroxyl and a 5'-deoxyribose phosphate residue.[2] Class III and class IV AP endonucleases also cleave DNA at the phosphate groups 3´ and 5´to the baseless site, but they generate a 3´-phosphate and a 5´-OH.[3]

I think the current term definition applies to only to Class I. It seems to me that there should be an umbrella term for AP endo activity independent of mechanism, with children for the classes. Based on the wikipedia article, it may turn out that most of the annotation to this term is incorrect wrt lyase vs nuclease.

[pgaudet]

Hi again,

I thought it was outside the scope of GO to capture reaction mechanisms. I am happy to create new terms if needed. I will bring that up at the next editors call.

Pascale

[pgaudet]

I checked a number of proteins annotated to GO:0003906_!_DNA-(apurinic_or_apyrimidinic_site)_lyase_activity to see how they were annotated in UniProt. UniProt has a note on all the ones I checked that says “The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.” This refers to the ‘ClassI’, mechanism, but there also Class 2 in that list (at least P87175), see: https://en.wikipedia.org/wiki/AP_endonuclease

Kristian Axelen from UniProt is looking into this.

@hdrabkin

Thanks, Pascale

A8JR14 CG6171 B9DFZ0 NTH2 G5EBR7 exo-3 G5EBR7 exo-3 O35980 Nthl1 P04418
P05523 mutM P05523 mutM P05750 RPS3 P0AB83 nth P0AB83 nth P17096 HMGA1 P17096 HMGA1 P19889 RpLP0 P22936 APN1 P22936 APN1 P22936 APN1 P23396 RPS3 P23396 RPS3 P23396 RPS3 P23396 RPS3 P23396 RPS3 P27695 APEX1 P27695 APEX1 P27695 APEX1 P27695 APEX1 P27695 APEX1 P27864 Rrp1 P31378 NTG1 P38207 APN2 P45951 ARP P50465 nei P50465 nei P52926 HMGA2 P62908 Rps3 P78549 NTHL1 P87175 apn2 P9WNB9 nei1 Q06559 RpS3 Q06559 RpS3 Q08214 NTG2 Q10002 apn-1 Q13686 ALKBH1 Q564V5 exo-3 Q564V5 exo-3 Q8IW19 APLF Q8K203 Neil3 Q8LK56 DME Q8TAT5 NEIL3 Q9SIC4 NTH1

[pgaudet]

The decision from the GO editors discussion is to represent all different activities.

[jimhu-tamu]

Hi Pascale, not sure I understand which way the discussion went. One term to represent different activities or all activities represented by their own terms? I'm OK with either as long as the definitions are consistent.

[pgaudet]

It would be different terms, since they need to have different parents. If you have suggestions for name and definitions those would be welcome !

Thanks, Pascale

[pgaudet]

Created 3 new terms: [Term] +id: GO:0140078 +name: class I DNA-(apurinic or apyrimidinic site) lyase activity +namespace: molecular_function +def: "Catalysis of the cleavage of an AP site 3' of the baseless site by a beta-lyase mechanism, leaving an unsaturated aldehyde, termed a 3'-(4-hydroxy-5-phospho-2-pentenal) residue, and a 5'-phosphate." [PMID:1698278, Wikipedia:AP_endonuclease] +synonym: "AP endonuclease class I activity" RELATED [] +xref: EC:4.2.99.18 +xref: MetaCyc:4.2.99.18-RXN +is_a: GO:0003906 ! DNA-(apurinic or apyrimidinic site) lyase activity +created_by: pg +creation_date: 2017-07-24T11:33:34Z + +[Term] +id: GO:0140079 +name: class II DNA-(apurinic or apyrimidinic site) lyase activity +namespace: molecular_function +def: "Catalysis of the cleavage of an AP site 5' of the baseless site, by a hydrolytic mechanism, leaving a 3'-hydroxyl and a 5'-deoxyribose phosphate residue." [PMID:1698278, Wikipedia:AP_endonuclease] +is_a: GO:0003906 ! DNA-(apurinic or apyrimidinic site) lyase activity +is_a: GO:0004518 ! nuclease activity +created_by: pg +creation_date: 2017-07-24T11:46:03Z + +[Term] +id: GO:0140080 +name: class III/IV DNA-(apurinic or apyrimidinic site) lyase activity +namespace: molecular_function +def: "Catalysis of the cleavage of an AP site 3' and 5' of the baseless site, generating a 3´-phosphate and a 5´-OH." [PMID:2519777, Wikipedia:AP_endonuclease] +synonym: "endonuclease III" RELATED [] +synonym: "endonuclease IV" RELATED [] +xref: EC:4.2.99.18 +xref: MetaCyc:4.2.99.18-RXN +is_a: GO:0003906 ! DNA-(apurinic or apyrimidinic site) lyase activity +created_by: pg +creation_date: 2017-07-24T11:48:18Z

====

Modified the parent of GO:0003906_!_DNA-(apurinic_or_apyrimidinic_site)_lyase_activity because it's not classified as a nuclease (ie, an hydrolyze) by EC, except for Class II. -is_a: GO:0004520 ! endodeoxyribonuclease activity

===

Added cross ref EC:4.2.99.18 to Class I and III, but not Class II because that's the enzyme with the hydrolytic mechanism. However EC lists APEX2_HUMAN as one member of the EC:4.2.99.18 class - I don't know why EC doesn't distinguish the different classes.

Pascale

[pgaudet]

Terms are in the ontology, I am waiting for feedback from K. Axelen before closing.

[pgaudet]

Message to Kristian Axelen:
Hello,

There are 3 types en endonucleases, Class I, II and III (see https://en.wikipedia.org/wiki/AP_endonuclease http://pubs.acs.org/doi/pdfplus/10.1021/cr980321h

According to wikipedia human APE1 (P27695) is a Class II. I wonder if its current EC number is correct, which refers to Class I (and possibly Class III ) reactions.

I am trying to fix the corresponding GO terms; and input would be much appreciated !

Thanks, Pascale

---

Reply: Hi Pascale,

You are right, APE1 is a class II AP endonuclease, and no EC 4.2.99.18 cannot be used as it only covers the class I enzymes. It took me a little while to understand the subject since also the wikipedia article was misleading by citing the EC number (as BRENDA 4.2.99.18) just after the name AP endonuclease. I have now corrected this error in wikipedia.

Next, it complicates matters that only the class I enzymes have a unique EC number. There are at least two EC numbers associated with class II enzymes, Exodeoxyribonuclease III (EX3_ECOLI), to which APE1 is similar, is covered by EC 3.1.11.2, while Endonuclease 4 (END4_ECOLI) to which APN1_YEAST (P22936) is covered by EC 3.1.21.2.

So, while I can quite easily correct the EC errors concerning APE1 and APN1, it will be a much larger task to verify the annotation of the 626 other Swiss-Prot entries annotated as EC 4.2.99.18 enzymes.

I will keep you updated when I more progress to report.

Cheers,

Kristian

[pgaudet]

This ticket is closed as far as GO is concerned. @kaxelsen : I am notifying you that I am closing this.

Thanks, Pascale