Obsolete GO:0018600 alpha-pinene dehydrogenase activity?

[sjm41]

id: GO:0018600
name: alpha-pinene dehydrogenase activity
namespace: molecular_function
def: "Catalysis of the reaction: alpha-pinene + O2 + 2 H+ + 2 e- = H2O + myrtenol." [UM-BBD_reactionID:r0709]
xref: EC:1.14.-.-
xref: UM-BBD_reactionID:r0709
is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen

The EC:1.14.-.- xref should be removed from GO:0018600 (it's already correctly on GO:0016705).
Actually, GO:0018600 could be obsoleted since it has no annotations and no obvious EC/RHEA term

[pgaudet]

Hi @emanuel-schmid
Looking at the eawag-bbd entry for this: http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=r0709
it cites this paper https://pubmed.ncbi.nlm.nih.gov/10192895/
I dont have access to the full text, but is there evidence that this activity exists? It seems from the abstract that some cell extracts gave some products, but it could be multi-steps reactions catalyzed by multiple proteins.

It may be more appropriate to map to 'GO:0033074 pinene catabolic process' and 'GO:0046249 alpha-pinene catabolic process' , since we dont have direct evidence of the enzymatic activity described by GO:0018600 alpha-pinene dehydrogenase activity.

What do you think?

Thanks, Pascale

[pgaudet]

• Removed EC
• Added references for pienene catabolic process

[pgaudet]

@emanuel-schmid

• similar question for related activity GO:0018847 alpha-pinene lyase activity > http://eawag-bbd.ethz.ch/servlets/pageservlet?ptype=r&reacID=r0712; no EC, RHEA no other evidence

[pgaudet]

alpha-pinene monooxygenase [NADH] activity is incorrectly mapped:
The reaction described is "Catalysis of the reaction: alpha-pinene + NADH + H+ + O2 = NAD+ + H2O + alpha-pinene oxide." and is correctly mapped to UM-BBD_reactionID:r0742

However we have a related term, alpha-pinene monooxygenase activity, describing UM-BBD_reactionID:r0716: Catalysis of the reaction: alpha-pinene + O2 + 2 H+ + 2 e- = H2O + pinocarveol.
GO and UM-BBD match; however that term has EC:1.14.13.155 and RHEA:32891, that correspond to alpha-pinene monooxygenase [NADH] activity .

• Move EC and RHEA from GO:0018595 to GO:0018634
• question for @emanuel-schmid: should we obsolete alpha-pinene monooxygenase activity, or is there evidence for that reaction?

[pgaudet]

pinene synthase activity : EC:4.2.3.14 : transferred to EC:4.2.3.119 and 4.2.3.120 .

However it seems that most enzymes can produce both the alpha and the beta form, sometimes one more efficiently than the other, but for now we can keep these as NARROW xrefs of GO:0050550.

Also add NARROW Xrefs RHEA:25488 and RHEA:25496

[pgaudet]

Discussed with Kathrin at EAWAG-BBD, and she agrees that there is no biochemical evidence for the two reactions being questionned:
GO:0018600 alpha-pinene dehydrogenase activity
GO:0018847 alpha-pinene lyase activity

Papers cited characterized the degradation of pinene, but the reactions are not know.

Pascale

[pgaudet]

Dear all,

The proposal has been made to obsolete
GO:0018600 alpha-pinene dehydrogenase activity
GO:0018847 alpha-pinene lyase activity

The reason for the obsoletion is that there is no evidence that these reactions exist. There are no annotations to these terms; these terms are not present in any subsets. The reactions have cross references to BBD database, but papers cited have no biochemical evidence.

You can comment on the ticket: #26207

Thanks, Pascale