search

geneontology / go-ontology

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

EC 7.1.-.- are NOT transporters #17988

Closed pgaudet closed 3 years ago

pgaudet commented 5 years ago

7.1.1.1 Proton-translocating NAD(P)(+) transhydrogenase 7.1.1.2 NADH:ubiquinone reductase (H(+)-translocating) 7.1.1.3 Ubiquinol oxidase (H(+)-transporting) 7.1.1.4 Caldariellaquinol oxidase (H(+)-transporting) 7.1.1.5 Menaquinol oxidase (H(+)-transporting) 7.1.1.6 Plastoquinol--plastocyanin reductase 7.1.1.7 Ubiquinol oxidase (electrogenic, proton-motive force generating) 7.1.1.8 Quinol--cytochrome-c reductase

@deustp01

hdrabkin commented 5 years ago

I can't find a EC:7.7.- class; It stops at EC:7.6

EC 7Translocases | Catalyse the movement of ions or molecules across membranes or their separation within membranes |   https://www.qmul.ac.uk/sbcs/iubmb/enzyme/EC7/ 6 subclasses 7.1 through 7.6 Did I say something that said 7.7; typo?

hdrabkin commented 5 years ago

see also https://www.qmul.ac.uk/sbcs/iubmb/enzyme/EC7/0101p.html

pgaudet commented 5 years ago

sorry I meant 7.1 - see list of ECs in the first comment.

ukemi commented 5 years ago

So is proton transport not a transport?

hdrabkin commented 5 years ago

Yes proton transport is covered here I think: EC 7.1 Catalysing the translocation of hydrons (aka proton H+) EC 7.1.1 Hydron translocation or charge separation linked to oxidoreductase reactions EC 7.1.2 Hydron translocation linked to the hydrolysis of a nucleoside triphosphate EC 7.1.3 Hydron translocation or charge separation linked to oxidoreductase reactions

deustp01 commented 5 years ago

So is proton transport not a transport?

Sure. What I was fretting about is that moving that proton necessarily also involves reducing something and oxidizing something. This reorganization has the effect of taking enzymes that were classified as enabling oxidation - reduction reactions (and not as enabling transport) and now classifying them as enabling transport (with oxidation - reduction smuggled in). Where is the gain in information accuracy and usability for whoever consumes GO (and EC) annotations?

pgaudet commented 5 years ago

Is the biological aim of this reaction to move a proton around or to reduce it ?

I think we need to think about this like what we did for ATP hydrolysis - a protein kinase is NOT going 'ATP catabolic process', it is phosphorylating a protein.

Do you see what I mean ?

pgaudet commented 3 years ago

The link to transporter was removed. Fixed EC:1.10.9.1 to EC:7.1.1.6.