ubiquitin conjugating/ligase activity

[gocentral]

Hi,

We recently noticed that GO:4840 was merged into 4842 (ubiquiting conjugating activity is now a synonym of ubiquiting protein ligase activity) based on an old SF item. Sorry, for not commenting earlier. It somehow fell off of our radar.

We would like to reopen this item for discussion and we recommend that the merge be reverted. Based on PMIDs: 7800044, 10581972, 10581972

The E3s have a ubiquitin protein ligase activity and hence it makes sense to keep the ligase and conjugating activity terms separate.

Thanks,

Rama

Reported by: rbalakri

Original Ticket: "geneontology/ontology-requests/3948":https://sourceforge.net/p/geneontology/ontology-requests/3948

[gocentral]

Logged In: YES user_id=554736 Originator: YES

I realized my reasoning was too cryptic for people to make much sense.

More details below (with much help from our inhouse expert Rob Nash). The basic process to refresh ourselves: 1) Ubiquitin first gets linked to a cysteine side chain of E1 (aka ubiquitin activating enzyme) protein. 2) This activated Ubiquitin molecule is then transferred to cysteines on E2 (ubiquitin conjugating enzyme) 3) E2s are mostly complexed with E3 enzymes (Ub ligase). The E3 is responsible for recognizing the signal on the target protein. 4) Ub is transferred to the target protein

There are four major classes of E3 ubiquitin ligases that have been identified (reviewed in 16633365 and 16250895):

RING-finger type HECT-type U-box type PHD-finger type

For at least some of the RING-finger type, such as SCF Ub ligases, the complexes function as target recognition modules with the F-box subunit interacting with the substrate, and helping to bring the E2 and substrates into close proximity, thereby facilitating substrate polyubiquitination (see PMID:10581972). Here we would argue that both the E2 and the E3 'contribute_to' 'ubiquitin protein ligase activity', as both are required for the transfer to occur.

For at least some of the HECT-type E3s, such as E6-AP, an E6 associated protein involved in the human papillomavirus induced ubiquitination of p53, the E3 enzyme is directly responsible for the transfer of Ub to p53 via a conserved cysteine residue required for the formation of the Ub thioester formation, an intermediate step in the ligase reaction (PMID:7800044). Here we would argue that since the E3 has the activity and should be annotated with the function term 'ubiquitin protein ligase activity'.

U box type E3s also apparently function as adaptor like molecules bringing the E2 and substrate close together to promoter the E2 catalyzed transfer (see 16250895). Here we would also argue that both the E2 and the E3 'contribute_to' 'ubiquitin protein ligase activity', as both are required for the transfer to occur.

Finally, the PHD-finger type E3s appear to be variants of the RING finger domain type and function as adaptor proteins, so we would argue should get a 'contribute_to' 'ubiquitin protein ligase activity' term (PMID:126956663).

So although several of these E3 classes as adaptors, contributing to the activity by bringing the substrate to the E2, there is at least one class of E3s, the HECT-type enzymes that catalyze the ligase reaction directly, so strongly argue against the recent merge of Ub conjugating and ligase activity terms

Thanks,

Rama (and Rob)

Original comment by: rbalakri

[gocentral]

Logged In: YES user_id=516865 Originator: NO

Hi Rama, Rob,

The old SF entry is 1237306

The original outcome was to resolve a discrepancy with the mappings which identified problems with the old arrangement (I think they were siblings)

Can you propose the exact defs (including reactions) and positions ?

The current def is Catalysis of the reaction: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine

I'll post a notice on the old SF entry to check in on this one.

Cheers

Val

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=554736 Originator: YES

Definitions, relationships for the conjugating enzyme activity, ligase acitivity terms are below. We have a comment on GO: 19787 (small conjugating protein ligase activity) also.

1) 'Ubiquitin conjugating enzyme activity' shd be child of 'small protein conjugating enzyme activity' (GO:8639) only. Definition- Facilitates the formation of an isopeptide bond between the the C-terminal glycine of ubiquitin and an epsilon-amino group of lysine residue(s) of the target protein, either by itself or in concert with an ubiquitin-protein ligase (E3). In some cases the ubiquitin conjugating enzyme, coupled to activated ubiquitin, mediates the transfer in the presence of an auxiliary factor that is involved in substrate selection (for example, as provided by the F-box protein component of a RING-domain containing E3), while in others cases activated ubiquitin is first transferred from the E2 enzyme to an E3, and is then transferred to substrate by the ligase activity associated with the E3 enzyme (for example, as is the case with E6-AP, a HECT-domain containing E3 enzyme).

Add Synonym-'ubiquitin-carrier enzymes'.

2) Ubiquitin ligase activity

Catalyses the formation of an isopeptide bond, either by itself, or in concert with an ubiquitin conjugating enzyme (E2) between the the C-terminal glycine of ubiquitin and an epsilon-amino group of a lysine residue of the target protein. In some cases the E3 enzyme catalyses this reaction directly, such as is the case for HECT domain containing enzymes, while in other cases, the E3 ubiquitin ligase is involved in substrate selection and recruitment, while the E2 enzyme actually catalyzes the transfer of activated ubiquitin to the substrate, such as is the case with RING-domain type ubiquitin protein ligases (e.g. SCF (Skp1-Cullin-F-box) ubiquitin ligases.

Remove the following synonyms- E2; ubiquitin-conjugating enzyme activity; ubiquitin conjugating enzyme activity;

3) Definition of 19787 should be revised as well- Catalysis of ATP-dependent isopeptide bond formation between the carboxy-terminal residues of a small conjugating protein such as ubiquitin or a ubiquitin-like protein, and a substrate lysine residue.

Change to- Catalysis of isopeptide bond formation between the carboxy-terminal residues of a small conjugating protein such as ubiquitin or a ubiquitin-like protein, and a substrate lysine residue.

Please let us know if you have any questions.

Thanks, Rob, Rama

Original comment by: rbalakri

[gocentral]

Logged In: YES user_id=516865 Originator: NO

These defs sound good.

My only thought is that the reactions should also be kept, but also that these are really 'gene product specific' distinctions as they essentially catalyse the same reaction. I think this was how the origina problem arose...in mapping the EC number to the GO terms. We need to check that these problems won't recur if the terms are reinstated.

Val

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=554736 Originator: YES

Hi,

After reviewing the literature, it has become evident that it is okay to represent conjugating activity and ligase activity together as one term.

However, we would like to request a new term related to the activity of E3, which is the activity of substrate recognition. I will make this a separate request on SF.

This item can be closed unless anybody else has comments.

Thanks and sorry for the delay,

Rama

Original comment by: rbalakri

[gocentral]

Logged In: YES user_id=436423 Originator: NO

All I have to say is: thanks for taking the time to investigate and confirm that what we have is OK. m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=436423 Originator: NO

It's been a month; looks safe to close. Thanks again! m

Original comment by: mah11

[gocentral]

• milestone: --> TermGenie
• assigned_to: nobody --> ramab
• status: open --> closed-works-for-me

Original comment by: mah11