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Question about ubiquitin thiolesterase activity #10710

Closed gocentral closed 9 years ago

gocentral commented 10 years ago

Hello,

I have doubts about the definition of "ubiquitin thiolesterase activity": Catalysis of the reaction: ubiquitin C-terminal thiolester + H2O = ubiquitin + a thiol. Hydrolysis of esters, including those formed between thiols such as dithiothreitol or glutathione and the C-terminal glycine residue of the polypeptide ubiquitin, and AMP-ubiquitin

If I understand well, this is supposed to correspond to EC 3.4.19.12: Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).

is that right ?

In any case, the way GO has the definition sounds like there is a thiol bond between the ubiquitin and the protein, but as far as I can tell the bond is actually an isopeptide bond.

Anyone familiar with ubiquitin biology ?

Thanks,

Pascale

Reported by: pgaudet

Original Ticket: geneontology/ontology-requests/10519

gocentral commented 10 years ago

Original comment by: ukemi

gocentral commented 10 years ago

I am not a ubiquitin expert, but the comment 'Note that this term is distinguished from 'ubiquitin-specific protease activity ; GO:0004843' in that it specifically refers to hydrolysis of thiolester bonds, but encompasses the removal of any substrate attached to ubiquitin via a thiolester bond.' suggests that this term really does refer to a thiolester bond.

Original comment by: ukemi

gocentral commented 10 years ago

Hi David,

This is also the way I understand the term. The definition should be changed to remove "ubiquitin C-terminal thiolester + H2O = ubiquitin + a thiol." and match what EC has (Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin) - although I dont see what the ester, thioester, amide, peptide bonds have to do with this.

Thanks,

Pascale

Original comment by: pgaudet

gocentral commented 10 years ago

Original comment by: ukemi

gocentral commented 10 years ago

Hi Pascale,

I am going to reassign this to Becky since she has been working on aligning catalytic activity terms with definitions from external resources.

-D

Original comment by: ukemi

gocentral commented 10 years ago

Original comment by: rebeccafoulger

gocentral commented 10 years ago

Hi Pascale,

ubiquitin thiolesterase activity ; GO:0004221 actually refers to EC:3.1.2.15. According to the various enzyme sites, this may be the same as EC 3.4.19.12. However, IUBMB etc still list them separately.

I've therefore kept the definition as EC:3.1.2.15 lists it but removed the confusing post-equation text. So it's now: ubiquitin C-terminal thioester + H2O = ubiquitin + a thiol.

The comments remain in place.

http://www.chem.qmul.ac.uk/iubmb/enzyme/EC3/1/2/15.html

Thanks, Becky

Original comment by: rebeccafoulger

gocentral commented 10 years ago

OK, thanks - the annotations must be incorrect then. I'll check with Rama and Rachael. You can close that.

Pascale

Original comment by: pgaudet

gocentral commented 10 years ago

Original comment by: rebeccafoulger

gocentral commented 10 years ago

Original comment by: rebeccafoulger

gocentral commented 10 years ago

Pascale has contacted Kristian who says 'ubiquitin thiolesterase activity ; GO:0004221' should be obsoleted, and annotations moved to ubiquitin-specific protease activity ; GO:0004843'.

In more detail (from Kristian): If you look at the EC entry in the official IUBMB version (see http://www.enzyme-database.org/query.php?ec=3.1.2.15), the comment reads: May be the same as EC 3.4.19.12, ubiquitinyl hydrolase 1. I think that this exactly is the case.

If you check ENZYME (http://enzyme.expasy.org/EC/3.1.2.15 or enzyme.dat) you will see that there are no links from this EC number to UniProtKB/Swiss-Prot at all.

I also found a review (Cantu et al 2010, 20506386) saying: "Ubiquitin carboxyl-terminal hydrolases (EC 3.1.2.15) cleave a wide variety of products ... These enzymes belong to a larger class of peptidases called deubiquitinating enzymes that hydrolyze lysine-glycine amide bonds in ubiquitinated proteins ... Several families of these enzymes can be found in MEROPS, the peptidase database. We identified 11 ubiquitin thiolesterase families by the methods described above, but we have not included them here or in the ThYme database, as peptidase activity is their main function, and they can be found in MEROPS. "

I am now trying to either get rid of EC 3.1.2.15, and if this cannot be done, then maybe add this EC number to all the entries with EC 3.4.19.12.

For the InterPro mappings: IPR001394: change the EC number from EC 3.1.2.15 to EC 3.4.19.12. IPR001578: EC mapping is missing. Add EC 3.4.19.12 IPR006615: EC mapping is missing. Add EC 3.4.19.12 IPR018200: change the EC number from EC 3.1.2.15 to EC 3.4.19.12.

Original comment by: rebeccafoulger

gocentral commented 10 years ago

Request for remapping of InterPro domains is here: https://sourceforge.net/p/geneontology/annotation-issues/1130/

Original comment by: rebeccafoulger

gocentral commented 10 years ago

I'm no ubiquitin expert either. However, while the detailed chemistries of ester, thioester, and peptide bond hydrolysis are closely related and some enzymes can catalyze more than one of these molecular functions (e.g., some enzymes whose in vivo function is the digestion of dietary polypeptides are assayed in vitro based on their abilities to cleave small ester molecules to yield colored products), the functions still look separate, so retiring the thioesterase term and suggesting that it be replaced with a protease (peptidase) term seems wrong.

Original comment by: deustp01

gocentral commented 10 years ago

There's been discussions off-list about the proposed obsoletion of ubiquitin thiolesterase activity ; GO:0004221 (EC:3.1.2.15). The summary is:

There was confusion about which bonds were covered by the EC 3.4.19.12 (ubiquitinyl hydrolase) reaction because:

Kristian Axelson confirmed that although one of its activities is to cleave peptide bonds, it can also cleave other types of bonds, as described in the reaction text. For EC this isn't a problem, and it only has to be decided what reaction should be regarded as the main one. In this case it was the peptidase one.

For GO this is more problematic, and the related term 'ubiquitin-specific protease activity ; GO:0004843' needs to be limited to cleavage of peptide bonds, to fit with its position in GO under 'peptidase activity'.

Therefore, we suggest making a new broader term to map to EC:3.4.19.12, and house GO:0004843 under this:

ubiquitinyl hydrolase activity ; GO:NEW (EC:3.4.19.12) --[isa]ubiquitin-specific protease activity ; GO:0004843 (specifically refers to peptide bonds)

ubiquitinyl hydrolase activity ; GO:NEW Catalysis of the thiol-dependent hydrolysis of a bond (ester, thioester, amide, peptide or isopeptide bond) formed by the C-terminal Gly of ubiquitin and a substrate. EC:3.4.19.12 is_a: hydrolase activity ; GO:0016787

STILL TO BE DECIDED: Whether ubiquitin thiolesterase activity ; GO:0004221 could be a child of 'ubiquitinyl hydrolase activity ; GO:NEW' instead of being obsoleted.

Original comment by: rebeccafoulger

gocentral commented 10 years ago

Kristian confirmed that the following structure makes sense:

ubiquitinyl hydrolase activity ; GO:NEW (EC:3.4.19.12) --[is_a]ubiquitin-specific protease activity ; GO:0004843 (Catalysis of the thiol-dependent hydrolysis of a peptide bond) --[is_a]ubiqutin-thiolesterase activity ; GO:0004221 (Catalysis of thiol-dependent hydrolysis of a thioester bond) (EC:3.1.2.15)

So I have created a new grouping term for EC:3.4.19.12 mappings: ubiquitinyl hydrolase activity ; GO:0036459 (NEW)

I'll update the InterPro ticket and mailing list.

Kristian Axelsen also says: Yes, except that I will try to have EC 3.1.2.15 deleted, since it is redundant in an "EC list" context. We have no examples of EC 3.1.2.15 that are not EC 3.4.19.12 also, and it was defined long time ago based on one article, where the authors did not do a very thorough investigation of the substrate specificity.

But for the time being, it makes perfectly sense. I don't know how long time it will take to have the deletion of EC 3.1.2.15 public, and there is also the option it does not get accepted, so maybe it will not be deleted at all.

Original comment by: rebeccafoulger

gocentral commented 10 years ago

Original comment by: rebeccafoulger

gocentral commented 10 years ago

Based on further email discussions with Pascale and David H, I added a comment to ubiquitin thiolesterase activity ; GO:0004221 to use the term with caution:

comment: Use GO:0004221 with caution because it is unclear if this activity exists. Consider instead annotating to 'ubiquitinyl hydrolase activity ; GO:0036459'.

That's this ticket closed (I hope!!).

Original comment by: rebeccafoulger

gocentral commented 10 years ago

I know there have been some long discussions on ubiquitin thiolesterase activity, but I think that this term is still causing some issues.

There are lots of annotations (AmiGO2 gives 721 hits) made with this term. Most are deubiquitinases and the intended/correct term should have been "ubiquitin-specific protease activity". From what I can see, ubiquitin thiolesterase activity has been mis-assigned and propagated via ISS and other routes.

I'm not sure what the best solution is: if the term were obsoleted then it would certainly clear out the mis-annotation but it would leave a lot of DUBs without a catalytic function term. As the intended term is reasonably clear, could there be some kind of substitution for "ubiquitin-specific protease activity"/"ubiquitinyl hydrolase activity"?

Original comment by: hattrill