carboxypeptidases

[gocentral]

Hi,

When I was curating some carboxypeptidase-encoding genes, I noticed a few parent:children relationships that seem to be missing in this part of the tree:

1. cysteine-type carboxypeptidase activity ; GO:0016807 ; EC:3.4.18.- metallocarboxypeptidase activity ; GO:0004181 ; EC:3.4.17.- (and children) serine carboxypeptidase activity ; GO:0004185 (and children)

should be made is_a children of carboxypeptidase activity ; GO:0004180.

A suggested def for carboxypeptidase activity ; GO:0004180. Catalysis of the hydrolysis of C-terminal amino acid residues from oligopeptides or polypeptides. ref: ISBN:0198506732

2. According to the dictionary def for exopeptidase (ISBN:0198506732), the following terms should be made is_a children of exopeptidase activity ; GO:0008238

also see http://www.chem.qmul.ac.uk/iubmb/enzyme/EC3/intro.html.

aminopeptidase activity ; GO:0004177 ; EC:3.4.11.- dipeptidase activity ; GO:0016805 ; EC:3.4.13.- dipeptidyl-peptidase and tripeptidyl-peptidase activity ; GO:0016806 ; EC:3.4.14.- peptidyl-dipeptidase activity ; GO:0008241 ; EC:3.4.15.- omega peptidase activity ; GO:0008242 ; EC:3.4.19.-

A suggested def for exopeptidase activity ; GO:0008238 def: Catalysis of the hydrolysis of peptide bonds adjacent to the terminal amino or carboxyl group of an oligopeptide or polypeptide. ref: ISBN:0198506732

3. cysteine-type endopeptidase activity ; GO:0004197 ; EC:3.4.22.- ; aspartic-type endopeptidase activity ; GO:0004190 threonine endopeptidase activity ; GO:0004298 ; EC:3.4.25.-

should be made is_a children of endopeptidase activity ; GO:0004175.

also see http://www.chem.qmul.ac.uk/iubmb/enzyme/EC3/intro.html.

4. Some suggested defs for terms in this part of the tree:

term: omega peptidase activity ; GO:0008242 ; EC:3.4.19.- def: Catalysis of the removal of terminal peptide residues that are substituted, cyclized or linked by isopeptide bonds (peptide linkages other than those of a-carboxyl to a-amino groups). ref: http://www.chem.qmul.ac.uk/iubmb/enzyme/EC3/intro.html

term: metallocarboxypeptidase activity ; GO:0004181 def: Catalysis of the hydrolysis of C-terminal amino acid residues from oligopeptides or polypeptides, where a bivalent cation is an essential component of the catalytic mechanism. ref: ISBN:0198506732

term: cysteine-type endopeptidase activity ; GO:0004197 ; EC:3.4.22.- def: Catalysis of the hydrolysis of nonterminal peptide linkages in oligopeptides or polypeptides, where a cysteine residue is at the active centre. ref: ISBN:0198506732

term: cysteine-type carboxypeptidase activity ; GO:0016807 ; EC:3.4.18.- def: Catalysis of the hydrolysis of carboxyl terminal peptide linkages in oligopeptides or polypeptides, where a cysteine residue is at the active centre. ref: ISBN:0198506732

term: cysteine-type peptidase activity ; GO:0008234, GO:0004220 ; EC:3.4.-.- def: Catalysis of the hydrolysis of peptide linkages in oligopeptides or polypeptides, where a cysteine residue is at the active centre. ref: ISBN:0198506732

term: aspartic-type endopeptidase activity ; GO:0004190 def: Catalysis of the hydrolysis of nonterminal peptide linkages in oligopeptides or polypeptides, where the optimum pH for the reaction is below 5 by virtue of an aspartic residue being involved in the catalytic process. ref: ISBN:0198506732

term: serine-type endopeptidase activity ; GO:0004252 def: Catalysis of the hydrolysis of nonterminal peptide linkages in oligopeptides or polypeptides, where a serine residue (and a histidine residue) are at the active centre. ref: ISBN:0198506732

term: serine-type peptidase activity ; GO:0008236 def: Catalysis of the hydrolysis of peptide linkages in oligopeptides or polypeptides, where a serine residue (and a histidine residue) are at the active centre. ref: ISBN:0198506732

Thanks, Becky

Reported by: beckyfoulger

Original Ticket: "geneontology/ontology-requests/965":https://sourceforge.net/p/geneontology/ontology-requests/965

[gocentral]

Logged In: YES user_id=482748

Also on the theme of carboxypeptidases:

GO:0004183, GO:0004184 GO:0008472 and GO:0004187 essentially have the same definitions. They have separate ECs but all remove C-terminal Lys or Arg. GO:0004187 is a serine-type peptidase but the other 3 are metallopeptidases. Do these 3 still count as separate GO functions? If they do, could a comment (and synonyms) be added to each to distinguish them for curators:

carboxypeptidase H activity ; GO:0004183 see: http://www.chem.qmul.ac.uk/iubmb/enzyme/EC3/4/17/10.html add synonym: carboxypeptidase E (this is now the IUBMB common name) add comment: carboxypeptidase H is a zinc enzyme that is activated by Co[2+] and inhibited by 1,10-phenanthroline and other chelating agents. # lysine (arginine) carboxypeptidase activity see http://www.chem.qmul.ac.uk/iubmb/enzyme/EC3/4/17/3.html Add synonym: carboxypeptidase N Add synonym: lysine carboxypeptidase (this is the IUBMB common name) add comment: lysine (arginine) carboxypeptidase is a zinc enzyme that inactivates bradykinin and anaphylatoxins in blood plasma. # metallocarboxypeptidase D activity ; GO:0008472 add comment: metallocarboxypeptidase D is activated by Co[2+] and inhibited by guanidinoethylmercaptosuccinic acid.

Original comment by: beckyfoulger

[gocentral]

• assigned_to: nobody --> girlwithglasses

Original comment by: girlwithglasses

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Logged In: YES user_id=473796

I've done all the stuff from the main part of the query; thanks for the info and the defs!

Re: the rather similar carboxypeptidases - I think there would be some outcry if I were to merge those activities even though the reaction catalyzed is the same / similar. I will put the extra information that distinguishes them from each other; in the longer term, they'd probably be good candidates for slots.

Thanks Becky!

Original comment by: girlwithglasses

[gocentral]

• milestone: --> TermGenie
• status: open --> closed-fixed

Original comment by: girlwithglasses