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Literature summary extracted from
- Pupylation as a signal for proteasomal degradation in bacteria (2014), Biochim. Biophys. Acta, 1843, 103-113.
Natural Substrates/ Products (Substrates)
| EC Number | Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 3.5.1.119 | [prokaryotic ubiquitin-like protein]-L-glutamine + H2O | Mycobacterium tuberculosis | deamidase (Dop) renders prokaryotic ubiquitin-like protein Pup competent for conjugation to substrates, which is then carried out by the Pup-ligase PafA. Pupylation is a signal for proteasomal degradation in bacteria | [prokaryotic ubiquitin-like protein]-L-glutamate + NH3 | - |
? |  |
| 3.5.1.119 | [prokaryotic ubiquitin-like protein]-L-glutamine + H2O | Mycobacterium tuberculosis ATCC 25618 | deamidase (Dop) renders prokaryotic ubiquitin-like protein Pup competent for conjugation to substrates, which is then carried out by the Pup-ligase PafA. Pupylation is a signal for proteasomal degradation in bacteria | [prokaryotic ubiquitin-like protein]-L-glutamate + NH3 | - |
? | |
| 6.3.1.19 | ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine | Mycobacterium tuberculosis | pupylation is a signal for proteasomal degradation in bacteria. The prokaryotic, ubiquitin-like protein (Pup) is conjugated through its C-terminal residue to lysine side chains of substrates via an isopeptide bond. Pup proteins are small, ranging from 60 to 70 residues in length with Gly-Gly-Glu or Gly-Gly-Gln as C-terminal residues. Deamidation of the C-terminal glutamine of Pup by the deamidase of Pup (Dop) renders Pup competent for conjugation to substrates, which is then carried out by the Pup-ligase PafA | ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine | - |
? | |
| 6.3.1.19 | ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine | Mycobacterium tuberculosis ATCC 25618 | pupylation is a signal for proteasomal degradation in bacteria. The prokaryotic, ubiquitin-like protein (Pup) is conjugated through its C-terminal residue to lysine side chains of substrates via an isopeptide bond. Pup proteins are small, ranging from 60 to 70 residues in length with Gly-Gly-Glu or Gly-Gly-Gln as C-terminal residues. Deamidation of the C-terminal glutamine of Pup by the deamidase of Pup (Dop) renders Pup competent for conjugation to substrates, which is then carried out by the Pup-ligase PafA | ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine | - |
? | |
Organism
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 3.5.1.119 | Mycobacterium tuberculosis | P9WNU9 | - |
- |
| 3.5.1.119 | Mycobacterium tuberculosis ATCC 25618 | P9WNU9 | - |
- |
| 6.3.1.19 | Mycobacterium tuberculosis | P9WNU7 | - |
- |
| 6.3.1.19 | Mycobacterium tuberculosis ATCC 25618 | P9WNU7 | - |
- |
Substrates and Products (Substrate)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 3.5.1.119 | N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine + H2O | the enzyme catalyzes the nucleophilic attack of water on the terminal carbonyl atom of Pup, releasing ammonium in the case of deamidation or the substrate lysine in case of depupylation | Mycobacterium tuberculosis | [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine | - |
? | |
| 3.5.1.119 | N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine + H2O | the enzyme catalyzes the nucleophilic attack of water on the terminal carbonyl atom of Pup, releasing ammonium in the case of deamidation or the substrate lysine in case of depupylation | Mycobacterium tuberculosis ATCC 25618 | [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine | - |
? | |
| 3.5.1.119 | [prokaryotic ubiquitin-like protein]-L-glutamine + H2O | deamidase (Dop) renders prokaryotic ubiquitin-like protein Pup competent for conjugation to substrates, which is then carried out by the Pup-ligase PafA. Pupylation is a signal for proteasomal degradation in bacteria | Mycobacterium tuberculosis | [prokaryotic ubiquitin-like protein]-L-glutamate + NH3 | - |
? | |
| 3.5.1.119 | [prokaryotic ubiquitin-like protein]-L-glutamine + H2O | the deamidase activity (Dop) renders prokaryotic ubiquitin-like protein Pup competent for conjugation to substrates, which is then carried out by the Pup-ligase PafA. The enzyme catalyzes the nucleophilic attack of water on the terminal carbonyl atom of Pup, releasing ammonium in the case of deamidation or the substrate lysine in case of depupylation | Mycobacterium tuberculosis | [prokaryotic ubiquitin-like protein]-L-glutamate + NH3 | - |
? | |
| 3.5.1.119 | [prokaryotic ubiquitin-like protein]-L-glutamine + H2O | deamidase (Dop) renders prokaryotic ubiquitin-like protein Pup competent for conjugation to substrates, which is then carried out by the Pup-ligase PafA. Pupylation is a signal for proteasomal degradation in bacteria | Mycobacterium tuberculosis ATCC 25618 | [prokaryotic ubiquitin-like protein]-L-glutamate + NH3 | - |
? | |
| 3.5.1.119 | [prokaryotic ubiquitin-like protein]-L-glutamine + H2O | the deamidase activity (Dop) renders prokaryotic ubiquitin-like protein Pup competent for conjugation to substrates, which is then carried out by the Pup-ligase PafA. The enzyme catalyzes the nucleophilic attack of water on the terminal carbonyl atom of Pup, releasing ammonium in the case of deamidation or the substrate lysine in case of depupylation | Mycobacterium tuberculosis ATCC 25618 | [prokaryotic ubiquitin-like protein]-L-glutamate + NH3 | - |
? | |
| 6.3.1.19 | ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine | pupylation is a signal for proteasomal degradation in bacteria. The prokaryotic, ubiquitin-like protein (Pup) is conjugated through its C-terminal residue to lysine side chains of substrates via an isopeptide bond. Pup proteins are small, ranging from 60 to 70 residues in length with Gly-Gly-Glu or Gly-Gly-Gln as C-terminal residues. Deamidation of the C-terminal glutamine of Pup by the deamidase of Pup (Dop) renders Pup competent for conjugation to substrates, which is then carried out by the Pup-ligase PafA | Mycobacterium tuberculosis | ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine | - |
? | |
| 6.3.1.19 | ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine | the prokaryotic, ubiquitin-like protein (Pup) is conjugated through its C-terminal residue to lysine side chains of substrates via an isopeptide bond. Pup proteins are small, ranging from 60 to 70 residues in length with Gly-Gly-Glu or Gly-Gly-Gln as C-terminal residues. Deamidation of the C-terminal glutamine of Pup by the deamidase of Pup (Dop) renders Pup competent for conjugation to substrates, which is then carried out by the Pup-ligase PafA. The enzyme turns over one molecule of ATP to ADP per conjugation cycle, suggesting that PafA activates Pup by phosphorylation of its C-terminal glutamate. The formation of this intermediate occurs even in the absence of substrate and is shown to be the rate-limiting step of the PafA catalyzed reaction. After activation, the phosphorylated Pup and ADP remain bound to PafA, awaiting the nucleophilic attack of the substrate lysine, which finally results in the formation of the isopeptide bond. The C-terminal residue of the ligation-competent PupE features two carboxylates, the C-terminal alpha-carboxylate and the gamma-carboxylate of the glutamyl side chain, both of which could in principle be used for Pup-attachment. NMR-experiments using the pupylated proteasomal substrate PanB show that only the gamma-carboxylate is used to form the isopeptide bond between Pup and the target | Mycobacterium tuberculosis | ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine | - |
? | |
| 6.3.1.19 | ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine | pupylation is a signal for proteasomal degradation in bacteria. The prokaryotic, ubiquitin-like protein (Pup) is conjugated through its C-terminal residue to lysine side chains of substrates via an isopeptide bond. Pup proteins are small, ranging from 60 to 70 residues in length with Gly-Gly-Glu or Gly-Gly-Gln as C-terminal residues. Deamidation of the C-terminal glutamine of Pup by the deamidase of Pup (Dop) renders Pup competent for conjugation to substrates, which is then carried out by the Pup-ligase PafA | Mycobacterium tuberculosis ATCC 25618 | ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine | - |
? | |
| 6.3.1.19 | ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine | the prokaryotic, ubiquitin-like protein (Pup) is conjugated through its C-terminal residue to lysine side chains of substrates via an isopeptide bond. Pup proteins are small, ranging from 60 to 70 residues in length with Gly-Gly-Glu or Gly-Gly-Gln as C-terminal residues. Deamidation of the C-terminal glutamine of Pup by the deamidase of Pup (Dop) renders Pup competent for conjugation to substrates, which is then carried out by the Pup-ligase PafA. The enzyme turns over one molecule of ATP to ADP per conjugation cycle, suggesting that PafA activates Pup by phosphorylation of its C-terminal glutamate. The formation of this intermediate occurs even in the absence of substrate and is shown to be the rate-limiting step of the PafA catalyzed reaction. After activation, the phosphorylated Pup and ADP remain bound to PafA, awaiting the nucleophilic attack of the substrate lysine, which finally results in the formation of the isopeptide bond. The C-terminal residue of the ligation-competent PupE features two carboxylates, the C-terminal alpha-carboxylate and the gamma-carboxylate of the glutamyl side chain, both of which could in principle be used for Pup-attachment. NMR-experiments using the pupylated proteasomal substrate PanB show that only the gamma-carboxylate is used to form the isopeptide bond between Pup and the target | Mycobacterium tuberculosis ATCC 25618 | ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine | - |
? | |
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 3.5.1.119 | depupylase | - |
Mycobacterium tuberculosis |
| 3.5.1.119 | depupylase/deamidase | - |
Mycobacterium tuberculosis |
| 3.5.1.119 | Dop | - |
Mycobacterium tuberculosis |
| 3.5.1.119 | Rv2112c | locus name | Mycobacterium tuberculosis |
| 6.3.1.19 | PafA | ambiguous | Mycobacterium tuberculosis |
| 6.3.1.19 | Rv2097c | locus name | Mycobacterium tuberculosis |
General Information
| EC Number | General Information | Comment | Organism |
|---|---|---|---|
| 3.5.1.119 | physiological function | the enzyme is involved in pupylation. Pupylation is a signal for proteasomal degradation in bacteria | Mycobacterium tuberculosis |
| 6.3.1.19 | malfunction | in a pafA knockout strain pupylated proteins are undetectable and proteasomal substrate proteins accumulate | Mycobacterium tuberculosis |
| 6.3.1.19 | physiological function | pupylation is a signal for proteasomal degradation in bacteria. The prokaryotic, ubiquitin-like protein (Pup) is conjugated through its C-terminal residue to lysine side chains of substrates via an isopeptide bond | Mycobacterium tuberculosis |
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