Literature summary for 6.3.1.19 extracted from

Striebel, F.; Imkamp, F.; �zcelik, D.; Weber-Ban, E.
Pupylation as a signal for proteasomal degradation in bacteria (2014), Biochim. Biophys. Acta, 1843, 103-113.

Search for more literature for 6.3.1.19

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
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	-	?
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

Organism	UniProt	Comment	Textmining
Mycobacterium tuberculosis	P9WNU7	-	-
Mycobacterium tuberculosis ATCC 25618	P9WNU7	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
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	-	?
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	-	?
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	-	?
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

Synonyms	Comment	Organism
PafA	ambiguous	Mycobacterium tuberculosis
Rv2097c	locus name	Mycobacterium tuberculosis

General Information

General Information	Comment	Organism
malfunction	in a pafA knockout strain pupylated proteins are undetectable and proteasomal substrate proteins accumulate	Mycobacterium tuberculosis
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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Release 2023.1 (January 2023)