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Literature summary for 2.7.7.59 extracted from

  • Emori, M.T.; Tomazini, L.F.; Souza, E.M.; Pedrosa, F.O.; Chubatsu, L.S.; Oliveira, M.A.S.
    The deuridylylation activity of Herbaspirillum seropedicae GlnD protein is regulated by the glutamine 2-oxoglutarate ratio (2018), Biochim. Biophys. Acta, 1866, 1216-1223 .
    View publication on PubMed

Activating Compound

Activating Compound Comment Organism Structure
ATP the wild-type GlnD shows maximum UR activity in the presence of ATP Herbaspirillum seropedicae
glutamine the presence of glutamine results in increased uridylyl-removing enzyme (UR) activity of GlnD (maximal activity at 2 mM), while it inhibits the uridylyl transferase (UTase) activity of GlnD Herbaspirillum seropedicae
additional information no activation of wild-type GlnD by ADP. Enzyme mutant GlnDDELTAACT is not affected by ADP or ATP Herbaspirillum seropedicae

Cloned(Commentary)

Cloned (Comment) Organism
gene glnD, cloning and recombinant expression of His-tagged wild-type and mutant enzyme in Escherichia coli strains TOP10 and BL21(lambdaDE3), respectively Herbaspirillum seropedicae

Protein Variants

Protein Variants Comment Organism
additional information generation of enzyme mutant GlnDDELTAACT. The amplified sequence corresponds to the 1 to 1779 nucleotide according to the Herbaspirillum seropedicae SmRI glnD sequence. This sequence encodes the Herbaspirillum seropedicae GlnD, lacking the last 258 amino acid residues, which corresponds to the two ACT domains. The wild-type GlnD seems more sensible to nucleotides and Mn2+ than the truncated enzyme Herbaspirillum seropedicae

Inhibitors

Inhibitors Comment Organism Structure
2-oxoglutarate 2-OG, inhibits the UR activity of GlnD Herbaspirillum seropedicae
EDTA
-
Herbaspirillum seropedicae
glutamine the presence of glutamine results in increased uridylyl-removing enzyme (UR) activity of GlnD, while it inhibits the uridylyl transferase (UTase) activity of GlnD Herbaspirillum seropedicae
UTP the higher the UTP concentration, the longer GlnK remains uridylylated with the wild-type enzyme, although not with GlnDDELTAACT mutant Herbaspirillum seropedicae

Metals/Ions

Metals/Ions Comment Organism Structure
Mn2+ Mn2+ ions, and not Mg2+, are required for the [protein-PII]-UMP uridylyl-removing enzyme (UR) activity of enzyme GlnD Herbaspirillum seropedicae

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
diphosphate + uridylyl-[protein-PII] Herbaspirillum seropedicae
-
UTP + [protein-PII]
-
r
diphosphate + uridylyl-[protein-PII] Herbaspirillum seropedicae SmR1
-
UTP + [protein-PII]
-
r
UTP + [protein-PII] Herbaspirillum seropedicae
-
diphosphate + uridylyl-[protein-PII]
-
r
UTP + [protein-PII] Herbaspirillum seropedicae SmR1
-
diphosphate + uridylyl-[protein-PII]
-
r

Organism

Organism UniProt Comment Textmining
Herbaspirillum seropedicae D8IU13
-
-
Herbaspirillum seropedicae SmR1 D8IU13
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
diphosphate + uridylyl-[protein-PII GlnK] substrate GlnK-UMP3, the enzyme acts on residue Tyr51 of GlnK Herbaspirillum seropedicae UTP + [protein-PII GlnK]
-
r
diphosphate + uridylyl-[protein-PII GlnK] substrate GlnK-UMP3, the enzyme acts on residue Tyr51 of GlnK Herbaspirillum seropedicae SmR1 UTP + [protein-PII GlnK]
-
r
diphosphate + uridylyl-[protein-PII]
-
Herbaspirillum seropedicae UTP + [protein-PII]
-
r
diphosphate + uridylyl-[protein-PII]
-
Herbaspirillum seropedicae SmR1 UTP + [protein-PII]
-
r
UTP + [protein-PII GlnK] the enzyme acts on residue Tyr51 of GlnK Herbaspirillum seropedicae diphosphate + uridylyl-[protein-PII GlnK]
-
r
UTP + [protein-PII GlnK] the enzyme acts on residue Tyr51 of GlnK Herbaspirillum seropedicae SmR1 diphosphate + uridylyl-[protein-PII GlnK]
-
r
UTP + [protein-PII]
-
Herbaspirillum seropedicae diphosphate + uridylyl-[protein-PII]
-
r
UTP + [protein-PII]
-
Herbaspirillum seropedicae SmR1 diphosphate + uridylyl-[protein-PII]
-
r

Synonyms

Synonyms Comment Organism
GlnD
-
Herbaspirillum seropedicae
PII uridylyltransferase UniProt Herbaspirillum seropedicae
uridylyl transferase
-
Herbaspirillum seropedicae
uridylyl-removing activity
-
Herbaspirillum seropedicae
UTase
-
Herbaspirillum seropedicae
[protein-PII]-UMP uridylyl-removing enzyme UR, UniProt Herbaspirillum seropedicae

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
assay at Herbaspirillum seropedicae

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.5
-
assay at Herbaspirillum seropedicae

General Information

General Information Comment Organism
malfunction the higher the UTP concentration, the longer GlnK remains uridylylated with the wild-type enzyme, while there is enough UTP, GlnDDELTAACT catalyzes the uridylylation/deuridylylation futile cycle, confirming the regulatory role of the ACT domain Herbaspirillum seropedicae
metabolism the PII proteins play an important role in this system by modulating the cellular metabolism through physical interaction with protein partners. Herbaspirillum seropedicae, a nitrogen-fixing bacterium, has two PII proteins paralogues, GlnB and GlnK. The interaction of Herbaspirillum seropedicae PII proteins with its targets is regulated by allosteric ligands and by reversible post-translational uridylylation. The interaction between PII proteins and its targets is regulated at two distinct levels: the allosteric binding of molecular effectors and the post-translational modification status. By controlling the post-translational state of PII proteins, the GlnD enzyme acts as a primary sensor of nitrogen in the cell. Regulatory role of the ACT domain Herbaspirillum seropedicae
physiological function control for PII interaction with target proteins involves the covalent modification of the T-loop, such as uridylylation, phosphorylation or adenylylation. The uridylylation of PII proteins occurs in a conserved residue of tyrosine (Tyr51) in the T-loop. Uridylylation of Tyr51 renders a T-loop more mobile in comparison with the unmodified protein. The PII uridylylation is catalyzed by the GlnD enzyme, which also catalyzes the removal of the uridylyl group from PII. The choice between uridylyl transferase (UTase) and the uridylyl-removing activities (UR) of GlnD is essential to the function of the Ntr system and is supposedly dependent on the in vivo fluctuation of key metabolites. The deuridylylation activity of Herbaspirillum seropedicae GlnD protein is regulated by the glutamine:2-oxoglutarate ratio. GlnD can sense the glutamine:2-oxoglutarate ratio. The ACT domains of GlnD are the protein sensor of environment clues of nitrogen availability. Regulatory role of the ACT domain Herbaspirillum seropedicae