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 (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 | 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 | 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 | 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 | 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 | UniProt | Comment | Textmining |
---|---|---|---|
Herbaspirillum seropedicae | D8IU13 | - |
- |
Herbaspirillum seropedicae SmR1 | D8IU13 | - |
- |
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 | 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 Maximum [°C] | Comment | Organism |
---|---|---|---|
37 | - |
assay at | Herbaspirillum seropedicae |
pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
---|---|---|---|
7.5 | - |
assay at | Herbaspirillum seropedicae |
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 |