ATP as effector of inorganic pyrophosphatase of Escherichia coli. Identification of the binding site for ATP

@article{Rodina2007ATPAE,
  title={ATP as effector of inorganic pyrophosphatase of Escherichia coli. Identification of the binding site for ATP},
  author={Elena V. Rodina and Natalia N. Vorobyeva and Svetlana A. Kurilova and Maxim S. Belenikin and Nataliya V Fedorova and T.I. Nazarova},
  journal={Biochemistry (Moscow)},
  year={2007},
  volume={72},
  pages={93-99}
}
The interaction of Escherichia coli inorganic pyrophosphatase (E-PPase) with effector ATP has been studied. The E-PPase has been chemically modified with the dialdehyde derivative of ATP. It has been established that in the experiment only one molecule of effector ATP is bound to each subunit of the hexameric enzyme. Tryptic digestion of the adenylated protein followed by isolation of a modified peptide by HPLC and its mass-spectrometric identification has showed that it is an amino group of… 

ATP as effector of inorganic pyrophosphatase of Escherichia coli. The role of residue Lys112 in binding effectors

Analysis of data confirms the proposed location of an effector binding site in a cluster of positively charged amino acid residues including the side chains of Arg43, Lys146, Lys112, and Lys115 (subunit B) and plays a key role in forming contacts with the phosphate groups of the three studied effectors.

Inhibition of Escherichia coli inorganic pyrophosphatase by fructose-1-phosphate

Fru-1-P is a physiological inhibitor of pyrophosphatase that acts via a regulatory site in this enzyme, and is demonstrated to be a mechanism not involving competition with substrate for binding to the active site.

Discovery of Allosteric and Selective Inhibitors of Inorganic Pyrophosphatase from Mycobacterium tuberculosis.

These inhibitors are the first examples of allosteric, species-selective inhibitors of PPiase, serving as a proof-of-principle that PPiases can be selectively targeted.

Adaptation of protein expression by Escherichia coli in the gastrointestinal tract of gnotobiotic mice.

The feasibility of analysing the bacterial response to the conditions in the digestive system by a proteomics-based approach is demonstrated and it is shown that the host-associated bacteria adapt their metabolism to the Conditions in the intestine by utilizing arginine, asparagine and aspartate as substrates.

Probing distal regions of the A2B adenosine receptor by quantitative structure-activity relationship modeling of known and novel agonists.

Four novel adenosine analogues, having elongated or bulky substitutions at N (6) position and/or 2 position, were synthesized and evaluated biologically and were potent, full agonists at the A 2B AR in adenylate cyclase studies.

References

SHOWING 1-10 OF 14 REFERENCES

ATP as effector of inorganic pyrophosphatase of Escherichia coli. The role of residue Lys112 in binding effectors

Analysis of data confirms the proposed location of an effector binding site in a cluster of positively charged amino acid residues including the side chains of Arg43, Lys146, Lys112, and Lys115 (subunit B) and plays a key role in forming contacts with the phosphate groups of the three studied effectors.

Metal-free PPi activates hydrolysis of MgPPi by an Escherichia coli inorganic pyrophosphatase

It is demonstrated that the noncompetitive activation of MgPPi hydrolysis by metal-free PPi can also explain kinetic features of hexameric forms of both the native enzyme and the specially obtained mutant E-PPase with a substituted residue Glu145 in a flexible loop 144–149.

Effectory Site in Escherichia coli Inorganic Pyrophosphatase is Revealed Upon Mutation at the Intertrimeric Interface

The Asp26Ala variant is the first example of hexameric E‐PPase demonstrated to have an activatory subsite, and the finding that the free form of methylenediphosphonate activates MgPPi hydrolysis though its magnesium complex is a competitive inhibitor.

Some features of hydrolysis of organic and inorganic substrates by Escherichia coli inorganic pyrophosphatase in the presence of various activator cations

The kinetics of hydrolysis of the inorganic and organic substrates by Escherichia coli inorganic pyrophosphatase and its mutant forms with Asp42 replaced by Ala, Asn, or Glu was studied and the reasons for the observed differences in the substrate specificity of the enzyme are discussed.

Mechanism of Ca2+-induced inhibition of Escherichia coli inorganic pyrophosphatase.

Ca2+, as a constituent of the non-hydrolyzable substrate analog CaPPi, competes with MgPPi at the M3 binding site, which proves that Ca2+ is incapable of properly activating the H2O molecule for nucleophilic attack on PPi.

The structures of Escherichia coli inorganic pyrophosphatase complexed with Ca(2+) or CaPP(i) at atomic resolution and their mechanistic implications.

This work has enabled us to locate PP(i) in the active site of the inorganic pyrophosphatases family in the presence of Ca(2+), which is an inhibitor of EPPase.

Toward a quantum-mechanical description of metal-assisted phosphoryl transfer in pyrophosphatase

These structures of the yeast PPase product complex and fluoride-inhibited complex visualize the active site in three different states: substrate-bound, immediate product bound, and relaxed product bound and provide strong evidence that a water molecule directly attacks PPi with a pKa vastly lowered by coordination to two metal ions and D117.

Thermodynamics of binding of the distal calcium to manganese peroxidase.

It was proposed that, at lower pH, calcium binding to manganese peroxidase was more thermodynamically favorable, but the rate of calcium binding decreased because the flexibility of the calcium binding site, and in turn exposure of the ligands to the incoming ion, decreased.