Nucleotide affinity for a stable phosphorylated intermediate of nucleoside diphosphate kinase

Schneider, Benoı̂t; Norda, Ameli; Karlsson, Anna; Véron, Michel; Deville‐Bonne, Dominique

doi:10.1110/ps.0204702

Cited by 6 publications

(2 citation statements)

References 35 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Binding of the substrate ATP with the enzyme was confirmed by the quenching of fluorescence intensity with increasing concentrations of ATP [18, 19]. The spectra for the enzyme with increasing ATP concentrations were recorded at 3 different pH conditions.…”

Section: Resultsmentioning

confidence: 99%

Cloning, Expression, and Purification of Nucleoside Diphosphate Kinase fromAcinetobacter baumannii

et al. 2013

View full text Add to dashboard Cite

Acinetobacter baumannii is a multidrug resistant pathogenic bacteria associated with hospital acquired infections. This bacterium possesses a variety of resistance mechanisms which makes it more difficult to control the bacterium with conventional drugs, and, so far no effective drug treatment is available against it. Nucleoside diphosphate kinase is an important enzyme, which maintains the total nucleotide triphosphate pool inside the cell by the transfer of γ-phosphate from NTPs to NDPs. The role of nucleoside diphosphate kinase (Ndk) has also been observed in pathogenesis in other organisms. However, intensive studies are needed to decipher its other putative roles in Acinetobacter baumannii. In the present study, we have successfully cloned the gene encoding Ndk and achieved overexpression in bacterial host BL-21 (DE3). The overexpressed protein is further purified by nickel-nitrilotriacetic acid (Ni-NTA) chromatography.

show abstract

Section: Resultsmentioning

confidence: 99%

Cloning, Expression, and Purification of Nucleoside Diphosphate Kinase fromAcinetobacter baumannii

et al. 2013

View full text Add to dashboard Cite

show abstract

“…NDPKs bind nucleotides with affinities in the range of 10-200 µM, and guanine nucleotides are somewhat preferred over other substrates Schneider et al, 2002). Therefore, the simplest explanation for the preferential release of NDPK from the Mt/Ves fraction by GTP is that it involves binding of the nucleotide directly to its catalytic site.…”

Section: The Binding Of Ndpk To Vesicles Is Controlled By Its Catalytmentioning

confidence: 99%

Association of Nucleoside Diphosphate Kinase with Microtubule-Based Structures

Mitchell¹

View full text Add to dashboard Cite

Covalent Nucleophilic Catalysis: Structures of Enzyme Intermediates in Covalent Enzyme Catalysis

Ringe¹

2021

Encyclopedia of Life Sciences

View full text Add to dashboard Cite

Enzyme catalysis relies on several factors, such as proper fit of the substrate to the enzyme active site and interactions between substrate and residues that will aid in the chemical reaction. The overall effect is to lower the energy barrier for the reaction. One factor that is observed in some reactions is the formation of an intermediate covalent adduct to a residue in the active site in what is considered the first half of the reaction. This intermediate then goes on to react with another substrate to finish the overall reaction. Sometimes these covalent intermediates can be captured and characterised structurally. The chemical structure of an intermediate can define how a reaction proceeds, how the enzyme responds to binding of substrate, which residues of the active site are involved in the chemical transformation and how the substrate undergoes the rearrangements needed to produce the products. Capture of intermediates is not straightforward and requires different strategies, such as trapping with altered reaction conditions, use of low temperature and the use of mutants that prevent the second half of the reaction to proceed. A number of residues are able to form adducts to a ligand, depending on the nucleophilicity of the atom which undergoes the addition to a substrate (or part of a substrate). Key Concepts Covalent intermediates can lower the energy barrier in an enzyme‐catalysed reaction. Catalysis by an enzyme allows a reaction to occur under conditions that would be unfavourable or exceedingly slow in the absence of the enzyme. Strategies to accomplish this feat depend on the structure and physical properties of the protein to promote precise orientation of a substrate relative to the catalytic residues in an active site and stabilising unstable species with polarising bonds and forming covalent adducts. Structures of covalent intermediates help to define the mechanism by which an enzyme achieves its catalytic power. The structure of covalent intermediates can be trapped by a number of strategies, such as altering reaction conditions such as pH, by drastically lowering the temperature in order to prevent the second half of the reaction to occur or using mutants that prevent the second half of the reaction to occur. The most common covalent intermediates involve acylation, phosphorylation, glycosylation and Schiff base formation. Formation of a covalent adduct can lower the energy barrier of a reaction.

show abstract

Nucleotide affinity for a stable phosphorylated intermediate of nucleoside diphosphate kinase

Cited by 6 publications

References 35 publications

Cloning, Expression, and Purification of Nucleoside Diphosphate Kinase fromAcinetobacter baumannii

Cloning, Expression, and Purification of Nucleoside Diphosphate Kinase fromAcinetobacter baumannii

Association of Nucleoside Diphosphate Kinase with Microtubule-Based Structures

Covalent Nucleophilic Catalysis: Structures of Enzyme Intermediates in Covalent Enzyme Catalysis

Contact Info

Product

Resources

About