Molecular Basis of the Antimutagenic Activity of the House-Cleaning Inosine Triphosphate Pyrophosphatase RdgB from Escherichia coli

Savchenko, Alexei; Proudfoot, Michael; Skarina, T.; Singer, A.U.; Litvinova, Olga; Sanishvili, Ruslan; Brown, Greg; Chirgadze, Nickolay Y.; Yakunin, Alexander F.

doi:10.1016/j.jmb.2007.10.012

Cited by 28 publications

(52 citation statements)

References 44 publications

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“…Due to the high pyrophosphatase activities towards ITP, dITP, XTP, we hypothesise that dXTP is also a good substrate for this enzyme. YJR069C-encoding enzyme has shown around two magnitude and higher differences in activity between "key" substrates (dITP, ITP and XTP) and dGTP or dATP, which is somewhat similar to what was reported previously in (9,10). Since YJR069C-encoding protein was found to have pyrophosphatase activity on ITP, dITP and XTP, and same activity was proposed for dXTP, enzyme is annotated as (d)ITP/ (d)XTPase.…”

Section: Resultssupporting

confidence: 81%

“…Previously, it has been suggested that the ITPA (inosine triphosphate pyrophosphatase, (E.C. 3.6.1.19) protein can hydrolyse these type of nucleosides and its homologues were at some extent characterised in E. coli (9,10). In order to characterise the S. cerevisiae counterpart, a homologues enzyme encoded by YJR069C (HAM1) and shown to possess deoxy-N-6-hydroxylaminopurine triphosphate and deoxyinosine triphosphate pyrophosphohydrolases activities (9) was investigated.…”

Section: Resultsmentioning

confidence: 99%

“…RdgB (E.C. 3.6.1.19), has been characterised as one of such enzymes in E. coli (9,10). S. cerevisiae homologue of RdgB is encoded by YJR069C and it has been shown to possess http://bmbreports.org o C, with 6.55 nM enzyme, determined using an inorganic pyrophosphatase coupled assay deoxyribonucleoside triphosphate pyrophosphohydrolase activity (E.C.…”

Section: Introductionmentioning

confidence: 99%

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Characterisation of multiple substrate-specific (d)ITP/(d)XTPase and modelling of deaminated purine nucleotide metabolism

Davies¹,

Mendes²,

Smallbone³

et al. 2012

BMB Reports

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Section: Resultssupporting

confidence: 81%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Characterisation of multiple substrate-specific (d)ITP/(d)XTPase and modelling of deaminated purine nucleotide metabolism

Davies¹,

Mendes²,

Smallbone³

et al. 2012

BMB Reports

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“…Kinetic parameters were determined by nonlinear curve fitting using GraphPad Prism software (version 4.00 for Windows). TLC analysis of the PPK2 reaction products was performed with cellulose plates (Sigma) as described (28).…”

Section: Resultsmentioning

confidence: 99%

“…Crystals of the SeMetlabeled PA3455 and SMc02148 were grown by the hanging-drop vapordiffusion method at 18°C as described (28). PA3455 was crystallized in the presence of 0.1 M Hepes-K (pH 7.0), 5% Tacsimate, and 10% PEG MME 5K, whereas the crystals of SMc02148 were grown in the presence of 0.1 M Bis-Tris (pH 7.5), 0.1 M Na-formate, 0.1 M Li-sulfate, and 0.3 M NDSB 211.…”

Section: Resultsmentioning

confidence: 99%

Polyphosphate-dependent synthesis of ATP and ADP by the family-2 polyphosphate kinases in bacteria

Nocek

Kochinyan

Proudfoot

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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Inorganic polyphosphate (polyP) is a linear polymer of tens or hundreds of phosphate residues linked by high-energy bonds. It is found in all organisms and has been proposed to serve as an energy source in a pre-ATP world. This ubiquitous and abundant biopolymer plays numerous and vital roles in metabolism and regulation in prokaryotes and eukaryotes, but the underlying molecular mechanisms for most activities of polyP remain unknown. In prokaryotes, the synthesis and utilization of polyP are catalyzed by 2 families of polyP kinases, PPK1 and PPK2, and polyphosphatases. Here, we present structural and functional characterization of the PPK2 family. Proteins with a single PPK2 domain catalyze polyP-dependent phosphorylation of ADP to ATP, whereas proteins containing 2 fused PPK2 domains phosphorylate AMP to ADP. Crystal structures of 2 representative proteins, SMc02148 from Sinorhizobium meliloti and PA3455 from Pseudomonas aeruginosa, revealed a 3-layer ␣/␤/␣ sandwich fold with an ␣-helical lid similar to the structures of microbial thymidylate kinases, suggesting that these proteins share a common evolutionary origin and catalytic mechanism. Alanine replacement mutagenesis identified 9 conserved residues, which are required for activity and include the residues from both Walker A and B motifs and the lid. Thus, the PPK2s represent a molecular mechanism, which potentially allow bacteria to use polyP as an intracellular energy reserve for the generation of ATP and survival.crystal structure ͉ mutagenesis ͉ Walker motif ͉ AMP phosphorylation ͉ ADP phosphorylation I norganic polyphosphate (polyP) is a linear polymer composed of tens to hundreds of orthophosphate residues (P i ) linked by the energy-rich phosphoanhydride bonds, and it is found in all prokaryotes and eukaryotes (1-3). PolyP has numerous biological functions that include substitution for ATP in kinase reactions, acting as an energy source or storage reservoir of P i , chelating metals, and adjusting cellular physiology during growth, development, stress, starvation, and virulence (1, 4). Bacteria with low intracellular polyP levels show defective responses to various stress conditions, biofilm formation, quorum sensing, motility, and other virulence properties (3,5). Depending on the physiological state of the bacterium, the intracellular concentration of polyP is 0

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Identification of the HcgB Enzyme in [Fe]‐Hydrogenase‐Cofactor Biosynthesis

et al. 2013

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[Fe]‐Hydrogenase benötigt für seine Aktivität einen Eisen‐Guanylylpyridinol(FeGP)‐Cofaktor. Die Funktion von HcgB, einem Enzym in der Biosynthese des Cofaktors FeGP, wurde durch strukturelle Genomik prognostiziert und durch Modellreaktionen und verschiedene analytische Methoden bestätigt: HcgB katalysiert die terminale Guanylyltransferase‐Reaktion zur Bildung von Guanylylpyridinol. GMP=Guanosinmonophosphat.

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Molecular Basis of the Antimutagenic Activity of the House-Cleaning Inosine Triphosphate Pyrophosphatase RdgB from Escherichia coli

Cited by 28 publications

References 44 publications

Characterisation of multiple substrate-specific (d)ITP/(d)XTPase and modelling of deaminated purine nucleotide metabolism

Characterisation of multiple substrate-specific (d)ITP/(d)XTPase and modelling of deaminated purine nucleotide metabolism

Polyphosphate-dependent synthesis of ATP and ADP by the family-2 polyphosphate kinases in bacteria

Identification of the HcgB Enzyme in [Fe]‐Hydrogenase‐Cofactor Biosynthesis

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