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The Protein Journal Oct 2017The mammalian NUDT13 protein possesses a sequence motif characteristic of the NADH pyrophosphohydrolase subfamily of Nudix hydrolases. Due to the persistent insolubility...
The mammalian NUDT13 protein possesses a sequence motif characteristic of the NADH pyrophosphohydrolase subfamily of Nudix hydrolases. Due to the persistent insolubility of the recombinant product expressed in Escherichia coli, active mouse Nudt13 was expressed in insect cells from a baculovirus vector as a histidine-tagged recombinant protein. In vitro, it efficiently hydrolysed NADH to NMNH and AMP and NADPH to NMNH and 2',5'-ADP and had a marked preference for the reduced pyridine nucleotides. Much lower activity was obtained with other nucleotide substrates tested. K and k values for NADH were 0.34 mM and 7 s respectively. Expression of Nudt13 as an N-terminal fusion to green fluorescent protein revealed that it was targeted exclusively to mitochondria by the N-terminal targeting peptide, suggesting that Nudt13 may act to regulate the concentration of mitochondrial reduced pyridine nucleotide cofactors and the NAD(P)/NAD(P)H ratio in this organelle and elsewhere. Future studies of the enzymology of pyridine nucleotide metabolism in relation to energy homeostasis, redox control, free radical production and cellular integrity should consider the possible regulatory role of Nudt13.
Topics: Animals; Baculoviridae; Cloning, Molecular; Intracellular Space; Mice; Mitochondrial Proteins; NAD; Pyrophosphatases; Recombinant Proteins; Sf9 Cells; Nudix Hydrolases
PubMed: 28755312
DOI: 10.1007/s10930-017-9734-x -
BMC Research Notes Mar 2019Planarians including Dugesia ryukyuensis (Dr) have strong regenerative abilities that require enhanced DNA replication. Knockdown of the DUT gene in Dr, which encodes...
OBJECTIVE
Planarians including Dugesia ryukyuensis (Dr) have strong regenerative abilities that require enhanced DNA replication. Knockdown of the DUT gene in Dr, which encodes deoxyuridine 5'-triphosphate pyrophosphatase (dUTPase), promotes DNA fragmentation, inhibits regeneration, and eventually leads to death. dUTPase catalyzes the hydrolysis of dUTP to dUMP and pyrophosphate. dUTPase is known to prevent uracil misincorporation in DNA by balancing the intracellular ratio between dUTP and dTTP, and contributes to genome stability. Nevertheless, the catalytic performance of Dr-dUTPase has not been reported.
RESULTS
To confirm the catalytic activity of Dr-dUTPase, we cloned and expressed Dr-DUT in E. coli. Then, we purified Dr-dUTPase using His-tag and removed the tag with thrombin. The resulting Dr-dUTPase had the leading peptide Gly-Ser-His- originating from the vector at the amino terminus, and a mutation, Arg66Lys, to remove the internal thrombin site. We observed the hydrolysis of dUTP by Dr-dUTPase using Cresol Red as a proton sensor. The K for dUTP was determined to be 4.0 µM, which is similar to that for human dUTPase. Dr-dUTPase exhibited a preference for dUTP over the other nucleotides. We conclude the Dr-dUTPase has catalytic activity.
Topics: Animals; Biocatalysis; Planarians; Pyrophosphatases; Regeneration
PubMed: 30902068
DOI: 10.1186/s13104-019-4191-6 -
Virology Oct 2016Deoxyuridine 5'-triphosphate pyrophosphatase (dUTPase), a ubiquitous enzyme that catalyzes the hydrolysis of dUTP to dUMP and found in many viruses, has yet to be...
Deoxyuridine 5'-triphosphate pyrophosphatase (dUTPase), a ubiquitous enzyme that catalyzes the hydrolysis of dUTP to dUMP and found in many viruses, has yet to be identified in fowl adenovirus 9 (FAdV-9). By a multiple alignment of dUTPase amino acid sequences, FAdV-9 ORF1 contained the five conserved motifs that define the protein family, and encoded a functional dUTPase. Moreover, transcription and protein expression patterns were characterized, indicating that dUTPase was transcribed from 2h post-infection (h.p.i.) and translated from 6h.p.i., and both continued to the late phase of virus infection. An HA-tagged dUTPase recombinant virus was generated, and dUTPase was found to be localized in both the cytoplasm and nucleus in chicken hepatoma cells (CH-SAH). A dUTPase knockout virus was generated and compared with the wild-type virus, showing that dUTPase upregulated the expression of type I interferons, but was not required for viral DNA or virus replication in CH-SAH cells.
Topics: Adenoviridae; Amino Acid Sequence; Animals; Cytokines; Enzyme Activation; Genome, Viral; Mutation; Open Reading Frames; Protein Biosynthesis; Protein Transport; Pyrophosphatases; RNA, Messenger; Transcription, Genetic
PubMed: 27498408
DOI: 10.1016/j.virol.2016.07.023 -
Scientific Reports Apr 2019ADP-ribosylation is a post-translational modification that occurs on chemically diverse amino acids, including aspartate, glutamate, lysine, arginine, serine and...
ADP-ribosylation is a post-translational modification that occurs on chemically diverse amino acids, including aspartate, glutamate, lysine, arginine, serine and cysteine on proteins and is mediated by ADP-ribosyltransferases, including a subset commonly known as poly(ADP-ribose) polymerases. ADP-ribose can be conjugated to proteins singly as a monomer or in polymeric chains as poly(ADP-ribose). While ADP-ribosylation can be reversed by ADP-ribosylhydrolases, this protein modification can also be processed to phosphoribosylation by enzymes possessing phosphodiesterase activity, such as snake venom phosphodiesterase, mammalian ectonucleotide pyrophosphatase/phosphodiesterase 1, Escherichia coli RppH, Legionella pneumophila Sde and Homo sapiens NudT16 (HsNudT16). Our studies here sought to utilize X-ray crystallographic structures of HsNudT16 in complex with monomeric and dimeric ADP-ribose in identifying the active site for binding and processing free and protein-conjugated ADP-ribose into phosphoribose forms. These structural data guide rational design of mutants that widen the active site to better accommodate protein-conjugated ADP-ribose. We identified that several HsNudT16 mutants (Δ17, F36A, and F61S) have reduced activity for free ADP-ribose, similar processing ability against protein-conjugated mono(ADP-ribose), but improved catalytic efficiency for protein-conjugated poly(ADP-ribose). These HsNudT16 variants may, therefore, provide a novel tool to investigate different forms of ADP-ribose.
Topics: ADP-Ribosylation; Catalytic Domain; Crystallography, X-Ray; Humans; Mutation; Poly Adenosine Diphosphate Ribose; Poly(ADP-ribose) Polymerases; Protein Conformation; Protein Processing, Post-Translational; Pyrophosphatases
PubMed: 30976021
DOI: 10.1038/s41598-019-39491-w -
Scientific Reports Apr 2022Inosine triphosphate pyrophosphatases (ITPases) are ubiquitous house-cleaning enzymes that specifically recognize deaminated purine nucleotides and catalyze their...
Inosine triphosphate pyrophosphatases (ITPases) are ubiquitous house-cleaning enzymes that specifically recognize deaminated purine nucleotides and catalyze their hydrolytic cleavage. In this work, we have characterized the Trypanosoma brucei ITPase ortholog (TbITPA). Recombinant TbITPA efficiently hydrolyzes (deoxy)ITP and XTP nucleotides into their respective monophosphate form. Immunolocalization analysis performed in bloodstream forms suggests that the primary role of TbITPA is the exclusion of deaminated purines from the cytosolic nucleoside triphosphate pools. Even though ITPA-knockout bloodstream parasites are viable, they are more sensitive to inhibition of IMP dehydrogenase with mycophenolic acid, likely due to an expansion of IMP, the ITP precursor. On the other hand, TbITPA can also hydrolyze the activated form of the antiviral ribavirin although in this case, the absence of ITPase activity in the cell confers protection against this nucleoside analog. This unexpected phenotype is dependant on purine availability and can be explained by the fact that ribavirin monophosphate, the reaction product generated by TbITPA, is a potent inhibitor of trypanosomal IMP dehydrogenase and GMP reductase. In summary, the present study constitutes the first report on a protozoan inosine triphosphate pyrophosphatase involved in the removal of harmful deaminated nucleotides from the cytosolic pool.
Topics: IMP Dehydrogenase; Inosine; Inosine Triphosphate; Nucleotides; Pyrophosphatases; Ribavirin; Trypanosoma brucei brucei
PubMed: 35436992
DOI: 10.1038/s41598-022-10149-4 -
Journal of Biological Inorganic... Feb 2021The Schizosaccharomyces pombe Asp1 protein is a bifunctional kinase/pyrophosphatase that belongs to the highly conserved eukaryotic diphosphoinositol pentakisphosphate...
The Schizosaccharomyces pombe Asp1 protein is a bifunctional kinase/pyrophosphatase that belongs to the highly conserved eukaryotic diphosphoinositol pentakisphosphate kinase PPIP5K/Vip1 family. The N-terminal Asp1 kinase domain generates specific high-energy inositol pyrophosphate (IPP) molecules, which are hydrolyzed by the C-terminal Asp1 pyrophosphatase domain (Asp1). Thus, Asp1 activities regulate the intracellular level of a specific class of IPP molecules, which control a wide number of biological processes ranging from cell morphogenesis to chromosome transmission. Recently, it was shown that chemical reconstitution of Asp1 leads to the formation of a [2Fe-2S] cluster; however, the biological relevance of the cofactor remained under debate. In this study, we provide evidence for the presence of the Fe-S cluster in Asp1 inside the cell. However, we show that the Fe-S cluster does not influence Asp1 pyrophosphatase activity in vitro or in vivo. Characterization of the as-isolated protein by electronic absorption spectroscopy, mass spectrometry, and X-ray absorption spectroscopy is consistent with the presence of a [2Fe-2S] cluster in the enzyme. Furthermore, we have identified the cysteine ligands of the cluster. Overall, our work reveals that Asp1 contains an Fe-S cluster in vivo that is not involved in its pyrophosphatase activity.
Topics: Biocatalysis; Cysteine; Cytoskeletal Proteins; Iron-Sulfur Proteins; Multifunctional Enzymes; Mutation; Phosphotransferases (Alcohol Group Acceptor); Pyrophosphatases; Schizosaccharomyces; Schizosaccharomyces pombe Proteins
PubMed: 33544225
DOI: 10.1007/s00775-020-01840-w -
Journal of Biomedical Science Oct 2016Human ITPase (encoded by the ITPA gene) is a protective enzyme which acts to exclude noncanonical (deoxy)nucleoside triphosphates ((d)NTPs) such as (deoxy)inosine... (Review)
Review
Human ITPase (encoded by the ITPA gene) is a protective enzyme which acts to exclude noncanonical (deoxy)nucleoside triphosphates ((d)NTPs) such as (deoxy)inosine 5'-triphosphate ((d)ITP), from (d)NTP pools. Until the last few years, the importance of ITPase in human health and disease has been enigmatic. In 2009, an article was published demonstrating that ITPase deficiency in mice is lethal. All homozygous null offspring died before weaning as a result of cardiomyopathy due to a defect in the maintenance of quality ATP pools. More recently, a whole exome sequencing project revealed that very rare, severe human ITPA mutation results in early infantile encephalopathy and death. It has been estimated that nearly one third of the human population has an ITPA status which is associated with decreased ITPase activity. ITPA status has been linked to altered outcomes for patients undergoing thiopurine or ribavirin therapy. Thiopurine therapy can be toxic for patients with ITPA polymorphism, however, ITPA polymorphism is associated with improved outcomes for patients undergoing ribavirin treatment. ITPA polymorphism has also been linked to early-onset tuberculosis susceptibility. These data suggest a spectrum of ITPA-related disease exists in human populations. Potentially, ITPA status may affect a large number of patient outcomes, suggesting that modulation of ITPase activity is an important emerging avenue for reducing the number of negative outcomes for ITPA-related disease. Recent biochemical studies have aimed to provide rationale for clinical observations, better understand substrate selectivity and provide a platform for modulation of ITPase activity.
Topics: Genotype; Humans; Metabolism, Inborn Errors; Mutation; Polymorphism, Single Nucleotide; Pyrophosphatases
PubMed: 27770805
DOI: 10.1186/s12929-016-0291-y -
Zeitschrift Fur Naturforschung. C,... 1999Trehalose has been described to protect several enzymes against destabilizing conditions. This sugar is naturally accumulated by yeast as a stress protectant. A common...
Trehalose has been described to protect several enzymes against destabilizing conditions. This sugar is naturally accumulated by yeast as a stress protectant. A common stress condition that yeast is normally submitted is the presence of ethanol, the by-product of fermentation process of several yeast. In this paper we show the effects of trehalose and ethanol, alone or together, on yeast pyrophosphatase, and the effects of these compounds on inhibition and unfolding of pyrophosphatase promoted by urea. We show that both trehalose and ethanol inhibit pyrophosphatase in a dose-dependent manner, and that the presence of ethanol does not modify the inhibition promoted by trehalose as well as the presence of trehalose does not modify the inhibition promoted by ethanol. The effects of trehalose on pyrophosphatase are completely reversible, but the inhibition caused by ethanol was only partially reversible. Incubation of pyrophosphatase with 10% (v/v) ethanol promoted an inhibition of 15%, and the control activity was completely recovered after removal of ethanol. On the other hand, when pyrophosphatase was incubated with 20% (v/v) ethanol an inhibition of 40% of the control activity was observed which persisted after removal of ethanol. Ethanol also potentiates the inhibition of pyrophosphatase promoted by urea, and contributes for an irreversible inactivation and unfolding of pyrophosphatase in the presence of urea. Trehalose, that protects this enzyme against the inhibition and unfolding promoted by the chaotropic compound urea, was inefficient to protect against the effects of ethanol. Trehalose was also efficient to prevent an irreversible inactivation induced by urea.
Topics: Ethanol; Inorganic Pyrophosphatase; Kinetics; Pyrophosphatases; Saccharomyces cerevisiae; Trehalose; Urea
PubMed: 10349738
DOI: 10.1515/znc-1999-3-408 -
Nature Communications Oct 2018ENPP1 (Ecto-nucleotide pyrophosphatase phosphodiesterase 1), a type II transmembrane glycoprotein, hydrolyzes ATP to produce AMP and diphosphate, thereby inhibiting bone...
ENPP1 (Ecto-nucleotide pyrophosphatase phosphodiesterase 1), a type II transmembrane glycoprotein, hydrolyzes ATP to produce AMP and diphosphate, thereby inhibiting bone mineralization. A recent study showed that ENPP1 also preferentially hydrolyzes 2'3'-cGAMP (cyclic GMP-AMP) but not its linkage isomer 3'3'-cGAMP, and negatively regulates the cGAS-STING pathway in the innate immune system. Here, we present the high-resolution crystal structures of ENPP1 in complex with 3'3'-cGAMP and the reaction intermediate pA(3',5')pG. The structures revealed that the adenine and guanine bases of the dinucleotides are recognized by nucleotide- and guanine-pockets, respectively. Furthermore, the structures indicate that 2'3'-cGAMP, but not 3'3'-cGAMP, binds to the active site in a conformation suitable for catalysis, thereby explaining the specific degradation of 2'3'-cGAMP by ENPP1. Our findings provide insights into how ENPP1 hydrolyzes both ATP and cGAMP to participate in the two distinct biological processes.
Topics: Adenosine Triphosphate; Catalysis; Cell Line; Cell Line, Tumor; HEK293 Cells; Humans; Membrane Proteins; Nucleotides, Cyclic; Phosphoric Diester Hydrolases; Protein Structure, Secondary; Pyrophosphatases; Signal Transduction
PubMed: 30356045
DOI: 10.1038/s41467-018-06922-7 -
The FEBS Journal Jul 2018The ecto-nucleotide pyrophosphatase/phosphodiesterase (NPP) enzyme family modulates purinergic signaling by degrading extracellular nucleotides. CD203c (NPP3, ENPP3)...
UNLABELLED
The ecto-nucleotide pyrophosphatase/phosphodiesterase (NPP) enzyme family modulates purinergic signaling by degrading extracellular nucleotides. CD203c (NPP3, ENPP3) regulates the inflammatory response of basophils via ATP hydrolysis and is a marker for allergen sensitivity on the surface of these cells. Multiple other roles and substrates have also been proposed for this protein. In order to gain insight into its molecular functions, we determined the crystal structure of human NPP3 as well as its complex with an ATP analog. The enzyme exhibits little preference for nucleobase type, and forms specific contacts with the alpha and beta phosphate groups of its ligands. Dimerization of the protein does not affect its catalytic activity. These findings expand our understanding of substrate recognition within the NPP family.
DATABASE
Structural data are available in the Protein Data Bank under the accession numbers 6C01 (human NPP3) and 6C02 (human NPP3 T205A N594S with AMPCPP).
Topics: Adenosine Triphosphate; Amino Acid Sequence; Animals; Crystallography, X-Ray; Humans; Models, Molecular; Nucleotides; Phosphoric Diester Hydrolases; Protein Binding; Protein Domains; Protein Multimerization; Pyrophosphatases; Sequence Homology, Amino Acid; Sf9 Cells; Spodoptera; Substrate Specificity
PubMed: 29717535
DOI: 10.1111/febs.14489