Relevant bibliographies by topics / Nucleoside Diphosphate Kinase (NDK)

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Academic literature on the topic 'Nucleoside Diphosphate Kinase (NDK)'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "Nucleoside Diphosphate Kinase (NDK)"

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López-Zavala, Alonso A., Idania E. Quintero-Reyes, Jesús S. Carrasco-Miranda, Vivian Stojanoff, Andrzej Weichsel, Enrique Rudiño-Piñera, and Rogerio R. Sotelo-Mundo. "Structure of nucleoside diphosphate kinase from pacific shrimp (Litopenaeus vannamei) in binary complexes with purine and pyrimidine nucleoside diphosphates." Acta Crystallographica Section F Structural Biology Communications 70, no. 9 (August 29, 2014): 1150–54. http://dx.doi.org/10.1107/s2053230x1401557x.

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Nucleoside diphosphate kinase (NDK; EC 2.7.4.6) is an enzyme that catalyzes the third phosphorylation of nucleoside diphosphates, leading to nucleoside triphosphates for DNA replication. Expression of the NDK fromLitopenaeus vannamei(LvNDK) is known to be regulated under viral infection. Also, as determined by isothermal titration calorimetry,LvNDK binds both purine and pyrimidine deoxynucleoside diphosphates with high binding affinity for dGDP and dADP and with no heat of binding interaction for dCDP [Quintero-Reyeset al.(2012),J. Bioenerg. Biomembr.44, 325–331]. In order to investigate the differences in selectivity,LvNDK was crystallized as binary complexes with both acceptor (dADP and dCDP) and donor (ADP) phosphate-group nucleoside diphosphate substrates and their structures were determined. The three structures with purine or pyrimidine nucleotide ligands are all hexameric. Also, the binding of deoxy or ribonucleotides is similar, as in the former a water molecule replaces the hydrogen bond made by Lys11 to the 2′-hydroxyl group of the ribose moiety. This allows Lys11 to maintain a catalytically favourable conformation independently of the kind of sugar found in the nucleotide. Because of this, shrimp NDK may phosphorylate nucleotide analogues to inhibit the viral infections that attack this organism.
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Jeudy, Sandra, Audrey Lartigue, Jean-Michel Claverie, and Chantal Abergel. "Dissecting the Unique Nucleotide Specificity of Mimivirus Nucleoside Diphosphate Kinase." Journal of Virology 83, no. 14 (May 13, 2009): 7142–50. http://dx.doi.org/10.1128/jvi.00511-09.

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ABSTRACT The analysis of the Acanthamoeba polyphaga mimivirus genome revealed the first virus-encoded nucleoside diphosphate kinase (NDK), an enzyme that is central to the synthesis of RNA and DNA, ubiquitous in cellular organisms, and well conserved among the three domains of life. In contrast with the broad specificity of cellular NDKs for all types of ribo- and deoxyribonucleotides, the mimivirus enzyme exhibits a strongly preferential affinity for deoxypyrimidines. In order to elucidate the molecular basis of this unique substrate specificity, we determined the three-dimensional (3D) structure of the Acanthamoeba polyphaga mimivirus NDK alone and in complex with various nucleotides. As predicted from a sequence comparison with cellular NDKs, the 3D structure of the mimivirus enzyme exhibits a shorter Kpn loop, previously recognized as a main feature of the NDK active site. The structure of the viral enzyme in complex with various nucleotides also pinpointed two residue changes, both located near the active site and specific to the viral NDK, which could explain its stronger affinity for deoxynucleotides and pyrimidine nucleotides. The role of these residues was explored by building a set of viral NDK variants, assaying their enzymatic activities, and determining their 3D structures in complex with various nucleotides. A total of 26 crystallographic structures were determined at resolutions ranging from 2.8 Å to 1.5 Å. Our results suggest that the mimivirus enzyme progressively evolved from an ancestral NDK under the constraints of optimizing its efficiency for the replication of an AT-rich (73%) viral genome in a thymidine-limited host environment.
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Zhu, Xiaoyan, Emiliya Poghosyan, Radhika Gopal, Yi Liu, Kristine S. Ciruelas, Yousif Maizy, Dennis R. Diener, Stephen M. King, Takashi Ishikawa, and Pinfen Yang. "General and specific promotion of flagellar assembly by a flagellar nucleoside diphosphate kinase." Molecular Biology of the Cell 28, no. 22 (November 2017): 3029–42. http://dx.doi.org/10.1091/mbc.e17-03-0156.

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Nucleoside diphosphate kinases (NDKs) play a central role in diverse cellular processes using the canonical NDK activity or alternative mechanisms that remain poorly defined. Our study of dimeric NDK5 in a flagellar motility control complex, the radial spoke (RS), has revealed new modalities. The flagella in Chlamydomonas ndk5 mutant were paralyzed, albeit only deficient in three RS subunits. RS morphology appeared severely changed in averaged cryo-electron tomograms, suggesting that NDK5 is crucial for the intact spokehead formation as well as RS structural stability. Intriguingly, ndk5’s flagella were also short, resembling those of an allelic spoke-less mutant. All ndk5’s phenotypes were rescued by expressions of NDK5 or a mutated NDK5 lacking the canonical kinase activity. Importantly, the mutated NDK5 that appeared fully functional in ndk5 cells elicited a dominant-negative effect in wild-type cells, causing paralyzed short flagella with hypophosphorylated, less abundant, but intact RSs, and accumulated hypophosphorylated NDK5 in the cell body. We propose that NDK5 dimer is an RS structural subunit with an additional mechanism that uses cross-talk between the two NDK monomers to accelerate phosphorylation-related assembly of RSs and entire flagella.
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Goswami, Samridhi C., Jung-Hoon Yoon, Bozena M. Abramczyk, Gerd P. Pfeifer, and Edith H. Postel. "Molecular and Functional Interactions between Escherichia coli Nucleoside-diphosphate Kinase and the Uracil-DNA Glycosylase Ung." Journal of Biological Chemistry 281, no. 43 (August 7, 2006): 32131–39. http://dx.doi.org/10.1074/jbc.m604937200.

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Escherichia coli nucleoside-diphosphate kinase (Ndk) catalyzes nucleoside triphosphate synthesis and maintains intracellular triphosphate pools. Mutants of E. coli lacking Ndk exhibit normal growth rates but show a mutator phenotype that cannot be entirely attributed to the absence of Ndk catalytic activity or to an imbalance in cellular triphosphates. It has been suggested previously that Ndk, similar to its human counterparts, possesses nuclease and DNA repair activities, including the excision of uracil from DNA, an activity normally associated with the Ung and Mug uracil-DNA glycosylases (UDGs) in E. coli. Here we have demonstrated that recombinant Ndk purified from wild-type E. coli contains significant UDG activity that is not intrinsic, but rather, is a consequence of a direct physical and functional interaction between Ung and Ndk, although a residual amount of intrinsic UDG activity exists as well. Co-purification of Ung and Ndk through multicolumn low pressure and nickel-nitrilotriacetic acid affinity chromatography suggests that the interaction occurs in a cellular context, as was also suggested by co-immunoprecipitation of endogenous Ung and Ndk from cellular extracts. Glutathione S-transferase pulldown and far Western analyses demonstrate that the interaction also occurs at the level of purified protein, suggesting that it is specific and direct. Moreover, significant augmentation of Ung catalytic activity by Ndk was observed, suggesting that the interaction between the two enzymes is functionally relevant. These findings represent the first example of Ung interacting with another E. coli protein and also lend support to the recently discovered role of nucleoside-diphosphate kinases as regulatory components of multiprotein complexes.
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Dar, Haider Hussain, and Pradip K. Chakraborti. "Intermolecular phosphotransfer is crucial for efficient catalytic activity of nucleoside diphosphate kinase." Biochemical Journal 430, no. 3 (August 27, 2010): 539–49. http://dx.doi.org/10.1042/bj20100026.

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NDK (nucleoside diphosphate kinase) is primarily involved in maintaining cellular nucleotide pools in both prokaryotes and eukaryotes. We cloned ndk from Salmonella typhimurium and expressed it in Escherichia coli as a histidine-tagged protein. The Ni-NTA (Ni2+-nitrilotriacetate)-purified protein (sNDK) was found to be tetrameric with a monomeric unit molecular mass of ~18 kDa. The sNDK exhibited bivalent-cation-dependent autophosphorylation at a wide range of pH values and the phosphorylation withstands acid or alkali treatment. Surprisingly, nucleoside diphosphates did not behave as ‘true inhibitors’ of autophosphorylation activity. The sNDK displayed phosphotransfer activity from nucleoside triphosphates to nucleoside diphosphates; however, it was Mg2+/Mn2+-dependent. Mutational analysis established His117 as the predominantly phosphorylating residue in sNDK. Although it is a histidine kinase, we found that substitution of Ser119 with alanine/glutamate significantly affected the autophosphorylation, as well as the NTP-synthesizing ability of sNDK. Interestingly, the mixture of inactive (H117A) and partially active (S119A) proteins was found to be catalytically more efficient than the presence of corresponding amounts of active population, advocating transfer of phosphate from phospho-His117 to Ser119. Consistent with this observation, the Ni-NTA-purified H117A protein, obtained following co-expression of both of the mutant constructs [His-tagged H117A and GST (glutathione transferase)-tagged S119A] in E. coli, exhibited autophosphorylation, thereby alluding to intermolecular phosphotransfer between His117 and Ser119. Although this housekeeping enzyme has long been discovered and characterized from different sources, the results of the present study portray how Ser119 in sNDK is phosphorylated. Furthermore, our findings illustrate for the first time that the intermolecular phosphotransfer is mandatory for the efficient NTP synthesis in any NDK.
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Lin, Xiaorong, Cory Momany, and Michelle Momany. "SwoHp, a Nucleoside Diphosphate Kinase, Is Essential in Aspergillus nidulans." Eukaryotic Cell 2, no. 6 (December 2003): 1169–77. http://dx.doi.org/10.1128/ec.2.6.1169-1177.2003.

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ABSTRACT The temperature-sensitive swoH1 mutant of Aspergillus nidulans was previously identified in a screen for mutants with defects in polar growth. In the present work, we found that the swoH1 mutant swelled, lysed, and did not produce conidia during extended incubation at the restrictive temperature. When shifted from the permissive to the restrictive temperature, swoH1 showed the temperature-sensitive swelling phenotype only after 8 h at the higher temperature. The swoH gene was mapped to chromosome II and cloned by complementation of the temperature-sensitive phenotype. The sequence showed that swoH encodes a homologue of nucleoside diphosphate kinases (NDKs) from other organisms. Deletion experiments showed that the swoH gene is essential. A hemagglutinin-SwoHp fusion complemented the mutant phenotype, and the purified fusion protein possessed phosphate transferase activity in thin-layer chromatography assays. Sequencing of the mutant allele showed a predicted V83F change. Structural modeling suggested that the swoH1 mutation would lead to perturbation of the NDK active site. Crude cell extracts from the swoH1 mutant grown at the permissive temperature had ∼20% of the NDK activity seen in the wild type and did not show any decrease in activity when assayed at higher temperatures. Though the data are not conclusive, the lack of temperature-sensitive NDK activity in the swoH1 mutant raises the intriguing possibility that the SwoH NDK is required for growth at elevated temperatures rather than for polarity maintenance.
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Sikarwar, Juhi, Sanket Kaushik, Mau Sinha, Punit Kaur, Sujata Sharma, and Tej P. Singh. "Cloning, Expression, and Purification of Nucleoside Diphosphate Kinase from Acinetobacter baumannii." Enzyme Research 2013 (April 11, 2013): 1–4. http://dx.doi.org/10.1155/2013/597028.

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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.
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Miller, Jeffrey H., Pauline Funchain, Wendy Clendenin, Tiffany Huang, Anh Nguyen, Erika Wolff, Annie Yeung, et al. "Escherichia coli Strains (ndk) Lacking Nucleoside Diphosphate Kinase Are Powerful Mutators for Base Substitutions and Frameshifts in Mismatch-Repair-Deficient Strains." Genetics 162, no. 1 (September 1, 2002): 5–13. http://dx.doi.org/10.1093/genetics/162.1.5.

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Abstract Nucleoside diphosphate (NDP) kinase is one of the enzymes that maintains triphosphate pools. Escherichia coli strains (ndk) lacking this enzyme have been shown to be modest base substitution mutators, and two members of the human family of NDP kinases act as tumor suppressors. We show here that in E. coli strains lacking NDP kinase high levels of mispairs are generated, but most of these are corrected by the mismatch-repair system. Double mutants that are ndk mutS, lacking both the NDP kinase and mismatch repair, have levels of base substitutions 15-fold higher and levels of certain frameshifts up to 10-fold higher than those of the respective mutations in mutS strains that are NDP kinase proficient. A sequence analysis of the specificity of base substitution mutations generated in ndk and ndk mutS backgrounds as well as other experiments suggests that NDP kinase deficiency stimulates polymerase errors that lead to A:T → G:C transitions and that the editing capacity of cells may be affected, leading to additional uncorrected mispairs and to A:T → T:A transversions.
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Kamath, Shilpa, M. L. Chen, and A. M. Chakrabarty. "Secretion of Nucleoside Diphosphate Kinase by Mucoid Pseudomonas aeruginosa 8821: Involvement of a Carboxy-Terminal Motif in Secretion." Journal of Bacteriology 182, no. 13 (July 1, 2000): 3826–31. http://dx.doi.org/10.1128/jb.182.13.3826-3831.2000.

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ABSTRACT Nucleoside diphosphate kinase (Ndk) is a ubiquitous enzyme which functions in balancing the nucleotide pool of the cell. We have recently reported that in addition to being intracellular in both mucoid and nonmucoid Pseudomonas aeruginosa, Ndk is also secreted into the extracellular environment by mucoid P. aeruginosa cells. This secreted Ndk has biochemical activity similar to the intracellular Ndk and is 16 kDa in size. To demonstrate that Ndk is indeed secreted and to localize the secretion motif, we constructed an ndk knockout mutant, which lacks both intracellular and extracellular forms of Ndk. In this study, we report the construction of deletion derivatives made from the carboxy-terminal region of Ndk. These deletion derivatives were introduced into thendk::Cm knockout mutant and were examined for the intracellular and extracellular presence of Ndk. It was observed that the carboxy-terminal 8-amino-acid region is required for the secretion of Ndk into the extracellular region. This region has the sequence DXXX, where X is a predominantly hydrophobic residue. Such sequences represent a conserved motif in proteins secreted by the type I secretory pathway in gram-negative microorganisms. To investigate the significance of this motif in the secretion of Ndk, we constructed a fusion protein of Ndk and the blue fluorescent protein (BFP) as well as a fusion protein of mutated Ndk (whose DTEV motif has been changed to AAAA) and the BFP. The presence of extracellular Ndk was detected only in the ndk::Cm knockout mutant harboring the wild-type BFP-Ndk protein fusion. We could not detect the presence of extracellular Ndk in the ndk::Cm knockout mutant containing the mutated BFP-Ndk protein fusion. In addition, we have also used immunofluorescence microscopy to localize the wild-type and mutated BFP-Ndk proteins in the cell. The significance of these observations is discussed.
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Dar, Haider Hussain, Deepshikha Prasad, Grish C. Varshney, and Pradip K. Chakraborti. "Secretory nucleoside diphosphate kinases from both intra- and extracellular pathogenic bacteria are functionally indistinguishable." Microbiology 157, no. 11 (November 1, 2011): 3024–35. http://dx.doi.org/10.1099/mic.0.049221-0.

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Nucleoside diphosphate kinase (NDK), responsible for the maintenance of NTP pools, is an ATP-utilizing enzyme secreted by different pathogens. We found that NDK from Salmonella enterica serovar Typhimurium (S. Typhimurium) is also secretory in nature. Secretory NDK is known to play a crucial role in the survival of pathogenic microbes within host cells through their interaction with extracellular ATP. To elucidate this aspect, we assessed the contribution of secretory products containing NDK from intracellular (Mycobacterium tuberculosis and S. Typhimurium) and extracellular (Vibrio cholerae) pathogens to the process of ATP-induced J774 mouse macrophage cell lysis by monitoring lactate dehydrogenase (LDH) release in the culture medium. Compared with an untreated control, our results demonstrate that S. Typhimurium secretory products caused a greater than twofold decrease in LDH release from J774 macrophage cells treated with ATP. Furthermore, the secretory products from an ndk-deleted strain of S. Typhimurium did not display such behaviour. Contrary to this observation, the secretory products containing NDK of V. cholerae were found to be cytotoxic to J774 cells. At the amino acid level, the sequences of both the NDKs (S. Typhimurium and V. cholerae) exhibited 65 % identity, and their biochemical characteristics (autophosphorylation and phosphotransfer activities) were indistinguishable. However, to our surprise, the secretory product of an ndk-deleted strain of S. Typhimurium, when complemented with V. cholerae ndk, was able to prevent ATP-induced cytolysis. Taken together, our results unambiguously imply that the intrinsic properties of secretory NDKs are identical in intra- and extracellular pathogens, irrespective of their mode of manifestation.
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Dissertations / Theses on the topic "Nucleoside Diphosphate Kinase (NDK)"

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SELLAM, OLIVIER. "La nucleoside diphosphate kinase des proprietes regulatrices pour une enzyme du metabolisme ? contribution a l'etude de la ndp kinase de dictyostelium discoideum." Paris 7, 1998. http://www.theses.fr/1998PA077149.

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La nucleoside diphosphate kinase (ndp kinase) est une enzyme du metabolisme qui catalyse la synthese des ribo- et desoxyribo-nucleosides triphosphates a partir de leurs precurseurs diphosphates selon un mecanisme de type ping-pong. C'est un hexamere de sous-unites identiques de 17 kda dont la structure tridimensionnelle est connue. L'implication de ndp kinases dans le developpement et la metastase a ete mise en evidence respectivement chez l'homme et la drosophile. Par ailleurs, il a ete recemment montre que la ndp kinase humaine est capable de se fixer sur le promoteur de l'oncogene c-myc et d'en stimuler la transcription. J'ai etudie plusieurs mutants de la ndp kinase de dictyostelium. L'etude du mutant h55a a montre le role crucial l'his 55 dans les proprietes de fluorescence de l'enzyme phosphorylee, et sa contribution faible dans la catalyse. Le mutant n119a a permis d'obtenir des co-cristaux de l'enzyme avec l'azt diphosphate. La structure obtenue permet d'expliquer la faible efficacite de phosphorylation de l'azt diphosphate in vivo. J'ai par ailleurs etudie la proteine mutante s124g de dictyostelium, correspondant a un mutant isole dans des lignees humaines de neuroblastomes. La mutation n'affecte pas la catalyse, mais modifie les proprietes de repliement du polypeptide. Les fonctions biologiques de la ndp kinase chez dictyostelium ont ete etudiees par surexpression des formes sauvage et mutantes du gene codant pour la ndp kinase cytosolique. J'ai egalement realise l'inactivation de ce gene par recombinaison homologue, et obtenu des transfectants viables. Dans tous les cas, aucune difference de phenotype avec la souche parentale n'a ete observee. Cette absence d'effet chez dictyostelium est discutee dans le contexte des observations realisees chez d'autres organismes.
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MILON, LAURENCE. "La famille des nm23/ndp kinases humaines clonage de l'adnc, caracterisation biochimique et localisation mitochondriale de la nucleoside diphosphate kinase nm23-h4." Paris 6, 2000. http://www.theses.fr/2000PA066332.

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Les nucleoside diphosphate kinases sont les enzymes responsables in vivo de la synthese des nucleosides triphosphates a partir de l'atp. Elles sont impliquees dans des fonctions cellulaires normales et pathologiques, eventuellement independamment de leur activite enzymatique mais les mecanismes mis en jeu sont actuellement mal definis. Chez l'homme, six isoformes sont decrites a ce jour : nm23-h1, nm23-h2, dr-nm23, nm23-h4, nm23-h5 et nm23-h6. Mon travail a consiste en l'etude de nm23-h4, dont l'existence a ete mise en evidence au laboratoire. J'ai clone l'adnc nm23-h4. Le gene est localise sur le chromosome 16p13. 3. L'expression de l'arnm nm23-h4 est variable selon les tissus et particulierement abondante dans la prostate et le foie. La proteine nm23-h4 (187 acides amines ; mr : 20650) se distingue des autres isoformes humaines, par la presence d'une extension n-terminale caracteristique d'un adressage mitochondrial. La proteine entiere et une forme tronquee sans l'extension ont ete exprimees chez e. Coli et purifiees. La forme tronquee possede l'activite ndp kinase tandis que la forme entiere est inactive, suggerant un effet inhibiteur de l'extremite n-terminale. L'analyse de la structure tridimensionnelle par diffraction aux rayons x, montre que nm23-h4 est hexamerique comme les autres ndp kinases eucaryotes. Nm23-h4 possede un residu serine en position 129 correspondant a la mutation conditionnelle letale dominante de la ndp kinase de la drosophile. Le mutant s129p, beaucoup plus stable aux agents denaturants, confirme l'importance de ce residu dans la stabilite de la proteine. Nous montrons par transfert de western et analyse confocale de cellules humaines sur-exprimant la proteine fusionnee a la gfp, que nm23-h4 est une ndp kinase mitochondriale, la premiere caracterisee chez les mammiferes. Son import dans l'organite s'accompagne d'un clivage proteolytique, vraisemblablement de l'extension n-terminale. Nm23-h4 semble etre associee aux sites de contact mitochondriaux entre les membranes interne et externe. Le role de nm23-h4 dans la mitochondrie est discutee dans le contexte des etudes anterieures sur l'activite ndp kinase mitochondriale et de son association aux sites de contact.
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Massé, Karine. "Caractérisation des isoformes C et D de la NDP kinase chez la souris : étude préliminaire du rôle des isoformes A et B sur l'expression du protooncogène." Bordeaux 2, 1999. http://www.theses.fr/1999BOR28669.

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XU, YING-WU. "Crystallographique etude de nucleoside diphosphate kinase." Paris 11, 1998. http://www.theses.fr/1998PA112087.

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La nucleoside diphosphate kinase (ndpk) est un enzyme ubiquitaire, qui catalyse la formation des nucleoside triphosphates a partir des diphosphates et maintient l'equilibre de leurs concentrations aux depens de l'atp. La reaction de type ping-pong est tres efficace et passe par un intermediaire phospho-histidine. La ndpk est un tetramere chez certaines bacteries, un hexamere chez les eucaryotes. La sous-unite comporte un domaine a/b organise autour d'un feuillet-b a 4 brins antiparalleles. Outre son role dans la biosynthese des nucleotides, l'enzyme humain aurait une activite histidine kinase et lierait l'adn. De plus, ell serait impliquee dans la proliferation des metastases et dans l'activation de la transcription de certains genes. Dans cette these, nous presentons six structures cristallines de la ndpk de dictyostelium complexee avec des substrats, des analogues ou des inhibiteurs. Elles permettent de mieux comprendre le mecanisme de la catalyse et l'interaction avec des analogues de nucleotides anti-viraux, en visant a la conception de medicaments et a la mutagenese fondee sur la structure. La structure du complexe ndpk. Adp. Alf3 decrit la geometrie de l'etat de transition de la reaction de transfert de phosphate. Alf3 mime le phosphate-g de l'atp lors de son transfert sur l'histidine du site actif par un mecanisme d'attaque en ligne passant par un intermediaire bipyramid trigonal. Des complexes ndp. Aif3 similaires ont depuis ete decrits dans d'autres kinases. La structure du complexe ndpk. Adp. Bef3 illustre le mode fixation de l'atp. Ces deux structures definissent les interactions enzyme-substrat et mettent en evidence deux elements essentiels de la catalyse : l'ion mg++ et le oh en 3 du sucre sur le nucleotide. Nous avons analyse les cinetiques de phosphorylation et dephosphorylation des nucleotides par la ndpk aal'aide de la fluorescence intrinseque de la proteine. Les analogues antiviraux derives de l'azt et de la ddt sont de mauvais substrats de la ndpk en comparaison du substrat naturel tdp. La faible phosphorylation de l'azt s'explique par deux facteurs structuraux : l'absence de la liaison hydrogene entre le 3oh et l'oxygene pontant les phosphates b et g ; le deplacement de la chaine laterale du residu lys 16. La structure cristalline du complexe avec l'azt diphosphate donne une base structurale a la conception de nucleosides antiviraux qui soient de meilleurs substrats de la ndpk. Celles des complexes ndpk avec les deux antiviraux 3-fluoro-udp et 3-amino-adp permet de comprendre pourquoi ce sont aussi de mauvais substrats ; dans les deux cas, la modification en 3 du sucre change l'interaction avec la proteine. Le 3'-phospho-adenosine-5-phosphosulfate (paps) est un inhibiteur puissant de l'activite enzymatique de la ndpk. La structure cristalline du complexe revele qu'il se fixe sur le meme site que l'adp, mais d'une facon differente, qui donne des indications sur le mode de fixation de l'adn.
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Johansson, Monika. "The role of nucleoside diphosphate kinase in plant mitochondria /." Uppsala : Dept. of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, 2006. http://epsilon.slu.se/200674.pdf.

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Hammargren, Jenni. "Novel functions of the mitochondrial nucleoside diphosphate kinase in plants /." Uppsala : Dept. of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, 2007. http://epsilon.slu.se/200787.pdf.

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Morera, Solange. "Etude cristallographie de la nucleoside diphosphate kinase de dictyostelium discoideum." Paris 11, 1994. http://www.theses.fr/1994PA112251.

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Les ndp kinases sont des enzymes ubiquitaires et sont la principale source des nucleosides triphosphates autre que l'atp. Elles catalysent le transfert du -phosphate d'un nucleoside triphosphate sur un nucleoside diphosphate avec une faible specificite de substrat et une forte activite. Le mecanisme de la reaction est dit de type ping-pong, avec la formation d'un intermediaire phosphohistidine (h122) au cours de la catalyse. En plus de leur role dans le metabolisme des nucleosides triphosphates, les ndp kinases sont impliquees dans le developpement chez la drosophile et dans les metastases de tumeurs chez l'homme. La ndp kinase de dictyostelium est un hexamere compose de six sous-unites identiques de 17 kda chacune. Grace au modele du mutant h122c, j'ai resolu les structures de l'enzyme sauvage et d'un complexe avec l'adp a respectivement 1,8 a et 2,2 a de resolution. Une sous-unite est constituee d'un domaine globulaire / avec un feuillet antiparallele a quatre brins. Sa topologie est differente de celle des autres phosphotransferases, cependant on la retrouve dans des proteines fixant des mononucleotides, de l'arn ou de l'adn. Chaque sous-unite possede un site actif. Le mode de fixation du nucleotide est different de celui observe chez les proteines fixant des nucleotides. En effet, il n'y a pas de liaisons polaires du nucleotide avec les atomes de la chaine principale et pas de sequence riche en glycines. Le manque de specificite est du a l'absence d'interaction polaire entre la base et l'enzyme. Le ribose et les phosphates font des liaisons hydrogenes avec les chaines laterales. Le monomere, le dimere et le site actif de la ndp kinase de dictyostelium sont les memes chez toutes les ndp kinases. Nous avons propose un mecanisme catalytique du transfert du phosphate sur le n de h122. Nous ne savons toujours pas si les autres fonctions des ndp kinases humaines et de drosophile dependent de leur structure quaternaire
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MEYER, PHILIPPE. "Structure et fonction de la nucleoside diphosphate kinase : interaction avec les analogues de nucleoside antiviraux." Paris 11, 2000. http://www.theses.fr/2000PA112117.

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Les ndpk sont des enzymes qui catalysent le transfert du phosphate gamma d'un nucleoside triphosphate sur un nucleoside diphosphate avec une faible specificite pour le substrat. Elles sont une source de nucleoside triphosphates et sont impliquees dans l'activation des analogues de nucleoside utilises contre le sida. L'activite antivirale de ces analogues est due a l'absence d'hydroxyle en 3 du sucre, cette particularite en fait de mauvais substrats de la ndpk. Cet hydroxyle essentiel a la catalyse forme une liaison hydrogene avec l'oxygene 07 pontant les phosphates beta et gamma. Nous avons determine la structure de trois complexes de la ndpk de dictyostelium avec des analogues de nucleotide. La premiere decrit l'interaction du mutant h122g avec le d4t triphosphate. Une liaison hydrogene c3h---o7 permet d'expliquer l'augmentation d'efficacite catalytique de la ndpk sur cet analogue par rapport a l'azt. Les deux autres structures decrivent l'interaction de la ndpk sauvage avec les nucleotides alpha-borano-phosphate qui sont de meilleurs substrats que leurs nucleotides parents. Les borano-phosphate conferent une resistance de la liaison phosphodiester a la pyrophosphorolyse, or celle-ci expliquerait la resistance du vih aux analogues actuellement utilises. La structure du complexe avec l'alpha-borano-tdp de configuration rp a permis d'expliquer la stereospecificite de la ndpk pour ce compose. La structure avec l'alpha-borano-d4t diphosphate de configuration sp explique pourquoi la ndpk n'a qu'une stereospecificite partielle sur les composes alpha-borano-phosphate derives du d4t. Pour etendre l'etude structurale aux ndpk humaines recemment decouvertes nous avons determine la structure de la ndpk mitochondriale h4. Cette structure a mis en evidence le changement conformationnel induit par la presence d'une serine en position 96 a la place d'une proline dans les autres ndpk et a permis de suggerer un role pour la serine 113 dans la reconnaissance de la guanine.
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Thomas, Simon. "Secretion of nucleoside diphosphate kinase by the parasitic nematode Trichinella Spiralis." Thesis, Imperial College London, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.405764.

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Schneider, Benoît. "Phosphorylation des analogues de nucleotides antiretroviraux par la nucleoside diphosphate kinase." Paris 6, 2001. http://www.theses.fr/2001PA066223.

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Les analogues de nucleotides administres dans les therapies antiretrovirales (ddn, azt, d4t, 3tc) sont transformes dans la cellule en triphosphate par des kinases cellulaires avant d'atteindre leur cible, la transcriptase inverse du virus vih. Cette activation implique les enzymes de la voie de recuperation des nucleotides. Le dernier phosphate est ajoute par la nucleoside diphosphate (ndp) kinase, veritable enzyme de menage, avec une specificite large pour tous les nucleotides. La reactivite de la ndp kinase avec les analogues antiretroviraux s'est averee beaucoup plus faible que supposee. A l'aide d'une methode mesurant la fluorescence intrinseque de la proteine, nous avons etudie la reactivite de l'enzyme avec differents analogues de nucleotides donneur (ntp) ou accepteur (ndp) de phosphate. Bien que l'equilibre de la reaction avec les ntp et ndp soit le meme que pour les nucleotides naturels, la vitesse de transfert de phosphate est tres diminuee (1000 a 10000 fois) pour les analogues antiviraux, substrats lents de la ndp kinase. L'affinite relative des ntp a ete mesuree directement pour un mutant inactif de l'enzyme. Tous les antiviraux se lient moins bien au site actif que leurs homologues naturels a l'exception du d4t triphosphate qui se lie a l'enzyme avec la meme affinite que la thymidine triphosphate. L'absence de 3'oh sur le ribose empeche l'etablissement d'une liaison hydrogene intramoleculaire avec l'o 7 du phosphate , cruciale pour une catalyse efficace. Seul le d4t est capable d'effectuer partiellement une interaction de ce type. C'est le meilleur antiviral phosphoryle par la ndp kinase. L'examen de la structure d'un nucleotide lie au site actif montre que l'oxygene pro-rp du phosphate du nucleotide n'interagit ni avec le mg 2 +, ni avec la proteine. En collaboration avec l'unite de chimie organique de l'institut pasteur, un groupement borano (-bh 3) a ete introduit a la place de cet oxygene. Les derives rp--bh 3 de l'azt et du d4t di- et triphosphate sont dix fois mieux phosphoryles par la ndp kinase, en raison de leur meilleure affinite pour l'enzyme. Le diastereoisomere rp est aussi un meilleur terminateur de chaine de l'activite transcriptase inverse : les nucleotides -borano sont plus efficacement incorpores dans l'adn viral. Ils sont egalement moins sensibles a l'excision (pyrophosphorolyse) par l'enzyme sauvage comme par des variants resistants de la polymerase virale. A cause du role essentiel de la fonction 3'oh du nucleotide, nous avons essaye de compenser son absence dans les analogues antiviraux en introduisant une fonction - oh dans le site actif de la ndp kinase. Plusieurs mutants ont ete crees par mutagenese dirigee : un seul mutant pour lequel l'asn 119 a ete substituee par une ser phosphoryle mieux les antiviraux avec une efficacite catalytique entre deux et dix fois superieure, due a une fixation plus aisee au site actif. L'introduction de la ser en 119 permet de restaurer le reseau de liaisons hydrogene indispensable au transfert de phosphate. En parallele, nous avons recherche de nouveaux inhibiteurs de la ndp kinase : l'adenosine 3 phosphate 5 phosphosulfate (paps) inhibe l'activite ndp kinase avec une affinite de 10 m. L'analyse des cocristaux de l'enzyme complexee avec le paps montre que l'analogue de nucleotide se lie au site actif selon un mode different du nucleotide naturel. Le paps represente ainsi l'inhibiteur de plus forte affinite connu pour cette enzyme.
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Books on the topic "Nucleoside Diphosphate Kinase (NDK)"

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Kaplan, Richard A. Affinity isolation and mechanism studies of a bovine liver nucleoside diphosphate kinase with heterologous subunits. 1986.

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Book chapters on the topic "Nucleoside Diphosphate Kinase (NDK)"

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Schomburg, Dietmar, and Dörte Stephan. "Nucleoside-diphosphate kinase." In Enzyme Handbook, 343–53. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-642-59025-2_66.

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Kimura, N. "Role of Nucleoside Diphosphate Kinase in G-Protein Action." In GTPases in Biology II, 485–98. Berlin, Heidelberg: Springer Berlin Heidelberg, 1993. http://dx.doi.org/10.1007/978-3-642-78345-6_31.

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Véron, Michel, Annemiek Tepper, Martin Hildebrandt, Ioan Lascu, Marie-Lise Lacombe, Joël Janin, Solange Moréra, Jaqueline Cherfils, Christian Dumas, and Max Chiadmi. "Nucleoside Diphosphate Kinase: an Old Enzyme with New Functions?" In Purine and Pyrimidine Metabolism in Man VIII, 607–11. Boston, MA: Springer US, 1995. http://dx.doi.org/10.1007/978-1-4615-2584-4_126.

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Postel, E. H. "NM23/Nucleoside Diphosphate Kinase as a Transcriptional Activator of c-myc." In Current Topics in Microbiology and Immunology, 233–52. Berlin, Heidelberg: Springer Berlin Heidelberg, 1996. http://dx.doi.org/10.1007/978-3-642-61109-4_11.

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Deville-Bonne, Dominique, Benoit Schneider, Julie Bourdais, and Michel Véron. "Reaction of 2′, 3′-Dideoxynucleotides Triphosphates with Recombinant Human Nucleoside Diphosphate Kinase." In Advances in Experimental Medicine and Biology, 569–73. Boston, MA: Springer US, 1998. http://dx.doi.org/10.1007/978-1-4615-5381-6_110.

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Mesnildrey, Sébastien, and Michel Véron. "Nucleoside Diphosphate Kinase: Effect of the P100S Mutation on Activity and Quaternary Structure." In Interacting Protein Domains, 213–16. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-642-60848-3_31.

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Kasahara, Masanori, Camilo Canel, E. Churchill McKinney, and Martin F. Flajnik. "Molecular Cloning of Nurse Shark cDNAs with High Sequence Similarity to Nucleoside Diphosphate Kinase Genes." In Molecular Evolution of the Major Histocompatibility Complex, 491–99. Berlin, Heidelberg: Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-84622-9_40.

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Weitzdoerfer, R., D. Stolzlechner, M. Dierssen, J. Ferreres, M. Fountoulakis, and G. Lubec. "Reduction of nucleoside diphosphate kinase B, Rab GDP- dissociation inhibitor beta and histidine triad nucleotide-binding protein in fetal Down Syndrome brain." In Protein Expression in Down Syndrome Brain, 347–59. Vienna: Springer Vienna, 2001. http://dx.doi.org/10.1007/978-3-7091-6262-0_29.

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"Nucleoside Diphosphate Kinase." In Encyclopedia of Genetics, Genomics, Proteomics and Informatics, 1375. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6754-9_11664.

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Lutz, Susanne, Hans-Jörg Hippe, Feraydoon Niroomand, and Thomas Wieland. "Nucleoside Diphosphate Kinase–Mediated Activation of Heterotrimeric G Proteins." In Methods in Enzymology, 403–18. Elsevier, 2004. http://dx.doi.org/10.1016/s0076-6879(04)90025-0.

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Conference papers on the topic "Nucleoside Diphosphate Kinase (NDK)"

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Jarrett, Stuart G., Marian Novak, Nathan Harris, Isabel Mellon, Andrezj Slominski, Sandrine Arnaud-Dabernat, Jean-Yves Daniel, and David M. Kaetzel. "Abstract 1445: The metastasis suppressor NM23-H1 promotes genomic stability through its 3’-5’ exonuclease and nucleoside diphosphate kinase activities following UV irradiation." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-1445.

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Gonzalez, Caleb, Kelly Flentie, Brandon Kocher, Jayne Jayne Marasa, and David Piwnica-Worms. "Abstract 4880: A high-throughput siRNA screen identifies Nucleoside Diphosphate Kinase (NME3) as a novel host regulator of NF-êB signaling in response toSalmonella-induced activation of TLR-5." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-4880.

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