Journal articles: '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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Kim, Yong-Jae, Jung-Hoon Lee, Yeji Lee, Jingyue Jia, Se-Hwan Paek, Hyong-Bai Kim, Shouguang Jin, and Un-Hwan Ha. "Nucleoside Diphosphate Kinase and Flagellin from Pseudomonas aeruginosa Induce Interleukin 1 Expression via the Akt/NF-κB Signaling Pathways." Infection and Immunity 82, no. 8 (May 27, 2014): 3252–60. http://dx.doi.org/10.1128/iai.02007-14.

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ABSTRACTInflammatory responses are a first line of host defense against a range of invading pathogens, consisting of the release of proinflammatory cytokines followed by attraction of polymorphonuclear neutrophils (PMNs) to the site of inflammation. Among the many virulence factors that contribute to the pathogenesis of infections, nucleoside diphosphate kinase (Ndk) mediates bacterially induced toxicity against eukaryotic cells. However, no study has examined how Ndk affects inflammatory responses. The present study examined the mechanisms by whichPseudomonas aeruginosaactivates inflammatory responses upon infection of cells. The results showed that bacterial Ndk, with the aid of an additional bacterial factor, flagellin, induced expression of the proinflammatory cytokines interleukin-1α (IL-1α) and IL-1β. Cytokine induction appeared to be dependent on the kinase activity of Ndk and was mediated via the NF-κB signaling pathway. Notably, Ndk activated the Akt signaling pathway, which acts upstream of NF-κB, as well as caspase-1, which is a key component of inflammasome. Thus, this study demonstrated thatP. aeruginosa, through the combined effects of Ndk and flagellin, upregulates the expression of proinflammatory cytokines via the Akt/NF-κB signaling pathways.

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Patel-King, Ramila S., Oksana Gorbatyuk, Sachiko Takebe, and Stephen M. King. "Flagellar Radial Spokes Contain a Ca2+-stimulated Nucleoside Diphosphate Kinase." Molecular Biology of the Cell 15, no. 8 (August 2004): 3891–902. http://dx.doi.org/10.1091/mbc.e04-04-0352.

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The radial spokes are required for Ca2+-initiated intraflagellar signaling, resulting in modulation of inner and outer arm dynein activity. However, the mechanochemical properties of this signaling pathway remain unknown. Here, we describe a novel nucleoside diphosphate kinase (NDK) from the Chlamydomonas flagellum. This protein (termed p61 or RSP23) consists of an N-terminal catalytic NDK domain followed by a repetitive region that includes three IQ motifs and a highly acidic C-terminal segment. We find that p61 is missing in axonemes derived from the mutants pf14 (lacks radial spokes) and pf24 (lacks the spoke head and several stalk components) but not in those from pf17 (lacking only the spoke head). The p61 protein can be extracted from oda1 (lacks outer dynein arms) and pf17 axonemes with 0.5 M KI, and copurifies with radial spokes in sucrose density gradients. Furthermore, p61 contains two classes of calmodulin binding site: IQ1 interacts with calmodulin-Sepharose beads in a Ca2+-independent manner, whereas IQ2 and IQ3 show Ca2+-sensitive associations. Wild-type axonemes exhibit two distinct NDKase activities, at least one of which is stimulated by Ca2+. This Ca2+-responsive enzyme, which accounts for ∼45% of total axonemal NDKase, is missing from pf14 axonemes. We found that purified radial spokes also exhibit NDKase activity. Thus, we conclude that p61 is an integral component of the radial spoke stalk that binds calmodulin and exhibits Ca2+-controlled NDKase activity. These observations suggest that nucleotides other than ATP may play an important role in the signal transduction pathway that underlies the regulatory mechanism defined by the radial spokes.

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Perina, Dragutin, Marina Korolija, Andreja Mikoč, Mirna Halasz, Maja Herak Bosnar, and Helena Ćetković. "Characterization of Nme5-Like Gene/Protein from the Red Alga Chondrus Crispus." Marine Drugs 18, no. 1 (December 21, 2019): 13. http://dx.doi.org/10.3390/md18010013.

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The Nme gene/protein family of nucleoside diphosphate kinases (NDPK) was originally named after its member Nm23-H1/Nme1, the first identified metastasis suppressor. Human Nme proteins are divided in two groups. They all possess nucleoside diphosphate kinase domain (NDK). Group I (Nme1-Nme4) display a single type NDK domain, whereas Group II (Nme5-Nme9) display a single or several different NDK domains, associated or not associated with extra-domains. Data strongly suggest that, unlike Group I, none of the members of Group II display measurable NDPK activity, although some of them autophosphorylate. The multimeric form is required for the NDPK activity. Group I proteins are known to multimerize, while there are no data on the multimerization of Group II proteins. The Group II ancestral type protein was shown to be conserved in several species from three eukaryotic supergroups. Here, we analysed the Nme protein from an early branching eukaryotic lineage, the red alga Chondrus crispus. We show that the ancestral type protein, unlike its human homologue, was fully functional multimeric NDPK with high affinity to various types of DNA and dispersed localization throughout the eukaryotic cell. Its overexpression inhibits both cell proliferation and the anchorage-independent growth of cells in soft agar but fails to deregulate cell apoptosis. We conclude that the ancestral gene has changed during eukaryotic evolution, possibly in correlation with the protein function.

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Neeld, Dennis, Yongxin Jin, Candace Bichsel, Jinghua Jia, Jianhui Guo, Fang Bai, Weihui Wu, Un-Hwan Ha, Naohiro Terada, and Shouguang Jin. "Pseudomonas aeruginosa injects NDK into host cells through a type III secretion system." Microbiology 160, no. 7 (July 1, 2014): 1417–26. http://dx.doi.org/10.1099/mic.0.078139-0.

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Pseudomonas aeruginosa is a Gram-negative opportunistic human pathogen possessing a type III secretion system (T3SS) which injects toxic effector proteins into mammalian host cells. In previous studies, P. aeruginosa strains lacking all of the known type III effectors were shown to cause cytotoxicity upon prolonged infection time. In this study, we report the identification of a new cytotoxin, nucleoside diphosphate kinase (NDK), which is injected into eukaryotic cells in a T3SS-dependent manner. Injection of NDK is inhibited by the presence of previously known effectors of the T3SS, with an effectorless strain injecting the highest amount, suggesting active competition with the known T3SS effectors. NDK is shown to cause a cytotoxic response when expressed in eukaryotic cells, and P. aeruginosa strains harbouring NDK also show a greater toxicity than strains lacking it. Interestingly, the cytotoxic effect of intracellular NDK is independent of its kinase activity. In previous studies, NDK was shown to be secreted into culture supernatants via a type I secretion system and cause cytotoxicity in a kinase-dependent manner. Therefore, the current study highlights an alternative route of NDK secretion as well as two different cytotoxic mechanisms of NDK, depending on the extra- or intra-cellular location of the protein.

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Araújo, Joabe Lima, Gardênia Taveira Santos, Lucas Aires de Sousa, Gabel Taveira Santos, Welson de Freitas Silva, Alice de Oliveira Sousa, and Jefferson Almeida Rocha. "Molecular docking of rutenum complex with epiisopyloturin and nitric oxide against nucleoside diphosphate kinase protein Leishmania." Research, Society and Development 9, no. 2 (January 1, 2020): e59922121. http://dx.doi.org/10.33448/rsd-v9i2.2121.

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Leishmaniasis is an infectious disease that affects both animals and humans, caused by flagellated parasites belonging to the genus Leishmania may present in different clinical forms depending on the infecting strain and the immune reaction of the host. The disease is estimated to reach about 700,000 to 1 million people, causing the deaths of 20 to 30,000 individuals annually. Thus, the present study aims to perform a molecular coupling simulation of the ruthenium complex with epiisopiloturin and nitric oxide against the protein Nucleoside diphosphate kinase from Leishmania amazonensis. The NDK 3D molecule was extracted from the PDB nucleic proteins and acids database. The 3D molecular structure of the Epiruno2 complex was designed using gaussview 5.0 software. The NDK target and Epiruno2 complex were prepared for docking simulations, where NDK was considered rigid and Epiruno2 was considered flexible. The Epiruno2 complex presented a good molecular affinity rate with the target protein, making it attractive for experimental trials in laboratories for Leishmania's NDK protein and NDKs of other pathogens, however, the drug miltefosin presented low molecular affinity for the same target, corroborating studies presented in the literature on the reduced efficacy of current drugs against leishmaniosis.

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Adam, Kevin, Jia Ning, Jeffrey Reina, and Tony Hunter. "NME/NM23/NDPK and Histidine Phosphorylation." International Journal of Molecular Sciences 21, no. 16 (August 14, 2020): 5848. http://dx.doi.org/10.3390/ijms21165848.

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The NME (Non-metastatic) family members, also known as NDPKs (nucleoside diphosphate kinases), were originally identified and studied for their nucleoside diphosphate kinase activities. This family of kinases is extremely well conserved through evolution, being found in prokaryotes and eukaryotes, but also diverges enough to create a range of complexity, with homologous members having distinct functions in cells. In addition to nucleoside diphosphate kinase activity, some family members are reported to possess protein-histidine kinase activity, which, because of the lability of phosphohistidine, has been difficult to study due to the experimental challenges and lack of molecular tools. However, over the past few years, new methods to investigate this unstable modification and histidine kinase activity have been reported and scientific interest in this area is growing rapidly. This review presents a global overview of our current knowledge of the NME family and histidine phosphorylation, highlighting the underappreciated protein-histidine kinase activity of NME family members, specifically in human cells. In parallel, information about the structural and functional aspects of the NME family, and the knowns and unknowns of histidine kinase involvement in cell signaling are summarized.

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Weiss, Bernard. "The Deoxycytidine Pathway for Thymidylate Synthesis in Escherichia coli." Journal of Bacteriology 189, no. 21 (September 7, 2007): 7922–26. http://dx.doi.org/10.1128/jb.00461-07.

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ABSTRACT When thymidylate production is diminished by a mutation affecting dCTP deaminase, Escherichia coli is known to use an alternate pathway involving deoxycytidine as an intermediate. The pathway requires the gene for any of three nucleoside diphosphate kinases (ndk, pykA, or pykF) and the gene for a 5′-nucleotidase (yfbR).

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Jeudy, Sandra, Bruno Coutard, Régine Lebrun, and Chantal Abergel. "Acanthamoeba polyphagamimivirus NDK: preliminary crystallographic analysis of the first viral nucleoside diphosphate kinase." Acta Crystallographica Section F Structural Biology and Crystallization Communications 61, no. 6 (June 1, 2005): 569–72. http://dx.doi.org/10.1107/s1744309105013904.

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Yu, Hua, Xiancai Rao, and Kebin Zhang. "Nucleoside diphosphate kinase (Ndk): A pleiotropic effector manipulating bacterial virulence and adaptive responses." Microbiological Research 205 (December 2017): 125–34. http://dx.doi.org/10.1016/j.micres.2017.09.001.

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Kapatral, Vinayak, Xiaowen Bina, and A. M. Chakrabarty. "Succinyl Coenzyme A Synthetase of Pseudomonas aeruginosa with a Broad Specificity for Nucleoside Triphosphate (NTP) Synthesis Modulates Specificity for NTP Synthesis by the 12-Kilodalton Form of Nucleoside Diphosphate Kinase." Journal of Bacteriology 182, no. 5 (March 1, 2000): 1333–39. http://dx.doi.org/10.1128/jb.182.5.1333-1339.2000.

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ABSTRACT Pseudomonas aeruginosa secretes copious amounts of an exopolysaccharide called alginate during infection in the lungs of cystic fibrosis patients. A mutation in the algR2 gene of mucoid P. aeruginosa is known to exhibit a nonmucoid (nonalginate-producing) phenotype and showed reduced activities of succinyl-coenzyme A (CoA) synthetase (Scs) and nucleoside diphosphate kinase (Ndk), implying coregulation of Ndk and Scs in alginate synthesis. We have cloned and characterized the sucCDoperon encoding the α and β subunits of Scs from P. aeruginosa and have studied the role of Scs in generating GTP, an important precursor in alginate synthesis. We demonstrate that, in the presence of GDP, Scs synthesizes GTP using ATP as the phosphodonor and, in the presence of ADP, Scs synthesizes ATP using GTP as a phosphodonor. In the presence of inorganic orthophosphate, succinyl-CoA, and an equimolar amount of ADP and GDP, Scs synthesizes essentially an equimolar amount of ATP and GTP. Such a mechanism of GTP synthesis can be an alternate source for the synthesis of alginate as well as for the synthesis of other macromolecules requiring GTP such as RNA and protein. Scs from P. aeruginosa is also shown to exhibit a broad NDP kinase activity. In the presence of inorganic orthophosphate (Pi), succinyl-CoA, and either GDP, ADP, UDP or CDP, it synthesizes GTP, ATP, UTP, or CTP. Scs was previously shown to copurify with Ndk, presumably as a complex. In mucoid cells ofP. aeruginosa, Ndk is also known to exist in two forms, a 16-kDa cytoplasmic form predominant in the log phase and a 12-kDa membrane-associated form predominant in the stationary phase. We have observed that the 16-kDa Ndk-Scs complex present in nonmucoid cells, synthesizes all three of the nucleoside triphosphates from a mixture of GDP, UDP, and CDP, whereas the 12-kDa Ndk-Scs complex specifically present in mucoid cell predominantly synthesizes GTP and UTP but not CTP. Such regulation may promote GTP synthesis in the stationary phase when the bulk of alginate is synthesized by mucoid P. aeruginosa.

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Dumais, Mitchell, Douglas R. Davies, Tao Lin, Bart L. Staker, Peter J. Myler, and Wesley C. Van Voorhis. "Structure and analysis of nucleoside diphosphate kinase fromBorrelia burgdorferiprepared in a transition-state complex with ADP and vanadate moieties." Acta Crystallographica Section F Structural Biology Communications 74, no. 6 (May 31, 2018): 373–84. http://dx.doi.org/10.1107/s2053230x18007392.

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Nucleoside diphosphate kinases (NDKs) are implicated in a wide variety of cellular functions owing to their enzymatic conversion of NDP to NTP. NDK fromBorrelia burgdorferi(BbNDK) was selected for functional and structural analysis to determine whether its activity is required for infection and to assess its potential for therapeutic inhibition. The Seattle Structural Genomics Center for Infectious Diseases (SSGCID) expressed recombinantBbNDK protein. The protein was crystallized and structures were solved of both the apoenzyme and a liganded form with ADP and vanadate ligands. This provided two structures and allowed the elucidation of changes between the apo and ligand-bound enzymes. Infectivity studies withndktransposon mutants demonstrated that NDK function was important for establishing a robust infection in mice, and provided a rationale for therapeutic targeting ofBbNDK. The protein structure was compared with other NDK structures found in the Protein Data Bank and was found to have similar primary, secondary, tertiary and quaternary structures, with conserved residues acting as the catalytic pocket, primarily using His132 as the phosphohistidine-transfer residue. Vanadate and ADP complexes model the transition state of this phosphoryl-transfer reaction, demonstrating that the pocket closes when bound to ADP, while allowing the addition or removal of a γ-phosphate. This analysis provides a framework for the design of potential therapeutics targetingBbNDK inhibition.

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Farkas, Zsolt, Metka Petric, Xianghua Liu, Floriane Herit, Éva Rajnavölgyi, Zsuzsa Szondy, Zsófia Budai, et al. "The nucleoside diphosphate kinase NDK‐1/NME1 promotes phagocytosis in concert with DYN‐1/Dynamin." FASEB Journal 33, no. 10 (July 17, 2019): 11606–14. http://dx.doi.org/10.1096/fj.201900220r.

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Wang, Zhuhong, Jun-Qing Ge, Hang Chen, Xiaoyan Cheng, Yiqun Yang, Jun Li, R. Jeff Whitworth, and Ming-Shun Chen. "An insect nucleoside diphosphate kinase (NDK) functions as an effector protein in wheat - Hessian fly interactions." Insect Biochemistry and Molecular Biology 100 (September 2018): 30–38. http://dx.doi.org/10.1016/j.ibmb.2018.06.003.

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Zaborina, Olga, Namita Misra, Jan Kostal, Shilpa Kamath, Vinayak Kapatral, M. El-Azami El-Idrissi, B. S. Prabhakar, and A. M. Chakrabarty. "P2Z-Independent and P2Z Receptor-Mediated Macrophage Killing by Pseudomonas aeruginosa Isolated from Cystic Fibrosis Patients." Infection and Immunity 67, no. 10 (October 1, 1999): 5231–42. http://dx.doi.org/10.1128/iai.67.10.5231-5242.1999.

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ABSTRACT We demonstrate that a mucoid, alginate-producing strain ofPseudomonas aeruginosa isolated from the lungs of a cystic fibrosis (CF) patient secretes multiple enzymes with nucleoside diphosphate kinase (Ndk), ATPase, adenylate kinase, 5′-nucleotidase, and ATP-modifying enzymatic activities. The secretion is triggered at high cell density and in complex media but is greatly reduced when the mucoid cells are grown in mineral salts media or in presence of 5.0 mM Ca2+ or Mg2+. Interestingly, the secretion is triggered primarily in the mucoid CF isolate of strain 8821M (or in strain FRD1) but not in a nonmucoid laboratory strain, PAO1. The purified secreted Ndk shows 100% match in its N-terminal amino acid sequence with that of purified intracellular Ndk and demonstrates similar enzymatic properties. The N-terminal sequence of the purified ATPase isolated from an ndk knockout mutant shows its identity with that of the heat shock chaperonin Hsp60. During fractionation, the flowthrough fraction from a Mono Q column demonstrates the presence of 5′-nucleotidase, adenylate kinase, and a putative ATP reductase activity. These fractions demonstrate high cytotoxic activities for murine peritoneal primary macrophages which can be further stimulated in the presence of ATP or inhibited by pretreatment of macrophages with oxidized ATP (oATP). The cytotoxicity associated with ATP-induced stimulation is believed to be due to activation of macrophage surface-associated P2Z (P2X7) receptors, which are one of the purinergic receptors responsible for pore formation on macrophage membrane. Blocking of these receptors by pretreatment with oATP blocks ATP-induced macrophage cell death. Thus mucoid P. aeruginosa cells elaborate enzymes that modulate the external ATP levels of macrophages, thereby modulating macrophage cell death through P2Z receptor activation. Evidence for the presence of secreted cytotoxic agents that act independently of P2Z receptor activation is also presented.

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Thomas, Reena Rosy, M. K. Chandra Prakash, M. Krishna Reddy, Sukhada Mohandas, and Riaz Mahmood. "Microsatellite Identification in Solanaceae Crops Associated with Nucleoside Diphosphate Kinase (NDK) Specific to Abiotic Stress Tolerance through in silico Analysis." Journal of Horticultural Sciences 8, no. 2 (December 31, 2013): 195–98. http://dx.doi.org/10.24154/jhs.v8i2.300.

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Abiotic stress often causes a series of morphological, physiological, biochemical and molecular changes that affect plant growth, development and productivity. To cope with abiotic stresses, it is necessary to understand plant responses to stresses that disturb homeostatic equilibrium at the cellular and molecular level. Genomic information on Capsicum annuum has been explored to identify microsatellite markers associated with abiotic stress tolerance and assign them to cognate functional groups related to specific stress responses. Several in silico methods have been used to identify simple sequence repeats associated with stress responsive gene candidates in Capsicum annuum. In this study, a microsatellite marker has been identified in Capsicum annuum associated with Nucleoside Diphosphate Kinase (NDK) having multiple environmental stress tolerance (oxidative, high temperature and salt stress) and which is also highly conserved in crops of Solanaceae. These are house-keeping enzymes that maintain intracellular levels of all nucleoside triphosphates (NTP) with the exception of adenosine triphosphate (ATP). These are also involved in phytochrome A response, UV-B signaling, auxin responses and oxidative stress signaling.

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Lima, Juliana Maria, Plínio Salmazo Vieira, Arthur Henrique Cavalcante de Oliveira, and Carmen Lúcia Cardoso. "Label-free offline versus online activity methods for nucleoside diphosphate kinase b using high performance liquid chromatography." Analyst 141, no. 15 (2016): 4733–41. http://dx.doi.org/10.1039/c6an00655h.

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Label-free methodologies for nucleoside diphosphate kinase fromLeishmaniaspp. (LmNDKb): anofflineLC-UV assay for solubleLmNDKb and anonlinetwo-dimensional LC-UV system based on immobilizedLmNDKb to help screenLmNDKb ligands and measure NDKb activity.

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Burger, Annette, Birgit Brandt, Urs SÃ¼sstrunk, Charles J. Thompson, and Wolfgang Wohlleben. "Analysis of aStreptomyces coelicolorA3(2) locus containing the nucleoside diphosphate kinase (ndk) and folylpolyglutamate synthetase (folC) genes." FEMS Microbiology Letters 159, no. 2 (February 1998): 283–91. http://dx.doi.org/10.1111/j.1574-6968.1998.tb12873.x.

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Lee, Bumkyu, Yusuke Yoshida, and Kohji Hasunuma. "Photomorphogenetic characteristics are severely affected in nucleoside diphosphate kinase-1 (ndk-1)-disrupted mutants in Neurospora crassa." Molecular Genetics and Genomics 275, no. 1 (November 24, 2005): 9–17. http://dx.doi.org/10.1007/s00438-005-0044-1.

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Rikhy, Richa, Mani Ramaswami, and K. S. Krishnan. "A Temperature-Sensitive Allele of Drosophila sesB Reveals Acute Functions for the Mitochondrial Adenine Nucleotide Translocase in Synaptic Transmission and Dynamin Regulation." Genetics 165, no. 3 (November 1, 2003): 1243–53. http://dx.doi.org/10.1093/genetics/165.3.1243.

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Abstract Rapidly reversible, temperature-sensitive (ts) paralytic mutants of Drosophila have been useful in delineating immediate in vivo functions of molecules involved in synaptic transmission. Here we report isolation and characterization of orangi (org), an enhancer of shibire (shi), a ts paralytic mutant in Drosophila dynamin. org is an allele of the stress sensitive B (sesB) locus that encodes a mitochondrial adenine nucleotide translocase (ANT) and results in a unique ts paralytic behavior that is accompanied by a complete loss of synaptic transmission in the visual system. sesBorg reduces the restrictive temperature for all shits alleles tested except for shits1. This characteristic allele-specific interaction of sesBorg with shi is shared by abnormal wing discs (awd), a gene encoding nucleoside diphosphate kinase (NDK). sesBorg shows independent synergistic interactions, an observation that is consistent with a shared pathway by which org and awd influence shi function. Genetic and electrophysiological analyses presented here, together with the observation that the sesBorg mutation reduces biochemically assayed ANT activity, suggest a model in which a continuous mitochondrial ANT-dependent supply of ATP is required to sustain NDK-dependent activation of presynaptic dynamin during a normal range of synaptic activity.

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Hama, H., C. Lerner, S. Inouye, and M. Inouye. "Location of the gene (ndk) for nucleoside diphosphate kinase on the physical map of the Escherichia coli chromosome." Journal of Bacteriology 173, no. 11 (1991): 3276. http://dx.doi.org/10.1128/jb.173.11.3276-.1991.

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Hama, H., C. Lerner, S. Inouye, and M. Inouye. "Location of the gene (ndk) for nucleoside diphosphate kinase on the physical map of the Escherichia coli chromosome.:." Journal of Bacteriology 173, no. 11 (June 1991): 3276. http://dx.doi.org/10.1128/jb.173.11.3276.1991.

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Willems, Roel, Herman Slegers, Inez Rodrigus, Adriaan C. Moulijn, Marc Lenjou, Griet Nijs, Zwi N. Berneman, and Dirk R. Van Bockstaele. "Extracellular nucleoside diphosphate kinase NM23/NDPK modulates normal hematopoietic differentiation." Experimental Hematology 30, no. 7 (July 2002): 640–48. http://dx.doi.org/10.1016/s0301-472x(02)00809-3.

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Anciaux, Katelijne, Kristof Van Dommelen, Roel Willems, Dirk Roymans, and Herman Slegers. "Inhibition of nucleoside diphosphate kinase (NDPK/nm23) by cAMP analogues." FEBS Letters 400, no. 1 (January 2, 1997): 75–79. http://dx.doi.org/10.1016/s0014-5793(96)01358-0.

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Zhang, Lei, Mingfang Song, Nuo Yang, XiuWen Zhang, Sayed Haidar Abbas Raza, Kaixiang Jia, Jiaxin Tian, et al. "Nucleoside Diphosphate Kinases (ndk) reveals a key role in adhesion and virulence of Aeromonas veronii." Microbial Pathogenesis 149 (December 2020): 104577. http://dx.doi.org/10.1016/j.micpath.2020.104577.

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Willems, Roel, Dirk R. Van Bockstaele, Filip Lardon, Marc Lenjou, Griet Nijs, Hans-Willem Snoeck, Zwi N. Berneman, and Herman Slegers. "Decrease in Nucleoside Diphosphate Kinase (NDPK/nm23) Expression during Hematopoietic Maturation." Journal of Biological Chemistry 273, no. 22 (May 29, 1998): 13663–68. http://dx.doi.org/10.1074/jbc.273.22.13663.

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Baughman, Cassandra, Jeanne Morin-Leisk, and Tina Lee. "Nucleoside Diphosphate Kinase B (NDKB) scaffolds endoplasmic reticulum membranes in vitro." Experimental Cell Research 314, no. 14 (August 2008): 2702–14. http://dx.doi.org/10.1016/j.yexcr.2008.06.005.

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Morin-Leisk, Jeanne, and Tina H. Lee. "Nucleotide-dependent self-assembly of Nucleoside Diphosphate Kinase (NDPK) in vitro." Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1784, no. 12 (December 2008): 2045–51. http://dx.doi.org/10.1016/j.bbapap.2008.07.011.

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38

Snider, Natasha T., Peter J. Altshuler, and M. Bishr Omary. "Modulation of cytoskeletal dynamics by mammalian nucleoside diphosphate kinase (NDPK) proteins." Naunyn-Schmiedeberg's Archives of Pharmacology 388, no. 2 (September 20, 2014): 189–97. http://dx.doi.org/10.1007/s00210-014-1046-5.

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Punj, Vasu, Olga Zaborina, Neelam Dhiman, Kim Falzari, M. Bagdasarian, and A. M. Chakrabarty. "Phagocytic Cell Killing Mediated by Secreted Cytotoxic Factors of Vibrio cholerae." Infection and Immunity 68, no. 9 (September 1, 2000): 4930–37. http://dx.doi.org/10.1128/iai.68.9.4930-4937.2000.

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ABSTRACT Vibrio cholerae strain VB1 secretes a number of enzymes into the outside medium that utilize ATP as a substrate. Such enzymes are found in the outside medium during the mid-log phase of growth, when the optical density at 650 nm is about 0.4, and they demonstrate nucleoside diphosphate kinase (Ndk), 5′ nucleotidase, and adenylate kinase (Ak) activities. We report that the filtered growth medium ofV. cholerae, as well as the flowthrough fraction of a green Sepharose column during fractionation of the growth medium, had very little cytotoxicity by itself towards macrophages and mast cells but exhibited significant cytotoxicity in the presence of exogenous ATP. Such fractions, harboring 5′ nucleotidase, Ndk, and presumably other ATP-utilizing enzymes, demonstrated enhanced macrophage and mast cell death; periodate-oxidized-ATP (oATP)-treated macrophage and mast cells or such cells exposed to 0.1 mM Mg2+, where surface-associated P2Z receptors could not be activated, were not susceptible to subsequent ATP addition. Microscopic visualization of mast cells clearly demonstrated cell morphological changes such as swelling, vacuolization, and nuclear fragmentation following treatment with ATP and the growth medium of V. cholerae; however, these effects were suppressed if the mast cells were pretreated with oATP. These results strongly imply that the secreted ATP-utilizing enzymes of V. cholerae modulate the external ATP levels of the macrophage and mast cells, leading to their accelerated death, presumably through activation of P2Z receptors. Thus, development of inhibitors for such enzymes may reduce the level of V. cholerae infection; alternatively, mutations in such genes may eliminate V. cholerae survival in the gut and contribute to a safer live vaccine.

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Crawford, Russell M., Kate J. Treharne, Sandrine Arnaud-Dabernat, Jean-Yves Daniel, Marc Foretz, Benoit Viollet, and Anil Mehta. "Understanding the Molecular Basis of the Interaction between NDPK-A and AMPK α1." Molecular and Cellular Biology 26, no. 15 (August 1, 2006): 5921–31. http://dx.doi.org/10.1128/mcb.00315-06.

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ABSTRACT Nucleoside diphosphate kinase (NDPK) (nm23/awd) belongs to a multifunctional family of highly conserved proteins (∼16 to 20 kDa) including two well-characterized isoforms (NDPK-A and -B). NDPK catalyzes the conversion of nucleoside diphosphates to nucleoside triphosphates, regulates a diverse array of cellular events, and can act as a protein histidine kinase. AMP-activated protein kinase (AMPK) is a heterotrimeric protein complex that responds to the cellular energy status by switching off ATP-consuming pathways and switching on ATP-generating pathways when ATP is limiting. AMPK was first discovered as an activity that inhibited preparations of acetyl coenzyme A carboxylase 1 (ACC1), a regulator of cellular fatty acid synthesis. We recently reported that NDPK-A (but not NDPK-B) selectively regulates the α1 isoform of AMPK independently of the AMP concentration such that the manipulation of NDPK-A nucleotide trans-phosphorylation activity to generate ATP enhanced the activity of AMPK. This regulation occurred irrespective of the surrounding ATP concentration, suggesting that “substrate channeling” was occurring with the shielding of NDPK-generated ATP from the surrounding medium. We speculated that AMPK α1 phosphorylated NDPK-A during their interaction, and here, we identify two residues on NDPK-A targeted by AMPK α1 in vivo. We find that NDPK-A S122 and S144 are phosphorylated by AMPK α1 and that the phosphorylation status of S122, but not S144, determines whether substrate channeling can occur. We report the cellular effects of the S122 mutation on ACC1 phosphorylation and demonstrate that the presence of E124 (absent in NDPK-B) is necessary and sufficient to permit both AMPK α1 binding and substrate channeling.

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Ambrosi, Cecilia, Federica Tiburzi, Francesco Imperi, Lorenza Putignani, and Paolo Visca. "Involvement of AlgQ in Transcriptional Regulation of Pyoverdine Genes in Pseudomonas aeruginosa PAO1." Journal of Bacteriology 187, no. 15 (August 1, 2005): 5097–107. http://dx.doi.org/10.1128/jb.187.15.5097-5107.2005.

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ABSTRACT In response to iron limitation, Pseudomonas aeruginosa produces the fluorescent siderophore pyoverdine. Transcription of pyoverdine biosynthetic (pvd) genes is driven by the iron starvation sigma factor PvdS, which is negatively regulated by the Fur-Fe(II) holorepressor. We studied the effect of AlgQ, the Escherichia coli Rsd orthologue, on pyoverdine production by P. aeruginosa PAO1. AlgQ is a global regulatory protein which activates alginate, ppGpp, and inorganic polyphosphate synthesis through a cascade involving nucleoside diphosphate kinase (Ndk). AlgQ is also capable of interacting with region 4 of RpoD. In a reconstituted E. coli system, PvdS-dependent transcription from the pvdA promoter was doubled by the multicopy algQ gene. The P. aeruginosa ΔalgQ mutant exhibited a moderate but reproducible reduction in pyoverdine production compared with wild-type PAO1, as a result of a decline in transcription of pvd genes. PvdS expression was not affected by the algQ mutation. Single-copy algQ fully restored pyoverdine production and expression of pvd genes in the ΔalgQ mutant, while ndk did not. An increased intracellular concentration of RpoD mimicked the ΔalgQ phenotype, whereas PvdS overexpression suppressed the algQ mutation. E. coli rsd could partially substitute for algQ in transcriptional modulation of pvd genes. We propose that AlgQ acts as an anti-sigma factor for RpoD, eliciting core RNA polymerase recruitment by PvdS and transcription initiation at pvd promoters. AlgQ provides a link between the pyoverdine and alginate regulatory networks. These systems have similarities in responsiveness and physiological function: both depend on alternative sigma factors, respond to nutrient starvation, and act as virulence determinants for P. aeruginosa.

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Yano, Akira, Masaaki Umeda, and Hirofumi Uchimiya. "Expression of functional proteins of cDNA encoding rice nucleoside diphosphate kinase (NDK) in Escherichia coli and organ-related alteration of NDK activities during rice seed germination (Oryza sativa L.)." Plant Molecular Biology 27, no. 5 (March 1995): 1053–58. http://dx.doi.org/10.1007/bf00037032.

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Qiyun, Zhou, Xie Zongming, Zhang Zhigang, Cao Yangrong, Zhang Jinsong, and Chen Shouyi. "Cloning, expression and characterization of a nucleoside diphosphate kinase (NDPK) gene from tobacco." Progress in Natural Science 17, no. 8 (August 1, 2007): 906–12. http://dx.doi.org/10.1080/10002007088537490.

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Allard, Laure, Pierre R. Burkhard, Pierre Lescuyer, Jennifer A. Burgess, Nadia Walter, Denis F. Hochstrasser, and Jean-Charles Sanchez. "PARK7 and Nucleoside Diphosphate Kinase A as Plasma Markers for the Early Diagnosis of Stroke." Clinical Chemistry 51, no. 11 (November 1, 2005): 2043–51. http://dx.doi.org/10.1373/clinchem.2005.053942.

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Abstract Background: Plasma markers for stroke could be useful in diagnosis and prognosis and in prediction of response of stroke patients to therapy. PARK7 and nucleoside diphosphate kinase A (NDKA) are increased in human postmortem cerebrospinal fluid (CSF), a model of global brain insult, suggesting that measurement in CSF and, more importantly, in plasma may be useful as a biomarker of stroke. Methods: We used ELISA to measure PARK7 and NDKA in plasma in 3 independent European and North American retrospective studies encompassing a total of 622 stroke patients and 165 control individuals. Results: Increases in both biomarkers were highly significant, with sensitivities of 54%–91% for PARK7 and 70%–90% for NDKA and specificities of 80%–97% for PARK7 and 90%–97% for NDKA. The concentrations of both biomarkers increased within 3 h of stroke onset. Conclusions: PARK7 and NDKA may be useful plasma biomarkers for the early diagnosis of stroke. In addition, this study demonstrated the utility of analysis of postmortem CSF proteins as a first step in the discovery of plasma markers of ischemic brain injury.

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Mishra, Arjun K., Nidhi Singh, Pragati Agnihotri, Shikha Mishra, Saurabh P. Singh, Bala K. Kolli, Kwang Poo Chang, Amogh A. Sahasrabuddhe, M. I. Siddiqi, and J. Venkatesh Pratap. "Discovery of novel inhibitors for Leishmania nucleoside diphosphatase kinase (NDK) based on its structural and functional characterization." Journal of Computer-Aided Molecular Design 31, no. 6 (May 27, 2017): 547–62. http://dx.doi.org/10.1007/s10822-017-0022-9.

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Shah, Syed Ali Raza, Hazir Rahman, Muhammad Qasim, Muhammad Safwan Akram, Yasemin Saygideger, Nanda Puspita, Burcu Saygıdeğer Demir, et al. "Differential Proteomics of Helicobacter pylori Isolates from Gastritis, Ulcer, and Cancer Patients: First Study from Northwest Pakistan." Medicina 58, no. 9 (August 28, 2022): 1168. http://dx.doi.org/10.3390/medicina58091168.

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Background and Objective: Helicobacter pylori is a human-stomach-dwelling organism that causes many gastric illnesses, including gastritis, ulcer, and gastric cancer. The purpose of the study was to perform differential proteomic analysis on H. pylori isolates from gastritis, ulcer, and gastric cancer patients. Materials and Methods: H. pylori was isolated from antrum and fundus biopsies obtained from patients who visited the Department of Gastroenterology. Using nano-LC-QTOF MS/MS analysis, differentially regulated proteins were identified through proteome profiling of pooled samples of H. pylori isolated from gastritis, ulcer, and gastric cancer patients. Antigenic scores and cellular localization of proteins were determined using additional prediction tools. Results: A total of 14 significantly regulated proteins were identified in H. pylori isolated from patients with either gastritis, ulcer, or gastric cancer. Comparative analysis of groups revealed that in the case of cancer vs. gastritis, six proteins were overexpressed, out of which two proteins, including hydrogenase maturation factor (hypA) and nucleoside diphosphate kinase (ndk) involved in bacterial colonization, were only upregulated in isolates from cancer patients. Similarly, in cancer vs. ulcer, a total of nine proteins were expressed. Sec-independent protein translocase protein (tatB), involved in protein translocation, and pseudaminic acid synthase I (pseI), involved in the synthesis of functional flagella, were upregulated in cancer, while hypA and ndk were downregulated. In ulcer vs. gastritis, eight proteins were expressed. In this group, tatB was overexpressed. A reduction in thioredoxin peroxidase (bacterioferritin co-migratory protein (bcp)) was observed in ulcer vs. gastritis and cancer vs. ulcer. Conclusion: Our study suggested three discrete protein signatures, hypA, tatB, and bcp, with differential expression in gastritis, ulcer, and cancer. Protein expression profiles of H. pylori isolated from patients with these gastric diseases will help to understand the virulence and pathogenesis of H. pylori.

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Lacombe, Marie-Lise, Malgorzata Tokarska-Schlattner, Mathieu Boissan, and Uwe Schlattner. "The mitochondrial nucleoside diphosphate kinase (NDPK-D/NME4), a moonlighting protein for cell homeostasis." Laboratory Investigation 98, no. 5 (February 28, 2018): 582–88. http://dx.doi.org/10.1038/s41374-017-0004-5.

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Prasad, Shashanka K., Smitha S. Bhat, Olga Koskowska, Jiraporn Sangta, Sheikh F. Ahmad, Ahmed Nadeem, and Sarana Rose Sommano. "Naringin from Coffee Inhibits Foodborne Aspergillus fumigatus via the NDK Pathway: Evidence from an In Silico Study." Molecules 28, no. 13 (July 4, 2023): 5189. http://dx.doi.org/10.3390/molecules28135189.

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In the tropics, coffee has been one of the most extensively cultivated economic crops, especially Arabica coffee (Coffea arabica L.). The coffee pulp, which includes phytochemicals with a proven antifungal action, is one of the most insufficiently utilized and neglected byproducts of coffee refining. In the current experiment, we carried out in silico screening of the isolated Arabica coffee phytochemicals for antifungal activity against Aspergillus fumigatus: a foodborne fungus of great public health importance. As determined by the molecular docking interactions of the library compounds indicated, the best interactions were found to occur between the nucleoside-diphosphate kinase protein 6XP7 and the test molecules Naringin (−6.771 kcal/mol), followed by Epigallocatechin gallate (−5.687 kcal/mol). Therefore, Naringin was opted for further validation with molecular dynamic simulations. The ligand–protein complex RMSD indicated a fairly stable Naringin-NDK ligand–protein complex throughout the simulation period (2–16 Å). In ADME and gastrointestinal absorbability testing, Naringin was observed to be orally bioavailable, with very low intestinal absorption and a bioavailability score of 0.17. This was further supported by the boiled egg analysis data, which clearly indicated that the GI absorption of the Naringin molecule was obscure. We found that naringin could be harmful only when swallowed at a median lethal dose between 2000 and 5000 mg/kg. In accordance with these findings, the toxicity prediction reports suggested that Naringin, found especially in citrus fruits and tomatoes, is safe for human consumption after further investigation. Overall, Naringin may be an ideal candidate for developing anti-A. fumigatus treatments and food packaging materials. Thus, this study addresses the simultaneous problems of discarded coffee waste management and antifungal resistance to available medications.

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Chatterjee, Anupriya, Rachana Eshwaran, Gernot Poschet, Santosh Lomada, Mahmoud Halawa, Kerstin Wilhelm, Martina Schmidt, Hans-Peter Hammes, Thomas Wieland, and Yuxi Feng. "Involvement of NDPK-B in Glucose Metabolism-Mediated Endothelial Damage via Activation of the Hexosamine Biosynthesis Pathway and Suppression of O-GlcNAcase Activity." Cells 9, no. 10 (October 19, 2020): 2324. http://dx.doi.org/10.3390/cells9102324.

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Our previous studies identified that retinal endothelial damage caused by hyperglycemia or nucleoside diphosphate kinase-B (NDPK-B) deficiency is linked to elevation of angiopoietin-2 (Ang-2) and the activation of the hexosamine biosynthesis pathway (HBP). Herein, we investigated how NDPK-B is involved in the HBP in endothelial cells (ECs). The activities of NDPK-B and O-GlcNAcase (OGA) were measured by in vitro assays. Nucleotide metabolism and O-GlcNAcylated proteins were assessed by UPLC-PDA (Ultra-performance liquid chromatography with Photodiode array detection) and immunoblot, respectively. Re-expression of NDPK-B was achieved with recombinant adenoviruses. Our results show that NDPK-B depletion in ECs elevated UDP-GlcNAc levels and reduced NDPK activity, similar to high glucose (HG) treatment. Moreover, the expression and phosphorylation of glutamine:fructose-6-phosphate amidotransferase (GFAT) were induced, whereas OGA activity was suppressed. Furthermore, overall protein O-GlcNAcylation, along with O-GlcNAcylated Ang-2, was increased in NDPK-B depleted ECs. Pharmacological elevation of protein O-GlcNAcylation using Thiamet G (TMG) or OGA siRNA increased Ang-2 levels. However, the nucleoside triphosphate to diphosphate (NTP/NDP) transphosphorylase and histidine kinase activity of NDPK-B were dispensable for protein O-GlcNAcylation. NDPK-B deficiency hence results in the activation of HBP and the suppression of OGA activity, leading to increased protein O-GlcNAcylation and further upregulation of Ang-2. The data indicate a critical role of NDPK-B in endothelial damage via the modulation of the HBP.

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Tsuiki, Hiromasa, Masayuki Nitta, Akiko Furuya, Nobuo Hanai, Toshiyoshi Fujiwara, Masaki Inagaki, Masato Kochi, Yukitaka Ushio, Hideyuki Saya, and Hideo Nakamura. "A novel human nucleoside diphosphate (NDP) kinase, Nm23-H6, localizes in mitochondria and affects cytokinesis." Journal of Cellular Biochemistry 76, no. 2 (February 1, 2000): 254–69. http://dx.doi.org/10.1002/(sici)1097-4644(20000201)76:2<254::aid-jcb9>3.0.co;2-g.

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

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