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Data of the interacting protein networks and nucleotide metabolism pathways related to NDK and NT5.

ABSTRACT: The data presented in this article are related to the research article entitled "Antibacterial mechanism of daptomycin antibiotic against Staphylococcus aureus based on a quantitative bacterial proteome analysis" (Ma et al., 2016) [1]. Nucleoside diphosphate kinase (NDK) and 5'-nucleotidase (NT5) are two proteins related to bacterial growth. Here, a bioinformatics analysis was presented to explore NDK and NT5-invovled in the interacting protein network and purine metabolism.

SUBMITTER: Zhang D

PROVIDER: S-EPMC5126131 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

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Data of the interacting protein networks and nucleotide metabolism pathways related to NDK and NT5.

Zhang Dan D Ma Wen W He Yu Y He Gu G Zhang Peng P Zhu Hongxia H Xu Ningzhi N Liang Shufang S

Data in brief 20161117

The data presented in this article are related to the research article entitled "Antibacterial mechanism of daptomycin antibiotic against <i>Staphylococcus aureus</i> based on a quantitative bacterial proteome analysis" (Ma et al., 2016) [1]. Nucleoside diphosphate kinase (NDK) and 5'-nucleotidase (NT5) are two proteins related to bacterial growth. Here, a bioinformatics analysis was presented to explore NDK and NT5-invovled in the interacting protein network and purine metabolism. ...[more]

PMID: 27921077

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Project description:IntroductionNucleoside diphosphate kinase (NDK), conserved across bacteria to humans, synthesises NTP from NDP and ATP. The eukaryotic homologue, the NDPK, uses ATP to phosphorylate the tubulin-bound GDP to GTP for tubulin polymerisation. The bacterial cytokinetic protein FtsZ, which is the tubulin homologue, also uses GTP for polymerisation. Therefore, we examined whether NDK can interact with FtsZ to convert FtsZ-bound GDP and/or free GDP to GTP to trigger FtsZ polymerisation.MethodsRecombinant and native NDK and FtsZ proteins of Mycobacterium smegmatis and Mycobacterium tuberculosis were used as the experimental samples. FtsZ polymersation was monitored using 90° light scattering and FtsZ polymer pelleting assays. The ?32P-GTP synthesised by NDK from GDP and ?32P-ATP was detected using thin layer chromatography and quantitated using phosphorimager. The FtsZ bound 32P-GTP was quantitated using phosphorimager, after UV-crosslinking, followed by SDS-PAGE. The NDK-FtsZ interaction was determined using Ni2+-NTA-pulldown assay and co-immunoprecipitation of the recombinant and native proteins in vitro and ex vivo, respectively.ResultsNDK triggered instantaneous polymerisation of GDP-precharged recombinant FtsZ in the presence of ATP, similar to the polymerisation of recombinant FtsZ (not GDP-precharged) upon the direct addition of GTP. Similarly, NDK triggered polymerisation of recombinant FtsZ (not GDP-precharged) in the presence of free GDP and ATP as well. Mutant NDK, partially deficient in GTP synthesis from ATP and GDP, triggered low level of polymerisation of MsFtsZ, but not of MtFtsZ. As characteristic of NDK's NTP substrate non-specificity, it used CTP, TTP, and UTP also to convert GDP to GTP, to trigger FtsZ polymerisation. The NDK of one mycobacterial species could trigger the polymerisation of the FtsZ of another mycobacterial species. Both the recombinant and the native NDK and FtsZ showed interaction with each other in vitro and ex vivo, alluding to the possibility of direct phosphorylation of FtsZ-bound GDP by NDK.ConclusionIrrespective of the bacterial species, NDK interacts with FtsZ in vitro and ex vivo and, through the synthesis of GTP from FtsZ-bound GDP and/or free GDP, and ATP (CTP/TTP/UTP), triggers FtsZ polymerisation. The possible biological context of this novel activity of NDK is presented.

Dataset Information

Data of the interacting protein networks and nucleotide metabolism pathways related to NDK and NT5.

Publications

Data of the interacting protein networks and nucleotide metabolism pathways related to NDK and NT5.

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