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| | ==Purification, characterization and structure of nucleoside diphosphate kinase from Drosophila S2 cells== | | ==Purification, characterization and structure of nucleoside diphosphate kinase from Drosophila S2 cells== |
| - | <StructureSection load='3wx8' size='340' side='right' caption='[[3wx8]], [[Resolution|resolution]] 1.95Å' scene=''> | + | <StructureSection load='3wx8' size='340' side='right'caption='[[3wx8]], [[Resolution|resolution]] 1.95Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3wx8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WX8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WX8 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3wx8]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WX8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WX8 FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">awd, K-pn, CG2210 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</td></tr> | + | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">awd, K-pn, CG2210 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </span></td></tr> | + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wx8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wx8 OCA], [http://pdbe.org/3wx8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wx8 RCSB], [http://www.ebi.ac.uk/pdbsum/3wx8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wx8 ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3wx8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wx8 OCA], [https://pdbe.org/3wx8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wx8 RCSB], [https://www.ebi.ac.uk/pdbsum/3wx8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wx8 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/NDKA_DROME NDKA_DROME]] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate.<ref>PMID:2849580</ref> <ref>PMID:2175255</ref> <ref>PMID:7559441</ref> | + | [[https://www.uniprot.org/uniprot/NDKA_DROME NDKA_DROME]] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate.<ref>PMID:2849580</ref> <ref>PMID:2175255</ref> <ref>PMID:7559441</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Nucleoside diphosphate kinase|Nucleoside diphosphate kinase]] | + | *[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Drome]] | | [[Category: Drome]] |
| | + | [[Category: Large Structures]] |
| | [[Category: Nucleoside-diphosphate kinase]] | | [[Category: Nucleoside-diphosphate kinase]] |
| | [[Category: Qian, L]] | | [[Category: Qian, L]] |
| Structural highlights
Function
[NDKA_DROME] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate.[1] [2] [3]
Publication Abstract from PubMed
Nucleoside diphosphate kinase (NDPK) is a ubiquitous enzyme found in all organisms and cell types, which catalyzes the transfer of the phosphoryl group from a nucleoside triphosphate to a nucleoside diphosphate. The gene encoding for NDPK from Drosophila melanogaster was amplified from the genomic DNA. The recombinant NDPK (rNDPK) was overexpressed in Escherichia coli and purified to homogeneity by Ni-NTA agarose affinity chromatography, HiTrap SP HP cation exchange chromatography and HiLoad 16/60 Superdex 200 gel filtration chromatography. The gel filtration chromatography and analytical ultracentrifugation showed that rNDPK was a trimer in solution. The binding affinity of NDPs with rNDPK, measured by isothermal titration calorimetry, indicated that the purines nucleotides show higher binding affinity compared with pyrimidines. The rNDPK had a definite nuclease activity in vitro, which could cleave supercoiled plasmid DNA, but had no effect on dsDNA and ssDNA. Furthermore, the structure for NDPK was determined by using the sitting drop vapor diffusion method. In the final model, the asymmetric unit is made of three molecules, each of which consists of a four-stranded anti-parallel beta-sheets and seven alpha-helices. Sequence alignment and structure comparison illustrated that the simulated nucleotide-binding active site are conserved.
Purification, characterization and structure of nucleoside diphosphate kinase from Drosophila melanogaster.,Qian L, Liu X Protein Expr Purif. 2014 Nov;103:48-55. doi: 10.1016/j.pep.2014.08.014. Epub 2014, Sep 4. PMID:25195176[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Biggs J, Tripoulas N, Hersperger E, Dearolf C, Shearn A. Analysis of the lethal interaction between the prune and Killer of prune mutations of Drosophila. Genes Dev. 1988 Oct;2(10):1333-43. PMID:2849580
- ↑ Biggs J, Hersperger E, Steeg PS, Liotta LA, Shearn A. A Drosophila gene that is homologous to a mammalian gene associated with tumor metastasis codes for a nucleoside diphosphate kinase. Cell. 1990 Nov 30;63(5):933-40. PMID:2175255
- ↑ Timmons L, Xu J, Hersperger G, Deng XF, Shearn A. Point mutations in awdKpn which revert the prune/Killer of prune lethal interaction affect conserved residues that are involved in nucleoside diphosphate kinase substrate binding and catalysis. J Biol Chem. 1995 Sep 29;270(39):23021-30. PMID:7559441
- ↑ Qian L, Liu X. Purification, characterization and structure of nucleoside diphosphate kinase from Drosophila melanogaster. Protein Expr Purif. 2014 Nov;103:48-55. doi: 10.1016/j.pep.2014.08.014. Epub 2014, Sep 4. PMID:25195176 doi:http://dx.doi.org/10.1016/j.pep.2014.08.014
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