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| | <StructureSection load='1nsq' size='340' side='right'caption='[[1nsq]], [[Resolution|resolution]] 2.18Å' scene=''> | | <StructureSection load='1nsq' size='340' side='right'caption='[[1nsq]], [[Resolution|resolution]] 2.18Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1nsq]] 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=1NSQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NSQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1nsq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NSQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NSQ FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=HIP:ND1-PHOSPHONOHISTIDINE'>HIP</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.18Å</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HIP:ND1-PHOSPHONOHISTIDINE'>HIP</scene></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=1nsq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nsq OCA], [https://pdbe.org/1nsq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nsq RCSB], [https://www.ebi.ac.uk/pdbsum/1nsq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nsq 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=1nsq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nsq OCA], [https://pdbe.org/1nsq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nsq RCSB], [https://www.ebi.ac.uk/pdbsum/1nsq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nsq ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[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>
| + | [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> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Drome]] | + | [[Category: Drosophila melanogaster]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Nucleoside-diphosphate kinase]]
| + | [[Category: Chiadmi M]] |
| - | [[Category: Chiadmi, M]] | + | [[Category: Janin J]] |
| - | [[Category: Janin, J]] | + | [[Category: Lascu I]] |
| - | [[Category: Lascu, I]] | + | [[Category: Lebras G]] |
| - | [[Category: Lebras, G]] | + | [[Category: Morera S]] |
| - | [[Category: Morera, S]] | + | |
| - | [[Category: Phosphotransferase]]
| + | |
| 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]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Nucleoside diphosphate kinase (NDP kinase) has a ping-pong mechanism with a phosphohistidine intermediate. Crystals of the enzymes from Dictyostelium discoideum and from Drosophila melanogaster were treated with phosphoramidate, and their X-ray structures were determined at 2.1 and 2.2 A resolution, respectively. The atomic models, refined to R factors below 20%, show no conformation change relative to the free proteins. In both enzymes, the active site histidine was phosphorylated on N delta, and it was the only site of phosphorylation. The phosphate group interacts with the hydroxyl group of Tyr56 and with protein-bound water molecules. Its environment is compared with that of phosphohistidines in succinyl-CoA synthetase and in phosphocarrier proteins. The X-ray structures of phosphorylated NDP kinase and of previously determined complexes with nucleoside diphosphates provide a basis for modeling the Michaelis complex with a nucleoside triphosphate, that of the phosphorylated protein with a nucleoside diphosphate, and the transition state of the phosphate transfer reaction in which the gamma-phosphate is pentacoordinated.
Mechanism of phosphate transfer by nucleoside diphosphate kinase: X-ray structures of the phosphohistidine intermediate of the enzymes from Drosophila and Dictyostelium.,Morera S, Chiadmi M, LeBras G, Lascu I, Janin J Biochemistry. 1995 Sep 5;34(35):11062-70. PMID:7669763[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
- ↑ Morera S, Chiadmi M, LeBras G, Lascu I, Janin J. Mechanism of phosphate transfer by nucleoside diphosphate kinase: X-ray structures of the phosphohistidine intermediate of the enzymes from Drosophila and Dictyostelium. Biochemistry. 1995 Sep 5;34(35):11062-70. PMID:7669763
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