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| | <StructureSection load='6xpu' size='340' side='right'caption='[[6xpu]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='6xpu' size='340' side='right'caption='[[6xpu]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6xpu]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspfu Aspfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XPU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6xpu]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_fumigatus_Af293 Aspergillus fumigatus Af293]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XPU FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IDP:INOSINE-5-DIPHOSPHATE'>IDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6xp4|6xp4]], [[6xp7|6xp7]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IDP:INOSINE-5-DIPHOSPHATE'>IDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ndk1, AFUA_5G03490 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=330879 ASPFU])</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'>[https://proteopedia.org/fgij/fg.htm?mol=6xpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xpu OCA], [https://pdbe.org/6xpu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xpu RCSB], [https://www.ebi.ac.uk/pdbsum/6xpu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xpu 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=6xpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xpu OCA], [https://pdbe.org/6xpu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xpu RCSB], [https://www.ebi.ac.uk/pdbsum/6xpu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xpu ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/NDK_ASPFU NDK_ASPFU]] 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.
| + | [https://www.uniprot.org/uniprot/NDK_ASPFU NDK_ASPFU] 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. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6xpu" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6xpu" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aspfu]] | + | [[Category: Aspergillus fumigatus Af293]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Nucleoside-diphosphate kinase]]
| + | [[Category: Bruning JB]] |
| - | [[Category: Bruning, J B]] | + | [[Category: Nguyen S]] |
| - | [[Category: Nguyen, S]] | + | |
| - | [[Category: Kinase]]
| + | |
| - | [[Category: Nucleoside diphosphate kinase]]
| + | |
| - | [[Category: Phosphotransferase]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
NDK_ASPFU 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.
Publication Abstract from PubMed
Aspergillus fumigatus infections are rising at a disconcerting rate in tandem with antifungal resistance rates. Efforts to develop novel antifungals has been hindered by the limited knowledge of fundamental biological and structural mechanisms of A. fumigatus propagation. Biosynthesis of NTPs, the building blocks of DNA and RNA, is catalysed by NDK. An essential enzyme in A. fumigatus, NDK poses as an attractive target for novel antifungals. NDK exhibits broad substrate specificity across species, using both purines and pyrimidines, but the selectivity of such nucleosides in A. fumigatus NDK is unknown, impeding structure-guided inhibitor design. Structures of NDK in unbound- and NDP-bound states were solved and NDK activity was assessed in the presence of various NTP substrates. We present the first instance of a unique substrate binding mode adopted by CDP and TDP specific to A. fumigatus NDK that illuminates the structural determinants of selectivity. Analysis of the oligomeric state reveals that A. fumigatus NDK adopts a hexameric assembly in both unbound- and NDP-bound states, contrary to previous reports suggesting it is tetrameric. Kinetic analysis revealed that ATP exhibited the greatest turnover rate (321 +/- 33.0 s(-1) ), specificity constant (626 +/- 110.0 mM(-1) s(-1) ) and binding free energy change (-37.0 +/- 3.5 kcal/mol). Comparatively, cytidine nucleosides displayed the slowest turnover rate (53.1 +/- 3.7 s(-1) ) and lowest specificity constant (40.2 +/- 4.4 mM(-1) s(-1) ). We conclude that NDK exhibits nucleoside selectivity whereby adenine nucleosides are used preferentially compared to cytidine nucleosides, and these insights can be exploited to guide drug design.
Nucleoside selectivity of Aspergillus fumigatus nucleoside-diphosphate kinase.,Nguyen S, Jovcevski B, Pukala TL, Bruning JB FEBS J. 2020 Oct 21. doi: 10.1111/febs.15607. PMID:33089641[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Nguyen S, Jovcevski B, Pukala TL, Bruning JB. Nucleoside selectivity of Aspergillus fumigatus nucleoside-diphosphate kinase. FEBS J. 2020 Oct 21. doi: 10.1111/febs.15607. PMID:33089641 doi:http://dx.doi.org/10.1111/febs.15607
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