6xps: Difference between revisions
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==Nucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 bound to GDP== | ==Nucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 bound to GDP== | ||
<StructureSection load='6xps' size='340' side='right'caption='[[6xps]]' scene=''> | <StructureSection load='6xps' size='340' side='right'caption='[[6xps]], [[Resolution|resolution]] 1.64Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XPS OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6xps]] 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=6XPS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XPS FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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='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=6xps FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xps OCA], [https://pdbe.org/6xps PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xps RCSB], [https://www.ebi.ac.uk/pdbsum/6xps PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xps ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== 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. | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:33089641</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6xps" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Aspfu]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Bruning | [[Category: Nucleoside-diphosphate kinase]] | ||
[[Category: Nguyen S]] | [[Category: Bruning, J B]] | ||
[[Category: Nguyen, S]] | |||
[[Category: Kinase]] | |||
[[Category: Nucleoside diphosphate kinase]] | |||
[[Category: Phosphotransferase]] | |||
[[Category: Transferase]] | |||
Revision as of 09:53, 14 April 2021
Nucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 bound to GDPNucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 bound to GDP
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 PubMedAspergillus 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. References
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