Enzymes
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Reaction participants Show >> << Hide
- Name help_outline ATP Identifier CHEBI:30616 (Beilstein: 3581767) help_outline Charge -4 Formula C10H12N5O13P3 InChIKeyhelp_outline ZKHQWZAMYRWXGA-KQYNXXCUSA-J SMILEShelp_outline Nc1ncnc2n(cnc12)[C@@H]1O[C@H](COP([O-])(=O)OP([O-])(=O)OP([O-])([O-])=O)[C@@H](O)[C@H]1O 2D coordinates Mol file for the small molecule Search links Involved in 1,280 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
- Name help_outline IDP Identifier CHEBI:58280 (Beilstein: 5786306) help_outline Charge -3 Formula C10H11N4O11P2 InChIKeyhelp_outline JPXZQMKKFWMMGK-KQYNXXCUSA-K SMILEShelp_outline O[C@@H]1[C@@H](COP([O-])(=O)OP([O-])([O-])=O)O[C@H]([C@@H]1O)n1cnc2c1nc[nH]c2=O 2D coordinates Mol file for the small molecule Search links Involved in 9 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
- Name help_outline ADP Identifier CHEBI:456216 (Beilstein: 3783669) help_outline Charge -3 Formula C10H12N5O10P2 InChIKeyhelp_outline XTWYTFMLZFPYCI-KQYNXXCUSA-K SMILEShelp_outline Nc1ncnc2n(cnc12)[C@@H]1O[C@H](COP([O-])(=O)OP([O-])([O-])=O)[C@@H](O)[C@H]1O 2D coordinates Mol file for the small molecule Search links Involved in 841 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
- Name help_outline ITP Identifier CHEBI:61402 Charge -4 Formula C10H11N4O14P3 InChIKeyhelp_outline HAEJPQIATWHALX-KQYNXXCUSA-J SMILEShelp_outline O[C@@H]1[C@@H](COP([O-])(=O)OP([O-])(=O)OP([O-])([O-])=O)O[C@H]([C@@H]1O)n1cnc2c1nc[nH]c2=O 2D coordinates Mol file for the small molecule Search links Involved in 11 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Cross-references
| RHEA:30347 | RHEA:30348 | RHEA:30349 | RHEA:30350 | |
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| Reaction direction help_outline | undefined | left-to-right | right-to-left | bidirectional |
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Related reactions help_outline
More general form(s) of this reaction
Publications
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Nucleoside selectivity of Aspergillus fumigatus nucleoside-diphosphate kinase.
Nguyen S., Jovcevski B., Pukala T.L., Bruning J.B.
Aspergillus fumigatus infections are rising at a disconcerting rate in tandem with antifungal resistance rates. Efforts to develop novel antifungals have been hindered by the limited knowledge of fundamental biological and structural mechanisms of A. fumigatus propagation. Biosynthesis of NTPs, th ... >> More
Aspergillus fumigatus infections are rising at a disconcerting rate in tandem with antifungal resistance rates. Efforts to develop novel antifungals have 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<sup>-1</sup> ), specificity constant (626 ± 110.0 mm<sup>-1</sup> ·s<sup>-1</sup> ) and binding free energy change (-37.0 ± 3.5 kcal·mol<sup>-1</sup> ). Comparatively, cytidine nucleosides displayed the slowest turnover rate (53.1 ± 3.7 s<sup>-1</sup> ) and lowest specificity constant (40.2 ± 4.4 mm<sup>-1</sup> ·s<sup>-1</sup> ). 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. ENZYMES: Nucleoside-diphosphate kinase (EC 2.7.4.6). DATABASE: Structural data are available in the PDB database under the accession numbers: Unbound-NDK (6XP4), ADP-NDK (6XP7), GDP-NDK (6XPS), IDP-NDK (6XPU), UDP-NDK (6XPT), CDP-NDK (6XPW), TDP-NDK (6XPV). << Less
FEBS J 288:2398-2417(2021) [PubMed] [EuropePMC]
This publication is cited by 4 other entries.