Analysis of ligand binding and resulting conformational changes in pyrophosphatase NUDT9

Gattkowski, Ellen; Rutherford, Trevor J.; Möckl, Franziska; Bauche, Andreas; Sander, Simon; Fliegert, Ralf; Tidow, Henning

doi:10.1111/febs.16097

Cited by 6 publications

(3 citation statements)

References 44 publications

(80 reference statements)

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“…NUDT9 plays a role in breast cancer [39]. The NUDT9 protein can dock with ADPR, and 218 amino acids directly participate in the docking [40]. We simulated the docking and found that the goose NUDT9 protein could dock with ADPR.…”

Section: Discussionmentioning

confidence: 99%

Whole Genome Resequencing Identifies Single-Nucleotide Polymorphism Markers of Growth and Reproduction Traits in Zhedong and Zi Crossbred Geese

Liu¹,

Guo²,

Zhao³

et al. 2023

Genes

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: The broodiness traits of domestic geese are a bottleneck that prevents the rapid development of the goose industry. To reduce the broodiness of the Zhedong goose and thus improve it, this study hybridized it with the Zi goose, which has almost no broody behavior. Genome resequencing was performed for the purebred Zhedong goose, as well as the F2 and F3 hybrids. The results showed that the F1 hybrids displayed significant heterosis in growth traits, and their body weight was significantly greater than those of the other groups. The F2 hybrids showed significant heterosis in egg-laying traits, and the number of eggs laid was significantly greater than those of the other groups. A total of 7,979,421 single-nucleotide polymorphisms (SNPs) were obtained, and three SNPs were screened. Molecular docking results showed that SNP11 located in the gene NUDT9 altered the structure and affinity of the binding pocket. The results suggested that SNP11 is an SNP related to goose broodiness. In the future, we will use the cage breeding method to sample the same half-sib families to accurately identify SNP markers of growth and reproductive traits.

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Section: Discussionmentioning

confidence: 99%

Whole Genome Resequencing Identifies Single-Nucleotide Polymorphism Markers of Growth and Reproduction Traits in Zhedong and Zi Crossbred Geese

Liu¹,

Guo²,

Zhao³

et al. 2023

Genes

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“…hsTRPM2), but here the preceding tetramerization step of the NUDT9H domains is absent (Huang et al, 2023). For the human NUDT9 enzyme a monomeric form of organization is assumed (Shen et al, 2003;Perraud et al, 2003;Gattkowski et al, 2021). Since the short stretch of amino acid residues critical for tetramerization of NUDT9H is absent in modern TRPM2 variants (Huang et al, 2023), it can be expected that our separately expressed hsNUDT9H domain also interacts as a monomer (Gattkowski et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

The essential inter-domain interaction between NUDT9H and channel domain of human TRPM2 is also accomplished in trans

Ehrlich,

Kühn

2023

Preprint

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Channel function of human transient receptor potential melastatin type 2 (hsTRPM2) essentially depends on its C-terminal domain NUDT9H, which is homologous to the human Nudix hydrolase NUDT9. This cytosolic enzyme specifically binds and cleaves adenosine 5′-diphosphate ribose (ADPR), which in turn represents the principal agonist of TRPM2. For hsTRPM2 the experimental data strongly suggest, that binding of ADPR to NUDT9H as well as to a separate N-terminal binding pocket induces channel gating. Recent cryogenic electron microscopy (cryo-EM) analyses have provided the first concrete clues as to how NUDT9H interacts with the channel domain. In the present study we take an alternative approach by testing co-expression of NUDT9H together with a C-terminally truncated non-functional variant of hsTRPM2. Our data obtained from co-immunoprecipitation and proximity ligation assays reveal that NUDT9H and channel domain also specifically interact when co-expressed as independent proteins. Most importantly, calcium imaging as well as whole-cell patch-clamp recordings demonstrate that this in-trans interaction restores channel function, after stimulation either with intracellular ADPR or with extracellular hydrogen peroxide. Moreover, point mutation N1326D within the NUDT9H domain previously shown to be essential for TRPM2 function significantly reduces co-immunoprecipitation of NUDT9H as well as ADPR-dependent channel activity. These findings open up new possibilities to identify the molecular determinants of this crucial inter-domain interaction.

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“…6; Fig. 1c), whereas ADPR hydrolysis in NUDT9-H occurs only in the presence of Mg 2+ but not Ca 2+ (ref 10,20 ). By contrast, vertebrate TRPM2 opens only in the presence of Ca 2+ with a lower open probability 21 , and cannot hydrolyze ADPR 22 .…”

Section: The Trpm2 Chanzyme Is Regulated By Five Ligand Binding Sitesmentioning

confidence: 94%

Coupling enzymatic activity and gating in an ancient TRPM chanzyme and its molecular evolution

Huang

Lü

2023

Preprint

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The canonical ion channels gated by chemical ligands use the free energy of agonist binding to open the channel pore, returning to a closed state upon agonist departure. A unique class of ion channels, known as channel-enzymes (chanzymes), possess additional enzymatic activity that is directly or indirectly linked to their channel function. Here we investigated a TRPM2 chanzyme from choanoflagellates, an evolutionary ancestor of all metazoan TRPM channels, which integrates two seemingly incompatible functions into a single peptide: a channel module activated by ADP ribose (ADPR) with high open probability and an enzyme module (NUDT9-H domain) consuming ADPR at a remarkably slow rate. Using time-resolved cryo-electron microscopy (cryo-EM), we captured a complete series of structural snapshots of the gating and catalytic cycles, revealing the coupling mechanism between channel gating and enzymatic activity. Our results showed that the slow kinetics of the NUDT9-H enzyme module confers a novel self-regulatory mechanism, whereby the enzyme module modulates channel gating in a binary manner. Binding of ADPR to NUDT9-H first triggers tetramerization of the enzyme modules, promoting channel opening, while the subsequent hydrolysis reaction reduces local ADPR availability, inducing channel closure. This coupling enables the ion-conducting pore to alternate rapidly between open and closed states, avoiding Mg2+ and Ca2+ overload. We further demonstrated how the NUDT9-H domain has evolved from a structurally semi-independent ADPR hydrolase module in early species TRPM2 to a fully integrated component of a gating ring essential for channel activation in advanced species TRPM2. Our study demonstrated an example of how organisms can adapt to their environments at the molecular level.

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Analysis of ligand binding and resulting conformational changes in pyrophosphatase NUDT9

Cited by 6 publications

References 44 publications

Whole Genome Resequencing Identifies Single-Nucleotide Polymorphism Markers of Growth and Reproduction Traits in Zhedong and Zi Crossbred Geese

Whole Genome Resequencing Identifies Single-Nucleotide Polymorphism Markers of Growth and Reproduction Traits in Zhedong and Zi Crossbred Geese

The essential inter-domain interaction between NUDT9H and channel domain of human TRPM2 is also accomplished in trans

Coupling enzymatic activity and gating in an ancient TRPM chanzyme and its molecular evolution

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