Pub Date : 2025-01-17DOI: 10.1016/j.str.2024.12.016
Jialin Yin, Vaishali P. Waman, Neeladri Sen, Mohd Firdaus-Raih, Su Datt Lam, Christine Orengo
ATP-pyrophosphatases (ATP-PPases) are the most primordial lineage of the large and diverse HUP (high-motif proteins, universal stress proteins, ATP-pyrophosphatase) superfamily. There are four different ATP-PPase substrate-specificity groups (SSGs), and members of each group show considerable sequence variation across the domains of life despite sharing the same catalytic function. Owing to the expansion in the number of ATP-PPase domain structures from advances in protein structure prediction by AlphaFold2 (AF2), we have characterized the two most populated ATP-PPase SSGs, the nicotinamide adenine dinucleotide synthases (NADSs) and guanosine monophosphate synthases (GMPSs). Local structural and sequence comparisons of NADS and GMPS identified taxonomic-group-specific functional motifs. As GMPS and NADS are potential drug targets of pathogenic microorganisms including Mycobacterium tuberculosis, bacterial GMPS and NADS specific functional motifs reported in this study, may contribute to antibacterial-drug development.
atp -焦磷酸酶（ATP-PPases）是大而多样的HUP（高基序蛋白，通用应激蛋白，atp -焦磷酸酶）超家族中最原始的谱系。有四个不同的ATP-PPase底物特异性组（ssg），尽管具有相同的催化功能，但每个组的成员在生命领域中表现出相当大的序列差异。由于AlphaFold2 （AF2）在蛋白质结构预测方面的进展扩大了ATP-PPase结构域的数量，我们已经鉴定了两个最普遍的ATP-PPase SSGs，烟酰胺腺嘌呤二核苷酸合成酶（NADSs）和鸟苷单磷酸合成酶（gmps）。NADS和GMPS的局部结构和序列比较确定了分类类群特异性功能基序。由于GMPS和NADS是包括结核分枝杆菌在内的病原微生物的潜在药物靶点，本研究报道的细菌GMPS和NADS特异性功能基序可能有助于抗菌药物的开发。
{"title":"Understanding the structural and functional diversity of ATP-PPases using protein domains and functional families in the CATH database","authors":"Jialin Yin, Vaishali P. Waman, Neeladri Sen, Mohd Firdaus-Raih, Su Datt Lam, Christine Orengo","doi":"10.1016/j.str.2024.12.016","DOIUrl":"https://doi.org/10.1016/j.str.2024.12.016","url":null,"abstract":"ATP-pyrophosphatases (ATP-PPases) are the most primordial lineage of the large and diverse HUP (high-motif proteins, universal stress proteins, ATP-pyrophosphatase) superfamily. There are four different ATP-PPase substrate-specificity groups (SSGs), and members of each group show considerable sequence variation across the domains of life despite sharing the same catalytic function. Owing to the expansion in the number of ATP-PPase domain structures from advances in protein structure prediction by AlphaFold2 (AF2), we have characterized the two most populated ATP-PPase SSGs, the nicotinamide adenine dinucleotide synthases (NADSs) and guanosine monophosphate synthases (GMPSs). Local structural and sequence comparisons of NADS and GMPS identified taxonomic-group-specific functional motifs. As GMPS and NADS are potential drug targets of pathogenic microorganisms including <em>Mycobacterium tuberculosis</em>, bacterial GMPS and NADS specific functional motifs reported in this study, may contribute to antibacterial-drug development.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"20 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142987472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-17DOI: 10.1016/j.str.2024.12.017
Karen Acosta, Christopher R. Brue, Polina Holubovska, Hee Jong Kim, Leland Mayne, Kenji Murakami, Elizabeth Rhoades
Tau plays an important role in modulating axonal microtubules in neurons, while intracellular tau aggregates are found in many neurodegenerative disorders. Tubulin binding sites are found in tau’s proline-rich region (PRR), microtubule binding repeats (MTBRs), and pseudo-repeat (R′). Tau phosphorylation sites, which cluster with high frequency within the PRR, regulate tubulin interactions and correlates with disease. Here, we use fluorescence correlation spectroscopy and structural mass spectrometry techniques to characterize the impact of phosphomimic mutations in the PRR on tau function. We find that phosphomimics cumulatively diminish tubulin dimer binding and slow microtubule polymerization. Additionally, we map two ∼15 residue regions of the PRR as primary tubulin dimer binding sites and propose a model in which PRR enhances lateral interactions between tubulin dimers, complementing the longitudinal interactions observed for MTBR. Our study provides insight into the previously overlooked relevance of tau’s PRR in functional interactions with tubulin dimers.
{"title":"Structural insights into the role of the proline rich region in tau function","authors":"Karen Acosta, Christopher R. Brue, Polina Holubovska, Hee Jong Kim, Leland Mayne, Kenji Murakami, Elizabeth Rhoades","doi":"10.1016/j.str.2024.12.017","DOIUrl":"https://doi.org/10.1016/j.str.2024.12.017","url":null,"abstract":"Tau plays an important role in modulating axonal microtubules in neurons, while intracellular tau aggregates are found in many neurodegenerative disorders. Tubulin binding sites are found in tau’s proline-rich region (PRR), microtubule binding repeats (MTBRs), and pseudo-repeat (R′). Tau phosphorylation sites, which cluster with high frequency within the PRR, regulate tubulin interactions and correlates with disease. Here, we use fluorescence correlation spectroscopy and structural mass spectrometry techniques to characterize the impact of phosphomimic mutations in the PRR on tau function. We find that phosphomimics cumulatively diminish tubulin dimer binding and slow microtubule polymerization. Additionally, we map two ∼15 residue regions of the PRR as primary tubulin dimer binding sites and propose a model in which PRR enhances lateral interactions between tubulin dimers, complementing the longitudinal interactions observed for MTBR. Our study provides insight into the previously overlooked relevance of tau’s PRR in functional interactions with tubulin dimers.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"5 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142987469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The human ATP-binding cassette (ABC) transporter ABCA7 participates in the lipidation of apolipoprotein ApoE, a commonly recognized risk factor for Alzheimer’s disease (AD). How ABCA7 is involved in the molecular pathogenesis of AD remains poorly understood. Using cryoelectron microscopy (cryo-EM), we determined ABCA7 structures in the apo and substrate-bound forms, respectively. Combined with activity assays, we assigned the residues that specifically bind two molecules of phosphatidylserine (PS) that are arranged in a “tail-to-tail” manner. Pull-down assays confirmed that ApoE directly interacts with ABCA7; and moreover, both ATPase and lipid transport activities of ABCA7 were significantly enhanced in the presence of ApoE. We also measured the activities of a familial AD variant and a protective clinically reported variant in the ABCA7 gene. Our findings not only give structural insights into ABCA7-mediated PS translocation, but we also provide first biochemical evidence for its link to AD by forwarding lipids to ApoE.
人类 ATP 结合盒（ABC）转运体 ABCA7 参与脂蛋白载脂蛋白的脂化，而脂蛋白载脂蛋白是公认的阿尔茨海默病（AD）风险因素。人们对ABCA7如何参与阿尔茨海默病的分子发病机制仍知之甚少。我们利用冷冻电子显微镜（cryo-EM）分别测定了ABCA7的载脂蛋白和底物结合型结构。结合活性测定，我们确定了以 "尾对尾 "方式特异性结合两分子磷脂酰丝氨酸（PS）的残基。下拉实验证实载脂蛋白与 ABCA7 直接相互作用；此外，在载脂蛋白存在的情况下，ABCA7 的 ATPase 和脂质转运活性都显著增强。我们还测定了ABCA7基因中一个家族性AD变体和一个临床报道的保护性变体的活性。我们的发现不仅从结构上揭示了 ABCA7 介导的 PS 转运，而且还首次提供了生化证据，证明它通过将脂质转运到载脂蛋白E而与 AD 联系在一起。
{"title":"Structural insights into human ABCA7-mediated lipid transport","authors":"Shu-Cheng Fang, Liang Wang, Meng-Ting Cheng, Da Xu, Zhi-Peng Chen, Jie Wang, Wenli Liao, Yanyan Li, Cong-Zhao Zhou, Wen-Tao Hou, Yuxing Chen","doi":"10.1016/j.str.2024.12.015","DOIUrl":"https://doi.org/10.1016/j.str.2024.12.015","url":null,"abstract":"The human ATP-binding cassette (ABC) transporter ABCA7 participates in the lipidation of apolipoprotein ApoE, a commonly recognized risk factor for Alzheimer’s disease (AD). How ABCA7 is involved in the molecular pathogenesis of AD remains poorly understood. Using cryoelectron microscopy (cryo-EM), we determined ABCA7 structures in the apo and substrate-bound forms, respectively. Combined with activity assays, we assigned the residues that specifically bind two molecules of phosphatidylserine (PS) that are arranged in a “tail-to-tail” manner. Pull-down assays confirmed that ApoE directly interacts with ABCA7; and moreover, both ATPase and lipid transport activities of ABCA7 were significantly enhanced in the presence of ApoE. We also measured the activities of a familial AD variant and a protective clinically reported variant in the ABCA7 gene. Our findings not only give structural insights into ABCA7-mediated PS translocation, but we also provide first biochemical evidence for its link to AD by forwarding lipids to ApoE.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"31 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142987468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-17DOI: 10.1016/j.str.2025.01.007
Erika Pellegrini, Pauline Juyoux, Jill von Velsen, Nicola J. Baxter, Hugh R.W. Dannatt, Yi Jin, Matthew J. Cliff, Jonathan P. Waltho, Matthew W. Bowler
(Structure 32, 1834–1846; October 3, 2024)
(结构32,1834-1846；2024年10月3日)
{"title":"Metal fluorides—multi-functional tools for the study of phosphoryl transfer enzymes, a practical guide","authors":"Erika Pellegrini, Pauline Juyoux, Jill von Velsen, Nicola J. Baxter, Hugh R.W. Dannatt, Yi Jin, Matthew J. Cliff, Jonathan P. Waltho, Matthew W. Bowler","doi":"10.1016/j.str.2025.01.007","DOIUrl":"https://doi.org/10.1016/j.str.2025.01.007","url":null,"abstract":"(Structure <em>32</em>, 1834–1846; October 3, 2024)","PeriodicalId":22168,"journal":{"name":"Structure","volume":"18 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142989515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-17DOI: 10.1016/j.str.2024.12.014
Sung-Hyun Hong, So Young An, Changkon Park, Youngim Kim, Eun-Hee Kim, Nak-Kyoon Kim, Jeong-Yong Suh
CRISPR-Cas is a bacterial defense system that employs RNA-guided endonucleases to destroy invading foreign nucleic acids. Bacteriophages produce anti-CRISPR (Acr) proteins to evade CRISPR-Cas defense during the infection. AcrIIC5, a type II-C Cas9 inhibitor, exhibits unusual variations in the local backbone fold between its orthologs. Here we investigated how the folding variations affect the inhibition of target Cas9 using AcrIIC5 orthologs. Structural comparison of free AcrIIC5Smu and AcrIIC5Nch confirmed that the folding variation correlated with characteristic indels in the helical region. Mutagenesis and biochemical assays combined with AlphaFold2 predictions identified key residues of AcrIIC5 orthologs important for Cas9 inhibition. Remarkably, AcrIIC5 orthologs employed divergent binding interfaces via folding variations to inhibit the Cas9 targets. Our study suggests that Acr proteins have evolved structural variants to diversify key interfaces for target Cas9, which could be beneficial for the adaptation of phages to evasive mutations on the Cas9 surface.
{"title":"Structural variants of AcrIIC5 inhibit Cas9 via divergent binding interfaces","authors":"Sung-Hyun Hong, So Young An, Changkon Park, Youngim Kim, Eun-Hee Kim, Nak-Kyoon Kim, Jeong-Yong Suh","doi":"10.1016/j.str.2024.12.014","DOIUrl":"https://doi.org/10.1016/j.str.2024.12.014","url":null,"abstract":"CRISPR-Cas is a bacterial defense system that employs RNA-guided endonucleases to destroy invading foreign nucleic acids. Bacteriophages produce anti-CRISPR (Acr) proteins to evade CRISPR-Cas defense during the infection. AcrIIC5, a type II-C Cas9 inhibitor, exhibits unusual variations in the local backbone fold between its orthologs. Here we investigated how the folding variations affect the inhibition of target Cas9 using AcrIIC5 orthologs. Structural comparison of free AcrIIC5<sub>Smu</sub> and AcrIIC5<sub>Nch</sub> confirmed that the folding variation correlated with characteristic indels in the helical region. Mutagenesis and biochemical assays combined with AlphaFold2 predictions identified key residues of AcrIIC5 orthologs important for Cas9 inhibition. Remarkably, AcrIIC5 orthologs employed divergent binding interfaces via folding variations to inhibit the Cas9 targets. Our study suggests that Acr proteins have evolved structural variants to diversify key interfaces for target Cas9, which could be beneficial for the adaptation of phages to evasive mutations on the Cas9 surface.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"4 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142987467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-15DOI: 10.1016/j.str.2024.12.013
Sebastian Kenny, Shalini Iyer, Clinton A. Gabel, Natalia Tegenfeldt, Andrew G. DeMarco, Mark C. Hall, Leifu Chang, V. Jo Davisson, Scott Vande Pol, Chittaranjan Das
High-risk human papillomavirus E6 oncoprotein is a model system for the recognition and degradation of cellular p53 tumor suppressor protein. There remains a gap in the understanding of the ubiquitin transfer reaction, including placement of the E6AP catalytic HECT domain of the ligase concerning the p53 substrate and how E6 itself is protected from ubiquitination. We determined the cryoelectron microscopy (cryo-EM) structure of the E6AP/E6/p53 complex, related the structure to in vivo modeling of the tri-molecular complex, and identified structural interactions associated with activation of the ubiquitin ligase function. The structure reveals that the N-terminal ordered domain (NOD) in E6AP has a terminal alpha helix that mediates the interaction of the NOD with the HECT domain of E6AP and protects the HPV-E6 protein from ubiquitination. In addition, this NOD helix is required for E6AP ligase function by contributing to the affinity of the E6-E6AP association, modulating E6 substrate recognition, while displacing UbcH7.
{"title":"Structure of E6AP in complex with HPV16-E6 and p53 reveals a novel ordered domain important for E3 ligase activation","authors":"Sebastian Kenny, Shalini Iyer, Clinton A. Gabel, Natalia Tegenfeldt, Andrew G. DeMarco, Mark C. Hall, Leifu Chang, V. Jo Davisson, Scott Vande Pol, Chittaranjan Das","doi":"10.1016/j.str.2024.12.013","DOIUrl":"https://doi.org/10.1016/j.str.2024.12.013","url":null,"abstract":"High-risk human papillomavirus E6 oncoprotein is a model system for the recognition and degradation of cellular p53 tumor suppressor protein. There remains a gap in the understanding of the ubiquitin transfer reaction, including placement of the E6AP catalytic HECT domain of the ligase concerning the p53 substrate and how E6 itself is protected from ubiquitination. We determined the cryoelectron microscopy (cryo-EM) structure of the E6AP/E6/p53 complex, related the structure to <em>in vivo</em> modeling of the tri-molecular complex, and identified structural interactions associated with activation of the ubiquitin ligase function. The structure reveals that the N-terminal ordered domain (NOD) in E6AP has a terminal alpha helix that mediates the interaction of the NOD with the HECT domain of E6AP and protects the HPV-E6 protein from ubiquitination. In addition, this NOD helix is required for E6AP ligase function by contributing to the affinity of the E6-E6AP association, modulating E6 substrate recognition, while displacing UbcH7.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"41 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142981362","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-13DOI: 10.1016/j.str.2024.12.012
Benjamin Russell Lewis, Muhammad R. Uddin, Katie M. Kuo, Laila M.N. Shah, Nicola J. Harris, Paula J. Booth, Dietmar Hammerschmid, James C. Gumbart, Helen I. Zgurskaya, Eamonn Reading
Tripartite resistance nodulation and cell division multidrug efflux pumps span the periplasm and are major drivers of multidrug resistance among gram-negative bacteria. Cations, such as Mg2+, become concentrated within the periplasm and, in contrast to the cytoplasm, its pH is sensitive to conditions outside the cell. Here, we reveal an interplay between Mg2+ and pH in modulating the structural dynamics of the periplasmic adapter protein, AcrA, and its function within the prototypical AcrAB-TolC multidrug pump from Escherichia coli. In the absence of Mg2+, AcrA becomes increasingly plastic within acidic conditions, but when Mg2+ is bound this is ameliorated, resulting instead in domain specific organization. We establish a unique histidine residue directs these dynamics and is essential for sustaining pump activity across acidic, neutral, and basic regimes. Overall, we propose Mg2+ conserves AcrA structural mobility to ensure optimal AcrAB-TolC function within rapidly changing environments commonly faced during bacterial infection and colonization.
{"title":"Mg2+-dependent mechanism of environmental versatility in a multidrug efflux pump","authors":"Benjamin Russell Lewis, Muhammad R. Uddin, Katie M. Kuo, Laila M.N. Shah, Nicola J. Harris, Paula J. Booth, Dietmar Hammerschmid, James C. Gumbart, Helen I. Zgurskaya, Eamonn Reading","doi":"10.1016/j.str.2024.12.012","DOIUrl":"https://doi.org/10.1016/j.str.2024.12.012","url":null,"abstract":"Tripartite resistance nodulation and cell division multidrug efflux pumps span the periplasm and are major drivers of multidrug resistance among gram-negative bacteria. Cations, such as Mg<sup>2+</sup>, become concentrated within the periplasm and, in contrast to the cytoplasm, its pH is sensitive to conditions outside the cell. Here, we reveal an interplay between Mg<sup>2+</sup> and pH in modulating the structural dynamics of the periplasmic adapter protein, AcrA, and its function within the prototypical AcrAB-TolC multidrug pump from <em>Escherichia coli</em>. In the absence of Mg<sup>2+</sup>, AcrA becomes increasingly plastic within acidic conditions, but when Mg<sup>2+</sup> is bound this is ameliorated, resulting instead in domain specific organization. We establish a unique histidine residue directs these dynamics and is essential for sustaining pump activity across acidic, neutral, and basic regimes. Overall, we propose Mg<sup>2+</sup> conserves AcrA structural mobility to ensure optimal AcrAB-TolC function within rapidly changing environments commonly faced during bacterial infection and colonization.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"39 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142967995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-13DOI: 10.1016/j.str.2024.12.011
Elżbieta Wątor-Wilk, Piotr Wilk, Przemysław Grudnik
Deoxyhypusination is the first rate-limiting step of the unique post-translational modification—hypusination—that is catalyzed by deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase (DOHH). This modification is essential for the activation of translation factor 5A in eukaryotes (eIF5A) and Archaea (aIF5A). This perspective focuses on the structural biology of deoxyhypusination complexes in eukaryotic and archaeal organisms. Based on recently published crystal and cryogenic electron microscopy (cryo-EM) structures of deoxyhypusination complexes from three different organisms, we compare the structural features and stoichiometries of DHS-IF5A complexes across different species. We discuss conserved elements in the active site architecture and binding interfaces as well as significant differences in their stoichiometry and regulation mechanisms. The structural insights provide a comprehensive understanding of the deoxyhypusination process and highlight evolutionary adaptations across the domains of life. Future research should focus on the regulatory mechanisms governing DHS activity and the functional implications of stoichiometric variations in different organisms.
{"title":"The structural biology of deoxyhypusination complexes","authors":"Elżbieta Wątor-Wilk, Piotr Wilk, Przemysław Grudnik","doi":"10.1016/j.str.2024.12.011","DOIUrl":"https://doi.org/10.1016/j.str.2024.12.011","url":null,"abstract":"Deoxyhypusination is the first rate-limiting step of the unique post-translational modification—hypusination—that is catalyzed by deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase (DOHH). This modification is essential for the activation of translation factor 5A in eukaryotes (eIF5A) and Archaea (aIF5A). This perspective focuses on the structural biology of deoxyhypusination complexes in eukaryotic and archaeal organisms. Based on recently published crystal and cryogenic electron microscopy (cryo-EM) structures of deoxyhypusination complexes from three different organisms, we compare the structural features and stoichiometries of DHS-IF5A complexes across different species. We discuss conserved elements in the active site architecture and binding interfaces as well as significant differences in their stoichiometry and regulation mechanisms. The structural insights provide a comprehensive understanding of the deoxyhypusination process and highlight evolutionary adaptations across the domains of life. Future research should focus on the regulatory mechanisms governing DHS activity and the functional implications of stoichiometric variations in different organisms.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"84 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142967974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-10DOI: 10.1016/j.str.2024.12.010
Michael DiDonato, Carolina Turk Simpson, Todd Vo, Mark Knuth, Bernhard Geierstanger, Joanna Jamontt, David H. Jones, John W. Fathman, Donnie DeLarosa, Tobias Junt, Damien Picard, Ulrike Sommer, Morten Bagger, Eric Peters, Shelly Meeusen, Glen Spraggon
Inflammatory bowel disease (IBD) consists of chronic conditions that severely impact a patient’s health and quality of life. Interleukin-10 (IL-10), a potent anti-inflammatory cytokine has strong genetic links to IBD susceptibility and has shown strong efficacy in IBD rodent models, suggesting it has great therapeutic potential. However, when tested in clinical trials for IBD, recombinant human IL-10 (rhIL-10) showed weak and inconsistent efficacy due to its short half-life and pro-inflammatory properties that counteract the anti-inflammatory efficacy. Here we present an engineered, IL-10, antibody-graft therapeutic (GFT-IL10M) designed to rectify these issues. GFT-IL10M combines the half-life extension properties of a monoclonal IgG antibody with altered IL-10 cell-type selective signaling, retaining desirable signaling on monocytes while reducing unwanted signaling on T, natural killer (NK), and B cells. Our structural and biochemical results indicate that the altered IL-10 topology in GFT-IL10M leads to a predominantly anti-inflammatory profile, potentially altering cell-type specific signaling patterns and extending half-life.
{"title":"A novel interleukin-10 antibody graft to treat inflammatory bowel disease","authors":"Michael DiDonato, Carolina Turk Simpson, Todd Vo, Mark Knuth, Bernhard Geierstanger, Joanna Jamontt, David H. Jones, John W. Fathman, Donnie DeLarosa, Tobias Junt, Damien Picard, Ulrike Sommer, Morten Bagger, Eric Peters, Shelly Meeusen, Glen Spraggon","doi":"10.1016/j.str.2024.12.010","DOIUrl":"https://doi.org/10.1016/j.str.2024.12.010","url":null,"abstract":"Inflammatory bowel disease (IBD) consists of chronic conditions that severely impact a patient’s health and quality of life. Interleukin-10 (IL-10), a potent anti-inflammatory cytokine has strong genetic links to IBD susceptibility and has shown strong efficacy in IBD rodent models, suggesting it has great therapeutic potential. However, when tested in clinical trials for IBD, recombinant human IL-10 (rhIL-10) showed weak and inconsistent efficacy due to its short half-life and pro-inflammatory properties that counteract the anti-inflammatory efficacy. Here we present an engineered, IL-10, antibody-graft therapeutic (GFT-IL10M) designed to rectify these issues. GFT-IL10M combines the half-life extension properties of a monoclonal IgG antibody with altered IL-10 cell-type selective signaling, retaining desirable signaling on monocytes while reducing unwanted signaling on T, natural killer (NK), and B cells. Our structural and biochemical results indicate that the altered IL-10 topology in GFT-IL10M leads to a predominantly anti-inflammatory profile, potentially altering cell-type specific signaling patterns and extending half-life.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"1 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142939573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-10DOI: 10.1016/j.str.2024.12.008
Sarah R. Stevenson, Svetomir B. Tzokov, Indrajit Lahiri, Kathryn R. Ayscough, Per A. Bullough
The core component of the actin cytoskeleton is the globular protein G-actin, which reversibly polymerizes into filaments (F-actin). Budding yeast possesses a single actin that shares 87%–89% sequence identity with vertebrate actin isoforms. Previous structural studies indicate very close overlap of main-chain backbones. Intriguingly, however, substitution of yeast ACT1 with vertebrate β-cytoplasmic actin severely disrupts cell function and the substitution with a skeletal muscle isoform is lethal. Here we report a 2.5 Å structure of budding yeast F-actin. Previously unresolved side-chain information allows us to highlight four main differences in the comparison of yeast and vertebrate ADP F-actins: a more open nucleotide binding pocket; a more solvent exposed C-terminus; a rearrangement of inter-subunit binding interactions in the vicinity of the D loop and changes in the hydrogen bonding network in the vicinity of histidine 73 (yeast actin) and methyl-histidine 73 (vertebrate actin).
肌动蛋白细胞骨架的核心成分是球形蛋白g -肌动蛋白，它可逆地聚合成细丝（f -肌动蛋白）。出芽酵母具有一个单一的肌动蛋白，与脊椎动物肌动蛋白同工型具有87%-89%的序列一致性。先前的结构研究表明，主链主干的重叠非常紧密。然而，有趣的是，用脊椎动物β-细胞质肌动蛋白替代酵母ACT1严重破坏细胞功能，并用骨骼肌同种异构体替代是致命的。在这里，我们报告了出芽酵母f -肌动蛋白的2.5 Å结构。先前未解决的侧链信息使我们能够突出酵母和脊椎动物ADP f -actin比较中的四个主要差异：更开放的核苷酸结合袋；一个更具溶剂性的暴露c端；D环附近亚基间结合相互作用的重排以及组氨酸73（酵母肌动蛋白）和甲基组氨酸73（脊椎动物肌动蛋白）附近氢键网络的变化。
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