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Ringing the changes: Regulation of Parkin activity by different ubiquitin and ubiquitin-like proteins 环形变化：不同泛素和泛素样蛋白对 Parkin 活性的调控
IF 5.7 2区 生物学
Structure Pub Date : 2024-11-07 DOI: 10.1016/j.str.2024.10.015
Shalini Iyer, Chittaranjan Das
{"title":"Ringing the changes: Regulation of Parkin activity by different ubiquitin and ubiquitin-like proteins","authors":"Shalini Iyer, Chittaranjan Das","doi":"10.1016/j.str.2024.10.015","DOIUrl":"https://doi.org/10.1016/j.str.2024.10.015","url":null,"abstract":"Phosphorylation of ubiquitin and the ubiquitin-like domain of Parkin, mediated by the kinase PINK1, is essential for the liberation of the E3 ligase from its autoinhibited state. In this issue of <em>Structure</em>, Lenka et al.<span><span><sup>1</sup></span></span> provide the structural basis for the specificity and stronger Parkin activation by phospho-NEDD8 compared to phospho-ubiquitin.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"95 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142596477","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}
引用次数: 0
Multi-step shapeshifting of SARS-CoV-2 Omicron spikes during fusion SARS-CoV-2 Omicron 穗状病毒在融合过程中的多步变形
IF 5.7 2区 生物学
Structure Pub Date : 2024-11-07 DOI: 10.1016/j.str.2024.10.017
Wang Xu, Yang Han, Maolin Lu
{"title":"Multi-step shapeshifting of SARS-CoV-2 Omicron spikes during fusion","authors":"Wang Xu, Yang Han, Maolin Lu","doi":"10.1016/j.str.2024.10.017","DOIUrl":"https://doi.org/10.1016/j.str.2024.10.017","url":null,"abstract":"In this issue of <em>Structure</em>, Dey et al.<span><span><sup>1</sup></span></span> employ single-molecule FRET to map the conformational trajectory of Omicron spikes during fusion, revealing a transition from pre-fusion to post-fusion through two intermediates. This study highlights the roles of acidic environments, Ca<sup>2+</sup>, and receptors in promoting SARS-CoV-2 cell entry.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"13 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142596478","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}
引用次数: 0
Traces of convergent evolution left in the structure of EgtB-IV EgtB-IV 结构中留下的趋同进化痕迹
IF 5.7 2区 生物学
Structure Pub Date : 2024-11-07 DOI: 10.1016/j.str.2024.10.006
Taku Mizutani, Ikuro Abe
{"title":"Traces of convergent evolution left in the structure of EgtB-IV","authors":"Taku Mizutani, Ikuro Abe","doi":"10.1016/j.str.2024.10.006","DOIUrl":"https://doi.org/10.1016/j.str.2024.10.006","url":null,"abstract":"The enzymatically regioselective catalyzed incorporation of cysteine sulfoxide into histidine generates physiologically important antioxidants such as ergothioneine and ovothiol. In this issue of <em>Structure</em>, Ireland et al.<span><span><sup>1</sup></span></span> report the crystal structure of EgtB-IV, which provides insights into the convergent evolution of sulfoxide synthase.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"9 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142596476","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}
引用次数: 0
Visualizing the dual interaction of calcineurin with PI4KA and FAM126A 钙调素与 PI4KA 和 FAM126A 的双重相互作用的可视化
IF 5.7 2区 生物学
Structure Pub Date : 2024-11-07 DOI: 10.1016/j.str.2024.10.010
Qingtong Zhou, Xiao Liu, Ming-Wei Wang
{"title":"Visualizing the dual interaction of calcineurin with PI4KA and FAM126A","authors":"Qingtong Zhou, Xiao Liu, Ming-Wei Wang","doi":"10.1016/j.str.2024.10.010","DOIUrl":"https://doi.org/10.1016/j.str.2024.10.010","url":null,"abstract":"In this issue of <em>Structure</em>, Shaw et al.<span><span><sup>1</sup></span></span> visualize the PI4KA-TTC7B-FAM126A-calcineurin complex by combining cryo-EM, HDX-MS, and AlphaFold3, and reveal a dual interaction of calcineurin with PI4KA and FAM126A. This work promotes our understanding of calcineurin-regulated PI4KA activity and paves the way for further exploration of the roles of PI4KA in the plasma membrane.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"18 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142598266","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}
引用次数: 0
Structure, function, surf, repeat: A week at Lorne Proteins 2024 结构、功能、冲浪、重复：2024 年洛恩蛋白质展一周回顾
IF 5.7 2区 生物学
Structure Pub Date : 2024-11-07 DOI: 10.1016/j.str.2024.10.007
Rosemary J. Cater, Renae M. Ryan, Jonathan S. Oakhill, Peter Czabotar, James M. Murphy, Melissa J. Call
{"title":"Structure, function, surf, repeat: A week at Lorne Proteins 2024","authors":"Rosemary J. Cater, Renae M. Ryan, Jonathan S. Oakhill, Peter Czabotar, James M. Murphy, Melissa J. Call","doi":"10.1016/j.str.2024.10.007","DOIUrl":"https://doi.org/10.1016/j.str.2024.10.007","url":null,"abstract":"Since 1976, the Lorne Proteins Conference has been a key gathering for protein scientists, combining cutting-edge research with community engagement in a picturesque corner of the world. Renowned for its diverse international speakers and collaborative spirit, the conference looks forward to its 50<sup>th</sup> anniversary in 2025.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"4 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142596475","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}
引用次数: 0
IspE kinase as an anti-infective target: Role of a hydrophobic pocket in inhibitor binding 作为抗感染靶标的 IspE 激酶：疏水袋在抑制剂结合中的作用
IF 5.7 2区 生物学
Structure Pub Date : 2024-11-06 DOI: 10.1016/j.str.2024.10.009
Rawia Hamid, Danica J. Walsh, Eleonora Diamanti, Diana Aguilar, Antoine Lacour, Mostafa M. Hamed, Anna K.H. Hirsch
{"title":"IspE kinase as an anti-infective target: Role of a hydrophobic pocket in inhibitor binding","authors":"Rawia Hamid, Danica J. Walsh, Eleonora Diamanti, Diana Aguilar, Antoine Lacour, Mostafa M. Hamed, Anna K.H. Hirsch","doi":"10.1016/j.str.2024.10.009","DOIUrl":"https://doi.org/10.1016/j.str.2024.10.009","url":null,"abstract":"Enzymes of the methylerythritol phosphate (MEP) pathway are potential targets for antimicrobial drug discovery. Here, we focus on 4-diphosphocytidyl-2-<em>C</em>-methyl-D-erythritol (IspE) kinase from the MEP pathway. We use biochemical and structural biology methods to investigate homologs from pathogenic microorganisms; <em>Escherichia coli</em>, <em>Klebsiella pneumoniae</em>, and <em>Acinetobacter baumannii</em>. We determined the X-ray crystal structures of IspE-inhibitor complexes and studied inhibitors’ binding modes targeting the substrate pocket. The experimental results indicate the need for distinct inhibitor strategies due to structural differences among IspE homologs, particularly for <em>A. baumannii</em> IspE, which displays a unique inhibitory profile due to a tighter hydrophobic subpocket in the substrate binding site. This study enhances our understanding of the MEP enzymes and sets the stage for structure-based drug design of selective inhibitors to combat pathogenic microorganisms.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"25 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142589076","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}
引用次数: 0
AI-driven mechanistic analysis of conformational dynamics in CNNM/CorC Mg2+ transporters 人工智能驱动的 CNNM/CorC Mg2+ 转运体构象动力学机理分析
IF 5.7 2区 生物学
Structure Pub Date : 2024-11-06 DOI: 10.1016/j.str.2024.10.021
Jie Ma, Xingyu Song, Yosuke Funato, Xinyu Teng, Yichen Huang, Hiroaki Miki, Wenning Wang, Motoyuki Hattori
{"title":"AI-driven mechanistic analysis of conformational dynamics in CNNM/CorC Mg2+ transporters","authors":"Jie Ma, Xingyu Song, Yosuke Funato, Xinyu Teng, Yichen Huang, Hiroaki Miki, Wenning Wang, Motoyuki Hattori","doi":"10.1016/j.str.2024.10.021","DOIUrl":"https://doi.org/10.1016/j.str.2024.10.021","url":null,"abstract":"The CNNM/CorC Mg<sup>2+</sup> transporters are widely conserved in eukaryotes (cyclin M [CNNM]) and prokaryotes (CorC) and participate in various biological processes. Previous structural analyses of the CorC transmembrane domain in the Mg<sup>2+</sup>-bound inward-facing conformation revealed the conserved Mg<sup>2+</sup> recognition mechanism in the CNNM/CorC family; however, the conformational dynamics in the Mg<sup>2+</sup> transport cycle remain unclear because structures in other conformations are unknown. Here, we used AlphaFold structure prediction to predict the occluded-like and outward-facing-like conformations of the CorC and CNNM proteins and identified conserved hydrophilic interactions close to the cytoplasmic side in these conformations. Molecular dynamics simulations and biochemical cross-linking showed that these conserved hydrophilic interactions are stable, especially in the outward-facing-like conformation. Furthermore, mutational analysis revealed that the residues involved in these hydrophilic interactions on the cytoplasmic side are important for Mg<sup>2+</sup> transport in the CorC and CNNM proteins. Our work provides mechanistic insights into the transport cycle of the CNNM/CorC family.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"19 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142588816","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}
引用次数: 0
Archaeal NusA2 is the ancestor of ribosomal protein eS7 in eukaryotes 古生物 NusA2 是真核生物核糖体蛋白 eS7 的祖先
IF 5.7 2区 生物学
Structure Pub Date : 2024-11-05 DOI: 10.1016/j.str.2024.10.019
Duy Khanh Phung, Simona Pilotto, Dorota Matelska, Fabian Blombach, Nikos Pinotsis, Ladislav Hovan, Francesco Luigi Gervasio, Finn Werner
{"title":"Archaeal NusA2 is the ancestor of ribosomal protein eS7 in eukaryotes","authors":"Duy Khanh Phung, Simona Pilotto, Dorota Matelska, Fabian Blombach, Nikos Pinotsis, Ladislav Hovan, Francesco Luigi Gervasio, Finn Werner","doi":"10.1016/j.str.2024.10.019","DOIUrl":"https://doi.org/10.1016/j.str.2024.10.019","url":null,"abstract":"N-utilization substance A (NusA) is a regulatory factor with pleiotropic functions in gene expression in bacteria. Archaea encode two conserved small proteins, NusA1 and NusA2, with domains orthologous to the two RNA binding K Homology (KH) domains of NusA. Here, we report the crystal structures of NusA2 from <em>Sulfolobus acidocaldarius</em> and <em>Saccharolobus solfataricus</em> obtained at 3.1 Å and 1.68 Å, respectively. NusA2 comprises an N-terminal zinc finger followed by two KH-like domains lacking the GXXG signature. Despite the loss of the GXXG motif, NusA2 binds single-stranded RNA. Mutations in the zinc finger domain compromise the structural integrity of NusA2 at high temperatures and molecular dynamics simulations indicate that zinc binding provides an energy barrier preventing the domain from reaching unfolded states. A structure-guided phylogenetic analysis of the KH-like domains supports the notion that the NusA2 clade is ancestral to the ribosomal protein eS7 in eukaryotes, implying a potential role of NusA2 in translation.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"10 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142580560","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}
引用次数: 0
Two cooperative lipid binding sites within the pleckstrin homology domain are necessary for AKT binding and stabilization to the plasma membrane pleckstrin同源结构域中的两个合作脂质结合位点是AKT与质膜结合和稳定的必要条件
IF 5.7 2区 生物学
Structure Pub Date : 2024-11-05 DOI: 10.1016/j.str.2024.10.020
Chrysa Soteriou, Mengfan Xu, Simon D. Connell, Arwen I.I. Tyler, Antreas C. Kalli, James L. Thorne
{"title":"Two cooperative lipid binding sites within the pleckstrin homology domain are necessary for AKT binding and stabilization to the plasma membrane","authors":"Chrysa Soteriou, Mengfan Xu, Simon D. Connell, Arwen I.I. Tyler, Antreas C. Kalli, James L. Thorne","doi":"10.1016/j.str.2024.10.020","DOIUrl":"https://doi.org/10.1016/j.str.2024.10.020","url":null,"abstract":"Almost four decades after the identification of the AKT protein and understanding of its role in cancer, barriers remain in the translation of AKT inhibitors for clinical applications. Here, we provide new molecular insight into the first step of AKT activation where AKT binds to the plasma membrane and its orientation is stabilized in a bilayer with lateral heterogeneity (L<sub>o</sub>-L<sub>d</sub> phase coexistence). We have applied molecular dynamic simulations and molecular and cell biology approaches, and demonstrate that AKT recruitment to the membrane requires a second binding site in the AKT pleckstrin homology (PH) domain that acts cooperatively with the known canonical binding site. Given the precision with which we have identified the protein-lipid interactions, the study offers new directions for AKT-targeted therapy and for testing small molecules to target these specific amino acid-PIP molecular bonds.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"129 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142580515","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}
引用次数: 0
Crystal structure of the alternative complex III from the phototrophic bacterium Chloroflexus aurantiacus 光营养细菌 Chloroflexus aurantiacus 的替代复合体 III 的晶体结构
IF 5.7 2区 生物学
Structure Pub Date : 2024-11-04 DOI: 10.1016/j.str.2024.10.014
Wenping Wu, Han Fang, Huimin He, Jingyi Wu, Zijun Gong, Chunyang Li, Xinkai Pei, Xiaoling Xu
{"title":"Crystal structure of the alternative complex III from the phototrophic bacterium Chloroflexus aurantiacus","authors":"Wenping Wu, Han Fang, Huimin He, Jingyi Wu, Zijun Gong, Chunyang Li, Xinkai Pei, Xiaoling Xu","doi":"10.1016/j.str.2024.10.014","DOIUrl":"https://doi.org/10.1016/j.str.2024.10.014","url":null,"abstract":"Alternative complex III (ACIII) is a multi-subunit quinol:electron acceptor oxidoreductase that couples quinol oxidation with transmembrane proton translocation in bacterial respiratory and photosynthetic electron transport chains. Four ACIII cryoelectron microscopy (cryo-EM) structures are known. However, the effects of cryo-EM versus X-ray crystallography structure determination on ACIII structure are unclear. Here, we report a 3.25 Å crystal structure of photosynthetic ACIII from <em>Chloroflexus aurantiacus</em> (<em>Ca</em>ACIIIp), revealing eight subunits (ActA–G and I) with four iron-sulfur clusters and six <em>c</em>-type hemes, a menaquinol-binding site, and two proton translocation passages. Structural comparisons with the previously reported cryo-EM structures reveal slight local conformational changes in the solvent-exposed regions of ActB, ActD, ActG, and the transmembrane (TM) helix of subunit I. The regions conferring structural flexibility possess low sequence conservation across species. However, the core functional modules containing the menaquinol-binding pocket, redox centers, and proton translocation passages remain unchanged, preserving the enzyme’s activity.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"73 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142574504","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}
引用次数: 0
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