Pub Date : 2025-01-29DOI: 10.1016/j.str.2025.01.001
Nicholas C. Morano, Yicheng Guo, Jordan E. Becker, Zhiteng Li, Jian Yu, David D. Ho, Lawrence Shapiro, Peter D. Kwong
Highly pathogenic avian influenza has spilled into many mammals, most notably cows and poultry, with several dozen human breakthrough infections. Zoonotic crossovers, with hemagglutinins mutated to enhance viral ability to use human α2-6-linked sialic acid receptors versus avian α2-3-linked ones, highlight the pandemic risk. To gain insight into these crossovers, we determined the cryoelectron microscopy (cryo-EM) structure of the hemagglutinin from the zoonotic H5N1 A/Texas/37/2024 strain (clade 2.3.4.4b) in complex with a previously reported neutralizing antibody. Surprisingly, we found that the receptor-binding site of this H5N1 hemagglutinin was already occupied by an α2-3-linked sialic acid and that this glycan emanated from asparagine N169 of a neighboring protomer on hemagglutinin itself. This structure thus highlights recognition by influenza hemagglutinin of an “auto”-α2-3-linked sialic acid from N169, an N-linked glycan conserved in 95% of H5 strains, and adds “auto-glycan recognition,” which may play a role in viral dispersal, to the complexities surrounding H5N1 zoonosis.
{"title":"Structure of a zoonotic H5N1 hemagglutinin reveals a receptor-binding site occupied by an auto-glycan","authors":"Nicholas C. Morano, Yicheng Guo, Jordan E. Becker, Zhiteng Li, Jian Yu, David D. Ho, Lawrence Shapiro, Peter D. Kwong","doi":"10.1016/j.str.2025.01.001","DOIUrl":"https://doi.org/10.1016/j.str.2025.01.001","url":null,"abstract":"Highly pathogenic avian influenza has spilled into many mammals, most notably cows and poultry, with several dozen human breakthrough infections. Zoonotic crossovers, with hemagglutinins mutated to enhance viral ability to use human α2-6-linked sialic acid receptors versus avian α2-3-linked ones, highlight the pandemic risk. To gain insight into these crossovers, we determined the cryoelectron microscopy (cryo-EM) structure of the hemagglutinin from the zoonotic H5N1 A/Texas/37/2024 strain (clade 2.3.4.4b) in complex with a previously reported neutralizing antibody. Surprisingly, we found that the receptor-binding site of this H5N1 hemagglutinin was already occupied by an α2-3-linked sialic acid and that this glycan emanated from asparagine N169 of a neighboring protomer on hemagglutinin itself. This structure thus highlights recognition by influenza hemagglutinin of an “auto”-α2-3-linked sialic acid from N169, an <em>N</em>-linked glycan conserved in 95% of H5 strains, and adds “auto-glycan recognition,” which may play a role in viral dispersal, to the complexities surrounding H5N1 zoonosis.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"31 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143055152","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}
Broadly neutralizing antibodies (nAbs) are vital therapeutic tools to counteract both pandemic and seasonal influenza threats. Traditional strategies for optimizing nAbs generally rely on labor-intensive, high-throughput mutagenesis screens. Here, we present an innovative structure-based design framework for the optimization of nAbs, which integrates epitope-paratope analysis, computational modeling, and rational design approaches, complemented by comprehensive experimental assessment. This approach was applied to optimize MEDI8852, a nAb targeting the stalk region of influenza A virus hemagglutinin (HA). The resulting variant, M18.1.2.2, shows a marked enhancement in both affinity and neutralizing efficacy, as demonstrated both in vitro and in vivo. Computational modeling reveals that this improvement can be attributed to the fine-tuning of interactions between the antibody’s side-chains and the epitope residues that are highly conserved across the influenza A virus HA stalk. Our dry-wet iterative protocol for nAb optimization presented here yielded a promising candidate for influenza intervention.
{"title":"Computational design and improvement of a broad influenza virus HA stem targeting antibody","authors":"Huarui Duan, Xiaojing Chi, Xuehua Yang, Shengnan Pan, Xiuying Liu, Peixiang Gao, Fangyuan Zhang, Xinhui Zhang, Xuemeng Dong, Yi Liao, Wei Yang","doi":"10.1016/j.str.2025.01.002","DOIUrl":"https://doi.org/10.1016/j.str.2025.01.002","url":null,"abstract":"Broadly neutralizing antibodies (nAbs) are vital therapeutic tools to counteract both pandemic and seasonal influenza threats. Traditional strategies for optimizing nAbs generally rely on labor-intensive, high-throughput mutagenesis screens. Here, we present an innovative structure-based design framework for the optimization of nAbs, which integrates epitope-paratope analysis, computational modeling, and rational design approaches, complemented by comprehensive experimental assessment. This approach was applied to optimize MEDI8852, a nAb targeting the stalk region of influenza A virus hemagglutinin (HA). The resulting variant, M18.1.2.2, shows a marked enhancement in both affinity and neutralizing efficacy, as demonstrated both <em>in vitro</em> and <em>in vivo</em>. Computational modeling reveals that this improvement can be attributed to the fine-tuning of interactions between the antibody’s side-chains and the epitope residues that are highly conserved across the influenza A virus HA stalk. Our dry-wet iterative protocol for nAb optimization presented here yielded a promising candidate for influenza intervention.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"112 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143055387","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 : 2025-01-29DOI: 10.1016/j.str.2025.01.003
Allen P. Zinkle, Ryan T. Morgan, Rie Nygaard, Filippo Mancia
Glycosyltransferases (GTs) catalyze the addition of sugars to diverse substrates facilitating complex glycoconjugate biosynthesis across all domains of life. When embedded in or associated with the membrane, these enzymes often depend on polyisoprenyl-phosphate or -pyrophosphate (PP) lipid carriers, including undecaprenyl phosphate in bacteria and dolichol phosphate in eukaryotes, to transfer glycan moieties. GTs that bind PP substrates (PP-GTs) are functionally diverse but share some common structural features within their family or subfamily, particularly with respect to how they interact with their cognate PP ligands. Recent advances in single-particle cryo-electron microscopy (cryo-EM) have provided insight into the structures of PP-GTs and the modes by which they bind their PP ligands. Here, we explore the structural landscape of PP-GTs, focusing mainly on those for which there is molecular-level information on liganded states, and highlight how PP coordination modalities may be shared or differ among members of this diverse enzyme class.
{"title":"Structural insights into polyisoprenyl-binding glycosyltransferases","authors":"Allen P. Zinkle, Ryan T. Morgan, Rie Nygaard, Filippo Mancia","doi":"10.1016/j.str.2025.01.003","DOIUrl":"https://doi.org/10.1016/j.str.2025.01.003","url":null,"abstract":"Glycosyltransferases (GTs) catalyze the addition of sugars to diverse substrates facilitating complex glycoconjugate biosynthesis across all domains of life. When embedded in or associated with the membrane, these enzymes often depend on polyisoprenyl-phosphate or -pyrophosphate (PP) lipid carriers, including undecaprenyl phosphate in bacteria and dolichol phosphate in eukaryotes, to transfer glycan moieties. GTs that bind PP substrates (PP-GTs) are functionally diverse but share some common structural features within their family or subfamily, particularly with respect to how they interact with their cognate PP ligands. Recent advances in single-particle cryo-electron microscopy (cryo-EM) have provided insight into the structures of PP-GTs and the modes by which they bind their PP ligands. Here, we explore the structural landscape of PP-GTs, focusing mainly on those for which there is molecular-level information on liganded states, and highlight how PP coordination modalities may be shared or differ among members of this diverse enzyme class.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"115 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143055153","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 : 2025-01-24DOI: 10.1016/j.str.2024.12.020
Kendra A. Ireland, Chase M. Kayrouz, Marissa L. Abbott, Mohammad R. Seyedsayamdost, Katherine M. Davis
Thio/selenoimidazole Nπ-methyltransferases are an emerging family of enzymes catalyzing the final step in the production of the S/Se-containing histidine-derived antioxidants ovothiol and ovoselenol. These enzymes, prevalent in prokaryotes, show minimal sequence similarity to other methyltransferases, and the structural determinants of their reactivities remain poorly understood. Herein, we report ligand-bound crystal structures of OvsM from the ovoselenol pathway as well as a member of a previously unknown clade of standalone ovothiol-biosynthetic Nπ-methyltransferases, which we have designated OvoM. Unlike previously reported ovothiol methyltransferases, which are fused as a C-terminal domain to the sulfoxide synthase OvoA, OvoMs function independently. Comparative structural analyses reveal conserved, ligand-induced conformational changes, suggesting similar behavior in dual-domain OvoA enzymes. Mutagenesis supports a model where OvoA domain rearrangement facilitates substrate recognition via a critical Tyr residue in the domain linker. Biochemical studies identify an essential active-site Asp, likely serving as a catalytic base in the SN2-like nucleophilic substitution reaction.
{"title":"Structural and functional analysis of SAM-dependent N-methyltransferases involved in ovoselenol and ovothiol biosynthesis","authors":"Kendra A. Ireland, Chase M. Kayrouz, Marissa L. Abbott, Mohammad R. Seyedsayamdost, Katherine M. Davis","doi":"10.1016/j.str.2024.12.020","DOIUrl":"https://doi.org/10.1016/j.str.2024.12.020","url":null,"abstract":"Thio/selenoimidazole <em>N</em>π-methyltransferases are an emerging family of enzymes catalyzing the final step in the production of the S/Se-containing histidine-derived antioxidants ovothiol and ovoselenol. These enzymes, prevalent in prokaryotes, show minimal sequence similarity to other methyltransferases, and the structural determinants of their reactivities remain poorly understood. Herein, we report ligand-bound crystal structures of OvsM from the ovoselenol pathway as well as a member of a previously unknown clade of standalone ovothiol-biosynthetic <em>N</em>π-methyltransferases, which we have designated OvoM. Unlike previously reported ovothiol methyltransferases, which are fused as a C-terminal domain to the sulfoxide synthase OvoA, OvoMs function independently. Comparative structural analyses reveal conserved, ligand-induced conformational changes, suggesting similar behavior in dual-domain OvoA enzymes. Mutagenesis supports a model where OvoA domain rearrangement facilitates substrate recognition via a critical Tyr residue in the domain linker. Biochemical studies identify an essential active-site Asp, likely serving as a catalytic base in the S<sub>N</sub>2-like nucleophilic substitution reaction.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"13 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143026723","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}
NSUN6 preferentially catalyzes the methylation of cytosine nucleotides in mRNA substrates, which enhances transcription. Dysregulation of NSUN6 catalysis drives the oncogenesis of certain cancers. In this study, we determined the crystal structure of human NSUN6 in complex with its S-adenosyl-L-methionine analog and a bound NECT-2 3′-UTR RNA substrate at 2.9 Å resolution. The complex structure reveals how NSUN6 recognizes the specific CUC[CU]A consensus motif of the substrate and facilitates the methyl transfer from S-adenosyl-L-methionine (SAM) to mRNA. By combining the structural data with nuclear magnetic resonance (NMR)-based fragment screening, a virtual screening, and a further comprehensive biochemical verification, we identified thiamine disulfide as a non-SAM analog lead compound that competes with the CUC[CU]A substrate for binding to NSUN6. Our findings pave the way for the discovery of potent inhibitors for the treatment of NSUN6-driven cancers in the future.
{"title":"NSUN6 inhibitor discovery guided by its mRNA substrate bound crystal structure","authors":"Fumei Zhong, Tian Pu, Qian Hu, Mingwei Li, Lei Wang, Suman Wang, Ke Ruan, Yunyu Shi, Beicheng Sun, Yiyang Jiang, Mengqi Lv","doi":"10.1016/j.str.2024.12.021","DOIUrl":"https://doi.org/10.1016/j.str.2024.12.021","url":null,"abstract":"NSUN6 preferentially catalyzes the methylation of cytosine nucleotides in mRNA substrates, which enhances transcription. Dysregulation of NSUN6 catalysis drives the oncogenesis of certain cancers. In this study, we determined the crystal structure of human NSUN6 in complex with its S-adenosyl-L-methionine analog and a bound NECT-2 3′-UTR RNA substrate at 2.9 Å resolution. The complex structure reveals how NSUN6 recognizes the specific CUC[CU]A consensus motif of the substrate and facilitates the methyl transfer from S-adenosyl-L-methionine (SAM) to mRNA. By combining the structural data with nuclear magnetic resonance (NMR)-based fragment screening, a virtual screening, and a further comprehensive biochemical verification, we identified thiamine disulfide as a non-SAM analog lead compound that competes with the CUC[CU]A substrate for binding to NSUN6. Our findings pave the way for the discovery of potent inhibitors for the treatment of NSUN6-driven cancers in the future.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"1 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143026722","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 : 2025-01-24DOI: 10.1016/j.str.2024.12.019
Yihu Xie, Bradley P. Clarke, Dongqi Xie, Menghan Mei, Prasanna Bhat, Pate S. Hill, Alexia E. Angelos, Tolga Çağatay, Mariam Haider, Scott E. Collier, Melissa G. Chambers, Vasilisa Aksenova, Mary Dasso, Beatriz M.A. Fontoura, Yi Ren
mRNAs are packaged with proteins into messenger ribonucleoprotein complexes (mRNPs) in the nucleus. mRNP assembly and export are of fundamental importance for all eukaryotic gene expression. Before export to the cytoplasm, mRNPs undergo dynamic remodeling governed by the DEAD-box helicase DDX39B (yeast Sub2). DDX39B/Sub2 primarily functions in the nucleus and leaves the mRNP prior to export through the nuclear pore complex; however, the underlying mechanisms remain elusive. Here, we identify the conserved TREX-2 complex as the long-sought factor that facilitates DDX39B/Sub2 to complete the mRNP remodeling cycle. Our crystallographic and cryoelectron microscopy (cryo-EM) analyses demonstrate that TREX-2 modulates the activities of DDX39B/Sub2 through multiple interactions. Critically, a conserved “trigger loop” from TREX-2 splits the two RecA domains of DDX39B/Sub2 and promotes the removal of DDX39B/Sub2 from mRNP. Our findings suggest that TREX-2 coordinates with DDX39B/Sub2 and the human export receptor NXF1-NXT1 (yeast Mex67-Mtr2) to complete the final steps of nuclear mRNP assembly.
{"title":"Structures and mRNP remodeling mechanism of the TREX-2 complex","authors":"Yihu Xie, Bradley P. Clarke, Dongqi Xie, Menghan Mei, Prasanna Bhat, Pate S. Hill, Alexia E. Angelos, Tolga Çağatay, Mariam Haider, Scott E. Collier, Melissa G. Chambers, Vasilisa Aksenova, Mary Dasso, Beatriz M.A. Fontoura, Yi Ren","doi":"10.1016/j.str.2024.12.019","DOIUrl":"https://doi.org/10.1016/j.str.2024.12.019","url":null,"abstract":"mRNAs are packaged with proteins into messenger ribonucleoprotein complexes (mRNPs) in the nucleus. mRNP assembly and export are of fundamental importance for all eukaryotic gene expression. Before export to the cytoplasm, mRNPs undergo dynamic remodeling governed by the DEAD-box helicase DDX39B (yeast Sub2). DDX39B/Sub2 primarily functions in the nucleus and leaves the mRNP prior to export through the nuclear pore complex; however, the underlying mechanisms remain elusive. Here, we identify the conserved TREX-2 complex as the long-sought factor that facilitates DDX39B/Sub2 to complete the mRNP remodeling cycle. Our crystallographic and cryoelectron microscopy (cryo-EM) analyses demonstrate that TREX-2 modulates the activities of DDX39B/Sub2 through multiple interactions. Critically, a conserved “trigger loop” from TREX-2 splits the two RecA domains of DDX39B/Sub2 and promotes the removal of DDX39B/Sub2 from mRNP. Our findings suggest that TREX-2 coordinates with DDX39B/Sub2 and the human export receptor NXF1-NXT1 (yeast Mex67-Mtr2) to complete the final steps of nuclear mRNP assembly.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"58 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143026724","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 : 2025-01-20DOI: 10.1016/j.str.2024.12.018
Arpita Chakravarti, Dinshaw J. Patel
Within the course of evolution, TIR (Toll/interleukin-1 receptor) domains acquired a myriad of functional specificities. This has significantly added to their well-established roles in innate immune signaling. These additional functions include nicotinamide adenine dinucleotide (NAD)(P) hydrolase, RNA/DNA nuclease (in plants), CN (cyclic nucleotide) cyclase, and base exchanger activities. Owing to these diverse functions, TIR domains can either generate CN second messengers or act as effectors, many of which can accomplish depletion of the essential metabolite NAD+, leading to cell death prior to pathogen-induced cell lysis. Despite their functional diversity, activated TIR domains have retained their ability to form multimers that adopt varying topologies, thereby creating composite NADase active sites between adjacent TIR monomers. This structure-based review on the functional diversity of TIR domains focuses primarily across bacterial antiphage defense systems while also addressing their eukaryotic counterparts, throughout highlighting multimerization, including filament formation, as the conserved topological characteristic.
在进化过程中，TIR（Toll/白细胞介素-1 受体）结构域获得了无数的功能特异性。这大大增加了它们在先天性免疫信号传导中的作用。这些附加功能包括烟酰胺腺嘌呤二核苷酸（NAD）（P）水解酶、RNA/DNA 核酸酶（在植物中）、CN（环核苷酸）环化酶和碱基交换活性。由于具有这些不同的功能，TIR 结构域可以产生 CN 第二信使，也可以充当效应器，其中许多效应器可以耗尽必需的代谢物 NAD+，导致细胞在病原体诱导的细胞溶解之前死亡。尽管功能多种多样，但活化的 TIR 结构域仍能形成拓扑结构各异的多聚体，从而在相邻的 TIR 单体之间形成复合的 NAD 酶活性位点。这篇基于结构的 TIR 结构域功能多样性综述主要关注细菌的抗虹吸虫防御系统，同时也探讨了真核生物的对应系统，重点强调了多聚体化（包括丝状体形成）这一保守的拓扑学特征。
{"title":"Structure-guided insights into TIR-mediated bacterial and eukaryotic immunity","authors":"Arpita Chakravarti, Dinshaw J. Patel","doi":"10.1016/j.str.2024.12.018","DOIUrl":"https://doi.org/10.1016/j.str.2024.12.018","url":null,"abstract":"Within the course of evolution, TIR (Toll/interleukin-1 receptor) domains acquired a myriad of functional specificities. This has significantly added to their well-established roles in innate immune signaling. These additional functions include nicotinamide adenine dinucleotide (NAD)(P) hydrolase, RNA/DNA nuclease (in plants), CN (cyclic nucleotide) cyclase, and base exchanger activities. Owing to these diverse functions, TIR domains can either generate CN second messengers or act as effectors, many of which can accomplish depletion of the essential metabolite NAD<sup>+</sup>, leading to cell death prior to pathogen-induced cell lysis. Despite their functional diversity, activated TIR domains have retained their ability to form multimers that adopt varying topologies, thereby creating composite NADase active sites between adjacent TIR monomers. This structure-based review on the functional diversity of TIR domains focuses primarily across bacterial antiphage defense systems while also addressing their eukaryotic counterparts, throughout highlighting multimerization, including filament formation, as the conserved topological characteristic.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"70 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142990087","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.2024.12.016
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}
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.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}
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