Pub Date : 2025-11-21DOI: 10.1016/j.str.2025.10.017
Xing-Yu Yue, Guang-Lei Wang, Mei-Juan Zou, Fei Ma, Zheng-Yu Wang-Otomo, Michael T. Madigan, Long-Jiang Yu
Aerobic anoxygenic phototrophic bacteria (AAPB) are widely distributed in nature and they are important members of the marine phototrophic community. However, a structural and functional understanding of the AAPB photosynthetic apparatus is still lacking. Here, we present cryo-EM structures of the LH1-RC (core) and LH2 (peripheral) photocomplexes from the model aerobic phototroph Erythrobacter (Ery.) sanguineus. The LH1 αβ-heterodimers bind the carotenoids bacteriorubixanthinal and caloxanthin—pigments that are absent from anaerobic anoxygenic phototrophs—to form a closed ring structure. Ery. sanguineus LH1-RC contains a lipid-anchored polypeptide unrelated to any of the auxiliary proteins identified in the core complexes of purple bacteria so far. The Ery. sanguineus LH2 complex shows unique absorption characteristics, with its Qy transition being blue-shifted to 814 nm. This work provides structural insights into the unusual photosynthetic properties of AAPB and points to new avenues to further explore their biology.
{"title":"Cryo-EM structures of photocomplexes from the free-living aerobic anoxygenic phototrophic bacterium Erythrobacter sanguineus","authors":"Xing-Yu Yue, Guang-Lei Wang, Mei-Juan Zou, Fei Ma, Zheng-Yu Wang-Otomo, Michael T. Madigan, Long-Jiang Yu","doi":"10.1016/j.str.2025.10.017","DOIUrl":"https://doi.org/10.1016/j.str.2025.10.017","url":null,"abstract":"Aerobic anoxygenic phototrophic bacteria (AAPB) are widely distributed in nature and they are important members of the marine phototrophic community. However, a structural and functional understanding of the AAPB photosynthetic apparatus is still lacking. Here, we present cryo-EM structures of the LH1-RC (core) and LH2 (peripheral) photocomplexes from the model aerobic phototroph <em>Erythrobacter (Ery.) sanguineus</em>. The LH1 αβ-heterodimers bind the carotenoids bacteriorubixanthinal and caloxanthin—pigments that are absent from anaerobic anoxygenic phototrophs—to form a closed ring structure. <em>Ery. sanguineus</em> LH1-RC contains a lipid-anchored polypeptide unrelated to any of the auxiliary proteins identified in the core complexes of purple bacteria so far. The <em>Ery. sanguineus</em> LH2 complex shows unique absorption characteristics, with its Q<sub>y</sub> transition being blue-shifted to 814 nm. This work provides structural insights into the unusual photosynthetic properties of AAPB and points to new avenues to further explore their biology.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"165 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145567382","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 : 2025-11-19DOI: 10.1016/j.str.2025.10.016
Daniel Wohlwend, Thilo Seifermann, Emmanuel Gnandt, Marta Vranas, Stefan Gerhardt, Thorsten Friedrich
Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is central to energy metabolism by coupling NADH oxidation and quinone reduction with proton translocation across the membrane. Electrons are transferred from the primary acceptor flavin mononucleotide via a chain of iron-sulfur clusters to quinone. The enigmatic cluster N1a is conserved, but not part of this electron transfer chain. We reported on variants of the complex in which N1a is not detectable by EPR spectroscopy. This was tentatively attributed to the lower redox potential of the variant N1a. However, it remained an open question, whether the variants contain this cluster at all. Here, we determined the structures of these variants by X-ray crystallography and cryogenic-electron microscopy. Cluster N1a is present in all variants and the shift of its redox potential is explained by nearby structural changes. A role of the cluster for the mechanism of the complex is discussed.
{"title":"Structural changes shifting the redox potential of the outlying cluster N1a in respiratory complex I","authors":"Daniel Wohlwend, Thilo Seifermann, Emmanuel Gnandt, Marta Vranas, Stefan Gerhardt, Thorsten Friedrich","doi":"10.1016/j.str.2025.10.016","DOIUrl":"https://doi.org/10.1016/j.str.2025.10.016","url":null,"abstract":"Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is central to energy metabolism by coupling NADH oxidation and quinone reduction with proton translocation across the membrane. Electrons are transferred from the primary acceptor flavin mononucleotide <em>via</em> a chain of iron-sulfur clusters to quinone. The enigmatic cluster N1a is conserved, but not part of this electron transfer chain. We reported on variants of the complex in which N1a is not detectable by EPR spectroscopy. This was tentatively attributed to the lower redox potential of the variant N1a. However, it remained an open question, whether the variants contain this cluster at all. Here, we determined the structures of these variants by X-ray crystallography and cryogenic-electron microscopy. Cluster N1a is present in all variants and the shift of its redox potential is explained by nearby structural changes. A role of the cluster for the mechanism of the complex is discussed.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"98 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145545801","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 : 2025-11-14DOI: 10.1016/j.str.2025.10.014
Charlie Lovatt, Thomas O’Sullivan, Clara Ortega-de San Luis, Tomás J. Ryan, René A.W. Frank
Memory is incorporated into the brain as physicochemical changes to engram cells. These neuronal populations form complex neuroanatomical circuits, are modified by experiences to store information, and allow memory recall. At the molecular level, learning modifies synaptic communication to rewire engram circuits. How macromolecules are organized within engram synapses is unknown. Here, we establish engram labeling technology combined with cryogenic correlated light and electron microscopy (cryoCLEM)-guided cryogenic electron tomography (cryoET) to visualize the in-tissue 3D macromolecular architecture of engram synapses of a contextual fear memory within the mouse hippocampus. Engram synapses exhibited structural diversity of macromolecular constituents and organelles in both pre- and postsynaptic compartments and within the synaptic cleft, including in membrane proteins, synaptic vesicle occupancy, and F-actin copy number. This “engram to tomogram” approach, harnessing in vivo functional neuroscience and structural biology, provides a methodological framework for testing fundamental molecular plasticity mechanisms within engram circuits.
记忆通过印记细胞的物理化学变化被纳入大脑。这些神经元群形成了复杂的神经解剖回路，通过经历来存储信息，并允许记忆回忆。在分子水平上，学习改变突触通讯，重新连接印痕电路。大分子如何在印痕突触内组织尚不清楚。在这里，我们建立了结合低温相关光和电子显微镜（cryoCLEM）引导的低温电子断层扫描（cryogenic electron tomography, cryoET）的印迹标记技术，以可视化小鼠海马内情境恐惧记忆的印迹突触的组织内3D大分子结构。印迹突触在突触前和突触后室以及突触间隙内均表现出大分子成分和细胞器的结构多样性，包括膜蛋白、突触囊泡占用和f -肌动蛋白拷贝数。这种“印痕到断层成像”的方法，利用体内功能神经科学和结构生物学，为测试印痕电路中的基本分子可塑性机制提供了一种方法框架。
{"title":"Memory engram synapse 3D macromolecular architecture visualized by cryoCLEM-guided cryoET","authors":"Charlie Lovatt, Thomas O’Sullivan, Clara Ortega-de San Luis, Tomás J. Ryan, René A.W. Frank","doi":"10.1016/j.str.2025.10.014","DOIUrl":"https://doi.org/10.1016/j.str.2025.10.014","url":null,"abstract":"Memory is incorporated into the brain as physicochemical changes to engram cells. These neuronal populations form complex neuroanatomical circuits, are modified by experiences to store information, and allow memory recall. At the molecular level, learning modifies synaptic communication to rewire engram circuits. How macromolecules are organized within engram synapses is unknown. Here, we establish engram labeling technology combined with cryogenic correlated light and electron microscopy (cryoCLEM)-guided cryogenic electron tomography (cryoET) to visualize the in-tissue 3D macromolecular architecture of engram synapses of a contextual fear memory within the mouse hippocampus. Engram synapses exhibited structural diversity of macromolecular constituents and organelles in both pre- and postsynaptic compartments and within the synaptic cleft, including in membrane proteins, synaptic vesicle occupancy, and F-actin copy number. This “engram to tomogram” approach, harnessing <em>in vivo</em> functional neuroscience and structural biology, provides a methodological framework for testing fundamental molecular plasticity mechanisms within engram circuits.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"119 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145509014","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 : 2025-11-06DOI: 10.1016/j.str.2025.10.007
Natalia Fuchs, Venera Weinhardt
In this issue of Structure, Deshmukh et al.1 reveal that β cells actively remodel insulin secretory granules in response to specific physiological cues, altering granule density, proinsulin processing, and spatial distribution. This stimulus-specific structural maturation highlights how β cells sculpt their secretory machinery, offering new insights into insulin release regulation.
{"title":"Soft X-ray tomography illuminates drug-induced changes in insulin granules","authors":"Natalia Fuchs, Venera Weinhardt","doi":"10.1016/j.str.2025.10.007","DOIUrl":"https://doi.org/10.1016/j.str.2025.10.007","url":null,"abstract":"In this issue of <em>Structure</em>, Deshmukh et al.<span><span><sup>1</sup></span></span> reveal that β cells actively remodel insulin secretory granules in response to specific physiological cues, altering granule density, proinsulin processing, and spatial distribution. This stimulus-specific structural maturation highlights how β cells sculpt their secretory machinery, offering new insights into insulin release regulation.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"105 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145447662","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}
Vibrio cholerae cytolysin (VCC) is a β-barrel pore-forming toxin (β-PFT). The membrane insertion of its pore-forming “pre-stem” motif is the most crucial step in the pore-formation mechanism. In the soluble monomeric form, pre-stem remains clamped against the central cytolysin domain by the so-called cradle loop. In the course of oligomeric pore-formation in the target membranes, the cradle loop gets detached from the pre-stem and reorients, thus allowing the pre-stem to extend and insert into the membrane. Here, we show that the specific cradle loop residue(s) play crucial roles in governing the pore-formation mechanism of VCC by establishing decisive interactions with the neighboring structural domains/modules. The alteration of the cradle loop residue, Y194 in particular, compromises the membrane-insertion of the pre-stem, and tends to arrest the membrane-bound toxin in the pre-pore-like oligomeric states. Our study suggests that the native cradle loop architecture, with its intact contacts with the surrounding interaction partners, is essential for VCC pore-formation.
{"title":"Cradle loop regulates β-barrel pore-formation mechanism of Vibrio cholerae cytolysin","authors":"Mahendra Singh, Arnab Chatterjee, Ananya Nayak, Prasenjit Naskar, Gurvinder Kaur, Jagannath Mondal, Somnath Dutta, Kausik Chattopadhyay","doi":"10.1016/j.str.2025.10.013","DOIUrl":"https://doi.org/10.1016/j.str.2025.10.013","url":null,"abstract":"<em>Vibrio cholerae</em> cytolysin (VCC) is a β-barrel pore-forming toxin (β-PFT). The membrane insertion of its pore-forming “pre-stem” motif is the most crucial step in the pore-formation mechanism. In the soluble monomeric form, pre-stem remains clamped against the central cytolysin domain by the so-called cradle loop. In the course of oligomeric pore-formation in the target membranes, the cradle loop gets detached from the pre-stem and reorients, thus allowing the pre-stem to extend and insert into the membrane. Here, we show that the specific cradle loop residue(s) play crucial roles in governing the pore-formation mechanism of VCC by establishing decisive interactions with the neighboring structural domains/modules. The alteration of the cradle loop residue, Y194 in particular, compromises the membrane-insertion of the pre-stem, and tends to arrest the membrane-bound toxin in the pre-pore-like oligomeric states. Our study suggests that the native cradle loop architecture, with its intact contacts with the surrounding interaction partners, is essential for VCC pore-formation.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"43 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145447659","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 : 2025-11-06DOI: 10.1016/j.str.2025.10.003
Yaxin Dai, Chia-Hsueh Lee
Why do certain drugs bind human OAT1 with much higher affinity than the rat ortholog? In this issue of Structure, Jeon et al.1 reveal that serine 203, which is present only in human OAT1, coordinates with a chloride ion and this S203-chloride interaction is crucial for the high-affinity binding of olmesartan and other drugs.
{"title":"Serine encodes drug selectivity in human OAT1","authors":"Yaxin Dai, Chia-Hsueh Lee","doi":"10.1016/j.str.2025.10.003","DOIUrl":"https://doi.org/10.1016/j.str.2025.10.003","url":null,"abstract":"Why do certain drugs bind human OAT1 with much higher affinity than the rat ortholog? In this issue of <em>Structure</em>, Jeon et al.<span><span><sup>1</sup></span></span> reveal that serine 203, which is present only in human OAT1, coordinates with a chloride ion and this S203-chloride interaction is crucial for the high-affinity binding of olmesartan and other drugs.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"12 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145447661","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 : 2025-11-06DOI: 10.1016/j.str.2025.10.008
Jessey Erath, Slavica Pavlovic Djuranovic
In a recent issue of Nature Structural & Molecular Biology, Anton et al.1 produce the first in situ visualization of Plasmodium falciparum ribosomes within infected erythrocytes. Using cryoelectron tomography and cryoelectron microscopy, ten ribosomal states are resolved, five previously unseen in eukaryotes, providing a more comprehensive parasite translation elongation cycle. The work describes parasite-specific translation dynamics, showing how the antimalarial cabamiquine disrupts elongation.
{"title":"Seeing is believing—Plasmodium falciparum translation in action","authors":"Jessey Erath, Slavica Pavlovic Djuranovic","doi":"10.1016/j.str.2025.10.008","DOIUrl":"https://doi.org/10.1016/j.str.2025.10.008","url":null,"abstract":"In a recent issue of <em>Nature Structural & Molecular Biology</em>, Anton et al.<span><span><sup>1</sup></span></span> produce the first <em>in situ</em> visualization of <em>Plasmodium falciparum</em> ribosomes within infected erythrocytes. Using cryoelectron tomography and cryoelectron microscopy, ten ribosomal states are resolved, five previously unseen in eukaryotes, providing a more comprehensive parasite translation elongation cycle. The work describes parasite-specific translation dynamics, showing how the antimalarial cabamiquine disrupts elongation.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"136 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145447675","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 : 2025-11-05DOI: 10.1016/j.str.2025.10.009
Huifang Yan, Fengyun Ni, Qinghua Wang, Jianpeng Ma
Propionyl-CoA carboxylase (PCC) is a biotin-dependent mitochondrial enzyme responsible for propionyl-CoA catabolism. Deficiencies in human PCC (hPCC) cause propionic acidemia, a severe metabolic disorder driven by toxic metabolite accumulation. Despite its therapeutic relevance, the structural basis of hPCC’s catalytic function remains unresolved. Here, we present high-resolution cryo-EM structures of hPCC in four distinct states, unliganded, ADP-, AMPPNP-, and ATP-bound/substrate-bound, capturing the full trajectory of the biotin carboxyl carrier protein (BCCP) domain as it translocates between active sites. Our results reinforce the crucial role of nucleotide-gated B-lid subdomain in synchronizing catalysis through coupling with BCCP movement. Structural and biochemical analysis of 10 disease-associated variants reveals how mutations disrupt key domain interfaces and dynamic motions required for activity. These new insights define the mechanistic principles governing hPCC functions, establish a structural framework for understanding PCC-related disorders, and lay the groundwork for future efforts to engineer functional replacements or modulators for metabolic therapy.
{"title":"Nanoscale conformational dynamics of human propionyl-CoA carboxylase","authors":"Huifang Yan, Fengyun Ni, Qinghua Wang, Jianpeng Ma","doi":"10.1016/j.str.2025.10.009","DOIUrl":"https://doi.org/10.1016/j.str.2025.10.009","url":null,"abstract":"Propionyl-CoA carboxylase (PCC) is a biotin-dependent mitochondrial enzyme responsible for propionyl-CoA catabolism. Deficiencies in human PCC (hPCC) cause propionic acidemia, a severe metabolic disorder driven by toxic metabolite accumulation. Despite its therapeutic relevance, the structural basis of hPCC’s catalytic function remains unresolved. Here, we present high-resolution cryo-EM structures of hPCC in four distinct states, unliganded, ADP-, AMPPNP-, and ATP-bound/substrate-bound, capturing the full trajectory of the biotin carboxyl carrier protein (BCCP) domain as it translocates between active sites. Our results reinforce the crucial role of nucleotide-gated B-lid subdomain in synchronizing catalysis through coupling with BCCP movement. Structural and biochemical analysis of 10 disease-associated variants reveals how mutations disrupt key domain interfaces and dynamic motions required for activity. These new insights define the mechanistic principles governing hPCC functions, establish a structural framework for understanding PCC-related disorders, and lay the groundwork for future efforts to engineer functional replacements or modulators for metabolic therapy.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"28 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145442016","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 : 2025-11-05DOI: 10.1016/j.str.2025.10.010
Paula Wagner Egea, Florent Delhommel, Ghulam Mustafa, Florian Leiss-Maier, Lisa Klimper, Thomas Badmann, Anna Heider, Idoia Wille, Michael Groll, Michael Sattler, Cathleen Zeymer
Incorporating metal cofactors into computationally designed protein scaffolds provides a versatile route to novel protein functions, including the potential for new-to-nature enzyme catalysis. However, a major challenge in protein design is to understand how the scaffold architecture influences conformational dynamics. Here, we characterized structure and dynamics of a modular de novo scaffold with flexible inter-domain linkers. Three rationally engineered variants with different metal specificity were studied by combining X-ray crystallography, NMR spectroscopy, and molecular dynamics simulations. The lanthanide-binding variant was initially trapped in an inactive conformational state, which impaired efficient metal coordination and cerium-dependent photocatalytic activity. Stabilization of the active conformation by AI-guided sequence optimization using ProteinMPNN led to accelerated lanthanide binding and a 10-fold increase in kcat/Km for a photoenzymatic model reaction. Our results suggest that modular scaffold architectures provide an attractive starting point for de novo metalloenzyme engineering and that ProteinMPNN-based sequence redesign can stabilize desired conformational states.
{"title":"Modular protein scaffold architecture and AI-guided sequence optimization facilitate de novo metalloenzyme engineering","authors":"Paula Wagner Egea, Florent Delhommel, Ghulam Mustafa, Florian Leiss-Maier, Lisa Klimper, Thomas Badmann, Anna Heider, Idoia Wille, Michael Groll, Michael Sattler, Cathleen Zeymer","doi":"10.1016/j.str.2025.10.010","DOIUrl":"https://doi.org/10.1016/j.str.2025.10.010","url":null,"abstract":"Incorporating metal cofactors into computationally designed protein scaffolds provides a versatile route to novel protein functions, including the potential for new-to-nature enzyme catalysis. However, a major challenge in protein design is to understand how the scaffold architecture influences conformational dynamics. Here, we characterized structure and dynamics of a modular <em>de novo</em> scaffold with flexible inter-domain linkers. Three rationally engineered variants with different metal specificity were studied by combining X-ray crystallography, NMR spectroscopy, and molecular dynamics simulations. The lanthanide-binding variant was initially trapped in an inactive conformational state, which impaired efficient metal coordination and cerium-dependent photocatalytic activity. Stabilization of the active conformation by AI-guided sequence optimization using <em>ProteinMPNN</em> led to accelerated lanthanide binding and a 10-fold increase in k<sub>cat</sub>/K<sub>m</sub> for a photoenzymatic model reaction. Our results suggest that modular scaffold architectures provide an attractive starting point for <em>de novo</em> metalloenzyme engineering and that <em>ProteinMPNN</em>-based sequence redesign can stabilize desired conformational states.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"1 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145442012","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 : 2025-11-05DOI: 10.1016/j.str.2025.10.012
René L. Bærentsen, Kristina Kronborg, Ditlev E. Brodersen, Yong Everett Zhang
Insights into bacterial metabolic adaptation during stress is crucial for understanding early mechanisms of antibiotic resistance. In the Gram-negative bacterium Escherichia coli, the universal stringent response produces the alarmones (p)ppGpp that target many cellular proteins. The cellular nucleosidase PpnN is regulated by (p)ppGpp and was shown to balance bacterial fitness and persistence during fluoroquinolone exposure. pppGpp and ppGpp both activate PpnN, but differentially regulate its cooperativity via an unknown mechanism; furthermore, the catalytic mechanism of PpnN has remained unclear. Here, we provide mechanistic insights into the interaction of PpnN with a substrate analogue, reaction products, and alarmone molecules, which allows us to understand the catalytic mechanism of this family of nucleosidases and the differential modes of regulation by ppGpp and pppGpp, respectively. Comparison to the homologous plant cytokinin-producing LOG proteins reveals that PpnN utilizes an evolutionarily conserved purine hydrolysis mechanism, which in bacteria is regulated by alarmones during stress.
{"title":"Catalytic mechanism and differential alarmone regulation of a conserved stringent nucleosidase","authors":"René L. Bærentsen, Kristina Kronborg, Ditlev E. Brodersen, Yong Everett Zhang","doi":"10.1016/j.str.2025.10.012","DOIUrl":"https://doi.org/10.1016/j.str.2025.10.012","url":null,"abstract":"Insights into bacterial metabolic adaptation during stress is crucial for understanding early mechanisms of antibiotic resistance. In the Gram-negative bacterium <em>Escherichia coli</em>, the universal stringent response produces the alarmones (p)ppGpp that target many cellular proteins. The cellular nucleosidase PpnN is regulated by (p)ppGpp and was shown to balance bacterial fitness and persistence during fluoroquinolone exposure. pppGpp and ppGpp both activate PpnN, but differentially regulate its cooperativity via an unknown mechanism; furthermore, the catalytic mechanism of PpnN has remained unclear. Here, we provide mechanistic insights into the interaction of PpnN with a substrate analogue, reaction products, and alarmone molecules, which allows us to understand the catalytic mechanism of this family of nucleosidases and the differential modes of regulation by ppGpp and pppGpp, respectively. Comparison to the homologous plant cytokinin-producing LOG proteins reveals that PpnN utilizes an evolutionarily conserved purine hydrolysis mechanism, which in bacteria is regulated by alarmones during stress.","PeriodicalId":22168,"journal":{"name":"Structure","volume":"28 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145442011","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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：