Acta crystallographica. Section F, Structural biology communications最新文献

{"title":"Structural insights into full-length human fascin1: a target for cancer treatment","authors":"Lucía Giraldo-Ruiz,&nbsp;Isabel Quereda-Moraleda,&nbsp;Alice Grieco,&nbsp;Javier Ruiz-Sanz,&nbsp;Irene Luque,&nbsp;Jose Manuel Martin-Garcia","doi":"10.1107/S2053230X25005254","DOIUrl":"10.1107/S2053230X25005254","url":null,"abstract":"<p>Fascin1 proteins are a family of globular proteins with actin-bundling activity that cross-link actin filaments together, allowing the formation of actin-rich structures involved in cell migration and adhesion, such as filopodia, invadopodia, stress fibers, micro-spikes and podocytes. The overexpression of human fascin1 has been linked to tumor progression in most human cancers, particularly during the epithelial–mesenchymal transition, making it a promising biomarker for cancer metastasis and a major target for the development of novel cancer therapies. X-ray crystallography has been instrumental in human fascin1-inhibition research since it provides detailed insights into the structure of the protein and its interactions with small-molecule inhibitors. This technique has allowed the characterization of a range of molecular conformations in which the protein naturally exists. However, human fascin1 has never been fully modeled until now. To the best of our knowledge, this study presents the first full-length structure of human fascin1 in which both copies are fully resolved. Comparison of this structure with the available wild-type and complexed structures provides new insights into the conformational plasticity of fascin1 that will facilitate subsequent studies on human fascin1 in the context of drug design for cancer-related therapies.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 7","pages":"319-331"},"PeriodicalIF":1.1,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1107/S2053230X25005254","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crystal structure of the sucrose phosphorylase from Alteromonas mediterranea shows a loop transition in the active site","authors":"Folmer Fredslund,&nbsp;Marine Goux,&nbsp;Bernard Offmann,&nbsp;Marie Demonceaux,&nbsp;Corinne André-Miral,&nbsp;Ditte Welner,&nbsp;David Teze","doi":"10.1107/S2053230X25004327","DOIUrl":"10.1107/S2053230X25004327","url":null,"abstract":"<p>Sucrose phosphorylases are essential enzymes regulating sucrose metabolism, and it has been shown that a loop rearrangement is essential to their catalytic cycle. Crystal structures of only six sucrose phosphorylase enzymes are available. Here, we present the crystal structure of a sucrose phosphorylase from a proteobacterium, <i>Alteromonas mediterranea</i>, at 2.15 Å resolution. The available sucrose phosphorylase structures have shown that an important conformational change occurs during the catalytic cycle or upon mutagenesis. Interestingly, our data present clear indications of the two major conformations in the same crystal.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 7","pages":"306-310"},"PeriodicalIF":1.1,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1107/S2053230X25004327","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crystal structure analysis of oxygen-induced degradation occurring in rsCherry","authors":"Thi Yen Hang Bui,&nbsp;Ludovic Pecqueur,&nbsp;Peter Dedecker,&nbsp;Luc Van Meervelt","doi":"10.1107/S2053230X25005485","DOIUrl":"10.1107/S2053230X25005485","url":null,"abstract":"<p>rsCherry was one of the first reversibly photoswitchable variants to be developed from mCherry. However, its practical applications have been limited due to several inherent drawbacks. We have recently shown that the purified protein undergoes oxygen-induced chromophore degradation in solution, resulting in the progressive loss of its fluorescence and color. In this work, we present four crystal structures of rsCherry that exhibit varying degrees of degradation. Our structural analysis indicates that oxygen-induced degradation of rsCherry predominantly affects the chromophore without altering the protein backbone. Changes were only observed in the conformation of Lys70, confirming the crucial role of this residue in chromophore damage in rsCherry. Overall, this study provides valuable insights into the structural changes triggered by oxygen exposure in rsCherry, offering suggestions for the development of stable red fluorescent proteins with improved resistance to oxidative damage.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 7","pages":"311-318"},"PeriodicalIF":1.1,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144473720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cryo-EM structures of Mycobacterium tuberculosis imidazole glycerol phosphate dehydratase in the apo state and in the presence of small molecules","authors":"Rahul Raina,&nbsp;Deepsikha Kar,&nbsp;Mohini Singla,&nbsp;Satish Tiwari,&nbsp;Swati Kumari,&nbsp;Sonanjali Aneja,&nbsp;Varun Kumar,&nbsp;Soumya Banerjee,&nbsp;Shivika Goyal,&nbsp;Ravi Kant Pal,&nbsp;Kutti R. Vinothkumar,&nbsp;Bichitra Biswal","doi":"10.1107/S2053230X25004595","DOIUrl":"10.1107/S2053230X25004595","url":null,"abstract":"<p>Unlike humans, <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>), the causative agent of human tuberculosis, has a <i>de novo</i> histidine-biosynthesis pathway. The enzyme imidazole glycerol phosphate dehydratase (IGPD), which catalyses the conversion of imidazole glycerol phosphate to imidazole acetol phosphate, has been studied extensively from various organisms and has become a major target for the development of antibacterial, antiweed and antifungal small molecules. In our previous studies, we have shown that in crystals IGPD forms a 24-mer oligomeric state in which the monomers are arranged in 432 symmetry. In order to gain insights into the oligomeric state of <i>Mtb</i> IGPD in solution, we determined cryogenic sample electron microscopy (cryo-EM) structures of apo IGPD at 2.2 and 3.1 Å resolution. In addition, we also determined the cryo-EM structure of IGPD in the presence of 3-amino-1,2,4-triazole (ATZ) to 2.8 Å resolution. The results of this work, which corroborate those from the crystallographic studies, indicate that IGPD forms a homo-oligomeric structure in solution comprising of 24 subunits. ATZ binds in the active-site pocket of the enzyme, which is located at the interface of three monomers and tethers 24 ATZ molecules. The results of this study suggest that cryo-EM, in addition to being a rapidly evolving and complementary imaging technology for elucidating 3D structures of biological macromolecules, can be useful in pinpointing the mode of binding small molecules of low mass (here ∼85 Da) and mapping protein-ligand interactions, which could assist in the design of accurate (high-potency) inhibitors.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 7","pages":"297-305"},"PeriodicalIF":1.1,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144245600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional and structural characterization of Stenotrophomonas maltophilia EntB, an unusual form of isochorismatase for siderophore synthesis","authors":"Megan Y. Nas,&nbsp;Jeffrey Gabell,&nbsp;Nicole Inniss,&nbsp;George Minasov,&nbsp;Ludmilla Shuvalova,&nbsp;Karla J. F. Satchell,&nbsp;Nicholas P. Cianciotto","doi":"10.1107/S2053230X2500490X","DOIUrl":"10.1107/S2053230X2500490X","url":null,"abstract":"<p>Clinical and environmental isolates of <i>Stenotrophomonas maltophilia</i> produce an enterobactin-like siderophore that promotes bacterial growth under low-iron conditions. Although prior mutational and bioinformatic analyses indicated that most of the enzymes encoded by the <i>S. maltophilia entCEBB′FA</i> locus are suitably reminiscent of their counterparts in <i>Escherichia coli</i> and other bacteria, <i>Stenotrophomonas</i> EntB was unusual. In bacteria producing enterobactin-related molecules, EntB and its homologs are usually multi-domain proteins in which the amino portion acts as an isochorismatase and the carboxy domain serves as an aryl carrier protein (ArCP). However, in <i>S. maltophilia</i> the isochorismatase and ArCP functions are encoded by two distinct genes: <i>entB</i> and <i>entB′</i>, respectively. Current mutant analysis was used to first confirm that <i>S. maltophilia entB</i> is needed for siderophore activity and bacterial growth in iron-depleted media. A crystal structure of <i>S. maltophilia</i> EntB was then obtained. The structure aligned with the N-terminal portion of EntB from <i>E. coli</i> and VibB from <i>Vibrio cholerae</i>, affirming the protein to be a single-domain isochorismatase. However, <i>S. maltophilia</i> EntB also aligned with the single-domain PhzD from <i>Pseudomonas aeruginosa</i>, which is a key enzyme involved in the biosynthesis of the antimicrobial compound phenazine. <i>BLASTP</i> searches indicated that <i>entB</i> and its neighboring genes are fully conserved amongst <i>S. maltophilia</i> strains but are variably present in other <i>Stenotrophomonas</i> species. The closest homologs to <i>S. maltophilia</i> EntB outside the genus were hypothetical proteins/putative isochorismatases in some Gram-negative bacteria (for example <i>Pseudomonas</i> spp. and <i>Xanthomonas</i> spp.), Gram-positive bacteria (<i>Streptomyces</i> spp. and <i>Bacillus subtilis</i>) and fungi (for example <i>Rhizopus arrhizus</i> and <i>Knufia peltigerae</i>).</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 7","pages":"287-296"},"PeriodicalIF":1.1,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1107/S2053230X2500490X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144214531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The structure of a family 168 glycoside hydrolase from the marine bacterium Muricauda eckloniae","authors":"Emily Knudson-Goerner,&nbsp;Alisdair B. Boraston","doi":"10.1107/S2053230X2500425X","DOIUrl":"10.1107/S2053230X2500425X","url":null,"abstract":"<p>The genome of the marine bacterium <i>Muricauda eckloniae</i> sp. DK169 contains an extensive polysaccharide-utilization locus that targets fucoidan from brown algae. Within this locus is a gene that encodes a putative fucoidan-degrading glycoside hydrolase (locus tag AAY42_01205) assigned to glycoside hydrolase family 168, which we call <i>Me</i>GH168. We present the 2.0 Å resolution X-ray crystal structure of <i>Me</i>GH168, demonstrating a (β/α)₈-barrel fold. The eight loop regions joining each α-helix and β-strand surround the catalytic groove. A comparison with the structure of a GH168, Fun168A, in complex with a fragment of fucoidan (PDB entry 8ya7) revealed conservation of key residues in the catalytic site. However, structural variation in positive-subsite loop regions may recontour the active site to create differences in substrate specificity between the two GH168s. The present data provide additional structural insights into the GH168 family, particularly expanding on sequence and structure conservation (and the lack thereof) in relation to substrate interactions.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 7","pages":"281-286"},"PeriodicalIF":1.1,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1107/S2053230X2500425X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144148796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preparing for successful protein crystallization experiments","authors":"Gabrielle R. Budziszewski,&nbsp;Vivian Stojanoff,&nbsp;Sarah E. J. Bowman","doi":"10.1107/S2053230X25004650","DOIUrl":"10.1107/S2053230X25004650","url":null,"abstract":"<p>Crystal-based structural methods, including X-ray crystallography, are frequently utilized for the determination of high-resolution structures of biomolecules. All crystal-based diffraction methods first require the preparation of biomolecular crystals, and careful sample preparation for crystallization experiments can increase the frequency of success. In this article, strategies to optimize factors that can impact crystallization are presented, from which buffers and reducing agents are most favorable to which crystallization techniques could be used.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 7","pages":"272-280"},"PeriodicalIF":1.1,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1107/S2053230X25004650","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144198030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crystal structure of the C1 domain of the surface-layer protein SlpM from Lactobacillus brevis: a module involved in protein self-assembly","authors":"Yi Xue,&nbsp;Xue Kang","doi":"10.1107/S2053230X25004194","DOIUrl":"10.1107/S2053230X25004194","url":null,"abstract":"<p>Surface-layer proteins (SLPs) play a crucial role in the self-assembly of bacterial surface layers, yet the structural details of their assembly domains remain largely unexplored. Here, we report the crystal structure of SlpM_C1, a structural module within the self-assembly domain of SlpM from <i>Lactobacillus brevis</i>. SlpM_C1 adopts a β-grasp fold, a conserved structural motif found in diverse protein families. Structural comparisons with ubiquitin and the SlpA_II domain from <i>L. acidophilus</i> reveal both shared and distinct features, highlighting elements of structural convergence despite sequence divergence. Furthermore, the dimerization patterns of SlpM_C1 and SlpA_II are compared and discussed. These findings provide new insights into the architecture and evolutionary adaptability of SLPs in <i>Lactobacillus</i> species.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 6","pages":"255-262"},"PeriodicalIF":1.1,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural analysis of YcdY, a member of the redox-enzyme maturation protein family","authors":"Hong Joon Choi,&nbsp;Su-jin Lee,&nbsp;Jee-Hyeon Kim,&nbsp;Young-Bong You,&nbsp;Sung-il Yoon","doi":"10.1107/S2053230X25003887","DOIUrl":"10.1107/S2053230X25003887","url":null,"abstract":"<p>Proteins of the NarJ subfamily from facultatively or obligately anaerobic bacteria play key roles as chaperones in folding and cofactor insertion for complex iron–sulfur molybdoenzymes (CISMs), which mediate energy production under anaerobic conditions. YcdY was identified as a NarJ subfamily member but was proposed to increase the catalytic activity of the non-CISM enzyme YcdX phosphatase, presumably by inserting a zinc cofactor into YcdX. To elucidate the structural features of YcdY required for its chaperone function, we determined the crystal structure of <i>Enterobacter cloacae</i> YcdY (enYcdY). enYcdY adopts a single-domain, curved helix-bundle structure decorated with α-helices. enYcdY contains an extensive dent on its concave side. The dent in enYcdY generally forms using hydrophobic or conserved residues. Based on comparative structural and sequence analyses, we propose that enYcdY uses the dent to recognize and fold the client protein. Interestingly, enYcdY did not increase the enzymatic activity of <i>E. cloacae</i> YcdX (enYcdX) in the presence or absence of Zn²⁺ ions, even for partially denatured enYCdX protein. The same results were obtained for the <i>Escherichia coli</i> counterparts, in contrast to a previous report. These observations suggest that YcdY functions as a chaperone for proteins other than YcdX.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 6","pages":"263-271"},"PeriodicalIF":1.1,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144092573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using resources generated by the Seattle Structural Genomics Center for Infectious Disease (SSGCID) for training early career researchers","authors":"Julie V. Early,&nbsp;Craig L. Smith,&nbsp;Oluwatoyin A. Asojo,&nbsp;Peter J. Myler","doi":"10.1107/S2053230X25003930","DOIUrl":"https://doi.org/10.1107/S2053230X25003930","url":null,"abstract":"<p>The focused issue on <i>Empowering education through structural genomics</i> is introduced. The virtual issue is available at https://journals.iucr.org/special_issues/2024/educationsg.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 6","pages":"222-225"},"PeriodicalIF":1.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144171316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}