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

{"title":"Crystal engineering of the hepatoma-derived growth factor-related protein 2 PWWP domain towards crystallographic fragment screening","authors":"Thibault Vantieghem,&nbsp;Evgenii M. Osipov,&nbsp;Steven Beelen,&nbsp;Sergei V. Strelkov","doi":"10.1107/S2053230X25006302","DOIUrl":"10.1107/S2053230X25006302","url":null,"abstract":"<p>Hepatoma-derived growth factor-related protein 2 (HRP-2) is a member of the HDGF-related protein family, which has been linked to multiple malignancies. A defining feature of this protein family is the presence of an N-terminal PWWP domain, which enables binding to nucleosomes carrying a dimethylation or trimethylation marker on residue Lys36 of histone H3. To support the rational design of small-molecule drugs that bind to the PWWP domain, crystallographic fragment screening was chosen. A critical requirement for such screening is the ability to reliably produce large batches of high-quality crystals, ideally grown under low-salt conditions to prevent the precipitation of drug-like fragments during crystal soaking. Initial crystallization of the wild-type (WT) HRP-2 PWWP domain only produced crystals under high-salt conditions and these significantly lost diffraction quality over two weeks. It was hypothesized that these complications were caused by oxidation of the solvent-exposed Cys64 residue. To overcome these difficulties, a Cys64Ser mutant was produced. This mutation revealed a substantially improved crystallization propensity, as eight crystal forms could be obtained and resolved versus two forms for the WT. Moreover, the mutant crystals could be grown in PEG-based low ionic strength conditions which are optimal for fragment soaking. Finally, the crystals did not lose their diffraction quality for up to six months. Importantly, systematic analysis of all obtained X-ray structures revealed that the Cys64/Ser64 residue lies at a key lattice interface which is conserved across all crystal forms. This suggests that even minor chemical changes at this position could disrupt important intermolecular contacts, explaining the demonstrated major benefit of the introduced mutation. The presented data underpin the substitution of surface-exposed cysteines as a general strategy to enhance protein crystallization and diffraction quality. Ultimately, the results presented here were pivotal to the successful execution of the crystallographic fragment-screening campaign with the HRP-2 PWWP domain.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 8","pages":"358-364"},"PeriodicalIF":1.1,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144705963","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":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 8","pages":"332-337"},"PeriodicalIF":1.1,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144740291","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":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 8","pages":"338-347"},"PeriodicalIF":1.1,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144740292","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 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}