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

{"title":"The crystal structures of apo and tryptophan-bound tryptophanyl-tRNA synthetase from Neisseria gonorrhoeae","authors":"Jessika Baral,&nbsp;David Song,&nbsp;Thomas E. Edwards,&nbsp;David M. Dranow,&nbsp;Donald D. Lorimer,&nbsp;Bart L. Staker,&nbsp;Peter Myler,&nbsp;Craig L. Smith","doi":"10.1107/S2053230X25001311","DOIUrl":"10.1107/S2053230X25001311","url":null,"abstract":"<p><i>Neisseria gonorrhoeae</i>, the causative agent of the human disease gonorrhea, is the second most common sexually transmitted pathogen in the United States. Gonorrhea has a significantly high morbidity rate due to the ability of <i>N. gonorrhoeae</i> to rapidly develop antibiotic resistance. In this paper, crystal structures of tryptophanyl-tRNA synthetase (TrpRS) from <i>N. gonorrhoeae</i> (<i>Ng</i>TrpRS) were determined in both its apo form and in complex with tryptophan. The structures reveal conserved HIGH and KMSKS motifs critical for ATP binding and catalysis, and highlight conformational changes in the active site upon tryptophan binding, including a methionine flip and the rearrangement of hydrogen-bonding residues. Structural alignments with human TrpRS isoforms demonstrate significant differences between the bacterial and human cytosolic forms, particularly in their active sites. While <i>Ng</i>TrpRS and human mitochondrial TrpRS share conserved catalytic residues that are essential for binding tryptophan and indolmycin, the cytosolic TrpRS contains substitutions that introduce steric hindrance, limiting the binding of indolmycin. These results provide insight for the development of inhibitors targeting bacterial TrpRS without affecting the human mitochondrial or cytosolic isoforms, contributing to efforts to combat antibiotic-resistant <i>N. gonorrhoeae</i> infections.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 4","pages":"130-137"},"PeriodicalIF":1.1,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143536335","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 4","pages":"124-129"},"PeriodicalIF":1.1,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143749406","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":"The first report of structural analysis of a nucleic acid using crystals grown in space.","authors":"Shin Ando, Moena Takahashi, Jiro Kondo","doi":"10.1107/S2053230X25000810","DOIUrl":"10.1107/S2053230X25000810","url":null,"abstract":"<p><p>For the success of structure-based drug design, three-dimensional structures solved by X-ray crystallography at atomic resolution are mandatory. In order to obtain high-quality single crystals with strong diffraction power, crystallization under microgravity conditions has been attempted for proteins. Since nucleic acid duplexes have chemical, structural and crystallographic characteristics that differ from those of globular proteins, such as intermolecular repulsion due to negative charge and molecular and crystallographic anisotropies, it is interesting to investigate whether microgravity crystallization improves the crystal growth of nucleic acids. However, to our knowledge there has been only one report on nucleic acid crystallization in a microgravity environment, and there have been no reports of successful structural analysis. Here, we conducted the crystallization of a DNA/RNA heteroduplex in space. The heteroduplex was successfully crystallized in a microgravity environment, and the size and appearance of the crystals were improved compared with control experiments conducted on Earth. Although the effect of the counter-diffusion method is likely to be more significant than the effect of microgravity in this study, we were able to analyze the structure at a higher resolution (1.4 Å) than our previously reported crystal structure (1.9 Å).</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"95-100"},"PeriodicalIF":1.1,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11866410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397667","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":"A two-in-one expression construct for biophysical and structural studies of the human pregnane X receptor ligand-binding domain, a pharmaceutical and environmental target.","authors":"Coralie Carivenc, Guillaume Laconde, Pauline Blanc, Muriel Amblard, William Bourguet, Vanessa Delfosse","doi":"10.1107/S2053230X2500069X","DOIUrl":"10.1107/S2053230X2500069X","url":null,"abstract":"<p><p>The ligand-binding domain (LBD) of the human nuclear receptor pregnane X receptor (PXR) is known to crystallize in two different crystal forms, P2₁2₁2₁ or P4₃2₁2, depending on the construct and the strategy used for protein production, as well as the presence or absence of the coactivator-derived peptide SRC-1. In order to facilitate biophysical and structural studies, a versatile construct was designed that allows access to both forms. This was achieved by introducing a thrombin cleavage site between the PXR_LBD and the SRC-1 peptide fused to its C-terminus. Here, we describe the expression, purification and crystallization processes of this novel construct and report two new structures of PXR_LBD that were obtained thanks to this strategy.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"85-94"},"PeriodicalIF":1.1,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11866411/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143373460","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":"Cryo-EM structures of apo and atorvastatin-bound human 3-hydroxy-3-methylglutaryl-coenzyme A reductase.","authors":"Manikandan Karuppasamy, Jason van Rooyen","doi":"10.1107/S2053230X25001098","DOIUrl":"10.1107/S2053230X25001098","url":null,"abstract":"<p><p>The enzyme 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR) regulates the level of cholesterol by catalysing the formation/production of mevalonate and has therefore become an important pharmaceutical target for coronary heart disease. Here, we report the cryo-EM structure of the catalytic part of the enzyme in the apo form and bound with its inhibitor atorvastatin, a commonly used drug in cardiovascular disease, at resolutions of 2.1 and 2.3 Å, respectively. In the cryo-EM maps, part of the N-domain corresponding to amino acids 439-487 is well ordered and could be modelled completely. Atorvastatin molecules were found to occupy all four active sites of the tetrameric complex, and the binding does not alter the conformation of the protein or the active site. The method described here exploits graphene oxide as an additional support and could be used as an alternative to elucidate the structures of pharmaceutical target compounds that are difficult to co-crystallize with human HMGR and for sparsely available samples in drug discovery.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"118-122"},"PeriodicalIF":1.1,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11866412/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456586","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":"Redox-dependent hydrogen-bond network rearrangement of ferredoxin-NADP⁺ reductase revealed by high-resolution X-ray and neutron crystallography.","authors":"Midori Uenaka, Yusuke Ohnishi, Akane Ise, Jiang Yu, Naomine Yano, Katsuhiro Kusaka, Hideaki Tanaka, Genji Kurisu","doi":"10.1107/S2053230X25000524","DOIUrl":"10.1107/S2053230X25000524","url":null,"abstract":"<p><p>High-resolution X-ray and neutron crystallography were employed to elucidate redox-dependent structural changes in ferredoxin-NADP⁺ reductase (FNR) from maize. This study focused on the rearrangement of hydrogen-bond networks upon FAD reduction. The X-ray structures of wild-type FNR in oxidized and reduced states were refined to 1.15 and 1.10 Å resolution, respectively, revealing no large structural changes in the main-chain backbones. Neutron crystallography provided complementary insights, confirming protonation at N1 and N5 of the isoalloxazine ring and visualizing hydrogen bonds that were undetectable by X-ray analysis. These findings illuminate the dynamic reorganization of water-mediated hydrogen-bond networks during redox transitions, which may underpin the redox-dependent modulation of partner binding by FNR. This integrated structural approach highlights the synergistic use of X-ray and neutron crystallography in studying redox-active proteins.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"73-84"},"PeriodicalIF":1.1,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11866413/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143363186","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":"LOPAC library screening identifies suramin as a TRIM21 binder with a unique binding mode revealed by crystal structure.","authors":"Yeojin Kim, Stefan Knapp, Andreas Krämer","doi":"10.1107/S2053230X25000913","DOIUrl":"10.1107/S2053230X25000913","url":null,"abstract":"<p><p>Differential scanning fluorimetry screening of the Library of Pharmacologically Active Compounds (LOPAC) identified four hits for the PRYSPRY domain of the human E3 ligase tripartite motif-containing protein 21 (TRIM21). Isothermal titration calorimetry subsequently confirmed suramin as a binder with micromolar affinity. To further investigate the binding mechanism, mouse TRIM21 was used as a structural surrogate due to its improved protein stability and high sequence similarity to the human counterpart. A crystal structure of the complex refined at 1.3 Å resolution revealed a unique binding mode, providing new avenues for targeting TRIM21 and for the development of proteolysis-targeting chimeras (PROTACs).</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"101-107"},"PeriodicalIF":1.1,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11866408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143424641","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":"Structure of Clostridium leptum carboxyspermidine decarboxylase and comparison to homologs prevalent within the human gut microbiome.","authors":"Savannah J Jones, Dawson J Bell, Jeffrey S McFarlane","doi":"10.1107/S2053230X25000482","DOIUrl":"10.1107/S2053230X25000482","url":null,"abstract":"<p><p>Polyamines are key signalling and substrate molecules that are made by all organisms. The polyamine known as spermidine is typically made by spermidine synthase, but in many bacterial species, including 70% of human gut microbes, carboxyspermidine decarboxylase (CASDC) performs the terminal step in the production of spermidine. An X-ray crystal structure of CASDC from the human gut microbe Clostridium leptum has been solved by molecular replacement at a resolution of 1.41 Å. CASDC is a homodimer, with each monomer composed of two domains: a β/α-barrel pyridoxal 5'-phosphate-binding domain that forms most of the active site and a β-barrel domain that extends the dimeric interface and contributes to the active site of the opposing monomer. We performed a structural comparison of CASDC enzymes for 15 common genera within the human gut flora. This analysis reveals structural differences occurring in the β6/β7 loop that acts as a `flap' covering the active site and in the α9/β12 loop that is connected to the α9 helix which is thought to select substrates by their chain length. This structural analysis extends our understanding of a key enzyme in spermidine biosynthesis in many bacterial species.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"66-72"},"PeriodicalIF":1.1,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11866407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063103","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":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 3","pages":"118-122"},"PeriodicalIF":1.1,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143497336","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":"Crystal structure of dihydroorotate dehydrogenase from Helicobacter pylori with bound flavin mononucleotide","authors":"Ashna A. Agarwal,&nbsp;John D. Georgiades,&nbsp;David M. Dranow,&nbsp;Donald D. Lorimer,&nbsp;Thomas Edwards,&nbsp;Kayleigh F. Barrett,&nbsp;Justin K. Craig,&nbsp;Wesley C. Van Voorhis,&nbsp;Peter J. Myler,&nbsp;Craig L. Smith","doi":"10.1107/S2053230X25000858","DOIUrl":"10.1107/S2053230X25000858","url":null,"abstract":"<p><i>Helicobacter pylori</i> is the primary causative agent of peptic ulcer disease, among other gastrointestinal ailments, and currently affects over half of the global population. Although some treatments exist, growing resistance to these drugs has prompted efforts to develop novel approaches to fighting this pathogen. To generate many of the nucleotides essential to biochemical processes, <i>H. pylori</i> relies exclusively on the <i>de novo</i> biosynthesis of these molecules. Recent drug-discovery efforts have targeted the first committed step of this pathway, catalysed by a class 2 dihydroorotate dehydrogenase (DHODH). However, these initiatives have been limited by the lack of a crystal structure. Here, we detail the crystal structure of <i>H. pylori</i> DHODH (<i>Hp</i>DHODH) at 2.25 Å resolution (PDB entry 6b8s). We performed a large-scale bioinformatics search to find evolutionary homologs. Our results indicate that <i>Hp</i>DHODH shows high conservation of both sequence and structure in its active site. We identified key polar interactions between the <i>Hp</i>DHODH protein and its requisite flavin mononucleotide (FMN) cofactor, identifying amino-acid residues that are critical to its function. Most notably, we found that <i>Hp</i>DHODH maintains several structural features that allow it to associate with the inner membrane and utilize ubiquinone to achieve catalytic turnover. We discovered a hydrophobic channel that runs from the putative membrane interface on the N-terminal microdomain to the core of the protein. We predict that this channel establishes a connection between the ubiquinone pool in the membrane and the FMN in the active site. These findings provide a structural explanation for the competitive inhibition of ubiquinone by pyrazole-based compounds that was determined biochemically in other studies. Understanding this mechanism may facilitate the development of new drugs targeting this enzyme and push the effort to find a resistance-free treatment for <i>H. pylori</i>.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 3","pages":"108-117"},"PeriodicalIF":1.1,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439351","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}