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

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Serendipitous high-resolution structure of Escherichia coli carbonic anhydrase 2. 大肠杆菌碳酸酐酶2的偶然高分辨率结构。
IF 1.1 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-02-01 Epub Date: 2025-01-15 DOI: 10.1107/S2053230X25000068
Michael R Rankin, Janet L Smith
{"title":"Serendipitous high-resolution structure of Escherichia coli carbonic anhydrase 2.","authors":"Michael R Rankin, Janet L Smith","doi":"10.1107/S2053230X25000068","DOIUrl":"10.1107/S2053230X25000068","url":null,"abstract":"<p><p>X-ray crystallography remains the dominant method of determining the three-dimensional structure of proteins. Nevertheless, this resource-intensive process may be hindered by the unintended crystallization of contaminant proteins from the expression source. Here, the serendipitous discovery of two novel crystal forms and one new, high-resolution structure of carbonic anhydrase 2 (CA2) from Escherichia coli that arose during a crystallization campaign for an unrelated target is reported. By comparing unit-cell parameters with those in the PDB, contaminants such as CA2 can be identified, preventing futile molecular-replacement attempts. Crystallographers can use these new lattice parameters to diagnose CA2 contamination in similar experiments.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"47-52"},"PeriodicalIF":1.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11783180/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142982328","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}
引用次数: 0
CryoCrane: an open-source GUI for analyzing cryo-EM screening data sets. crycrrane：用于分析低温电镜筛选数据集的开源GUI。
IF 1.1 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-02-01 Epub Date: 2025-01-13 DOI: 10.1107/S2053230X25000081
Jakob Ruickoldt, Petra Wendler
{"title":"CryoCrane: an open-source GUI for analyzing cryo-EM screening data sets.","authors":"Jakob Ruickoldt, Petra Wendler","doi":"10.1107/S2053230X25000081","DOIUrl":"10.1107/S2053230X25000081","url":null,"abstract":"<p><p>Screening of cryo-EM samples is essential for the generation of high-resolution cryo-EM structures. Often, it is cumbersome to correlate the appearance of specific grid squares and micrograph quality. Here, CryoCrane (Correlate atlas and exposures), a visualization tool for cryo-EM screening data, is presented. It aims to provide an intuitive way to visualize micrographs and to speed up data analysis.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"62-65"},"PeriodicalIF":1.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11783181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142968756","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}
引用次数: 0
Structural insights into the role of the prosegment binding loop in a papain-superfamily cysteine protease from Treponema denticola 齿状密螺旋体中木瓜蛋白酶超家族半胱氨酸蛋白酶前段结合环作用的结构见解。
IF 1.1 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-01-23 DOI: 10.1107/S2053230X25000378
N. D. Clark, C. Li, M. G. Malkowski
{"title":"Structural insights into the role of the prosegment binding loop in a papain-superfamily cysteine protease from Treponema denticola","authors":"N. D. Clark,&nbsp;C. Li,&nbsp;M. G. Malkowski","doi":"10.1107/S2053230X25000378","DOIUrl":"10.1107/S2053230X25000378","url":null,"abstract":"<p>Periodontal diseases afflict 20–50% of the global population and carry serious health and economic burdens. Chronic periodontitis is characterized by inflammation of the periodontal pocket caused by dysbiosis. This dysbiosis is coupled with an increase in the population of <i>Treponema denticola</i>, a spirochete bacterium with high mobility and invasivity mediated by a number of virulence factors. One such virulence factor is TDE0362, a multidomain protein with a carboxy-terminal papain-superfamily cysteine protease (C0362). Most papain-superfamily cysteine proteases are produced as proenzymes with a prodomain that interacts with the prosegment binding loop (PBL), requiring proteolytic processing for full activation. Previous studies have indicated that C0362 is not produced as a proenzyme, suggesting an alternative regulatory mechanism. We previously determined the crystal structure of C0362 captured in an inactive conformation with an oxidized catalytic cysteine and a disordered PBL. In this follow-up study, we evaluated the active-site architecture and the PBL in two mutant (Y559A and C412S) structures and an inhibitor-bound (E64) structure to provide insight into the role that the PBL plays in the generation of active enzyme. Our results implicate Tyr559 as playing a critical role in the transition of the enzyme to an active state. We subsequently utilized the structural information to generate models of C0362 bound to human complement factors C3 and C4. Collectively, our results provide insight into the regulatory mechanism and putative substrate-binding interfaces of C0362, highlighting avenues of further research towards inhibition of this essential virulence factor.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 2","pages":"53-61"},"PeriodicalIF":1.1,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021740","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}
引用次数: 0
IF 1.1 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-01-15
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 2","pages":"47-52"},"PeriodicalIF":1.1,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143114914","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}
引用次数: 0
IF 1.1 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-01-13
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 2","pages":"62-65"},"PeriodicalIF":1.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143114728","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}
引用次数: 0
Crystallographic analysis of the Escherichia coli tRNA seleno-modification enzyme in complex with tRNA 大肠杆菌tRNA硒修饰酶与tRNA复合物的结晶学分析。
IF 1.1 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-01-13 DOI: 10.1107/S2053230X25000044
Takuya Usui, Sayaka Ono, Akiyoshi Nakamura, Koji Kato, Toyoyuki Ose, Min Yao
{"title":"Crystallographic analysis of the Escherichia coli tRNA seleno-modification enzyme in complex with tRNA","authors":"Takuya Usui,&nbsp;Sayaka Ono,&nbsp;Akiyoshi Nakamura,&nbsp;Koji Kato,&nbsp;Toyoyuki Ose,&nbsp;Min Yao","doi":"10.1107/S2053230X25000044","DOIUrl":"10.1107/S2053230X25000044","url":null,"abstract":"<p>The bacterial enzyme tRNA 2-selenouridine synthase (SelU) catalyzes the conversion of 5-substituted 2-thiouridine (R5S2U) to 5-substituted 2-selenouridine (R5Se2U) at the wobble positions of several tRNAs. Seleno-modification potentially regulates translation efficiency in response to selenium availability. Notably, SelU uses the 2-geranylthiouridine (R5geS2U) intermediate for sulfur removal, and this geranylthiol (geS) is a unique leaving group among tRNA-maturation enzymes. However, the underlying sequence of the SelU reaction remains unclear. Here, a crystallographic study of the <i>Escherichia coli</i> SelU–tRNA complex is reported. Robust and well formed SelU–tRNA crystals were obtained after several optimizations, including co-expression with tRNA and additive screening. Diffraction data were collected at a resolution of 3.10 Å using a wavelength of 1.0000 Å. The crystals belonged to space group <i>C</i>2, and the phase was determined by molecular replacement using the <i>AlphaFold</i>2-predicted SelU structure as a search model. Electron-density mapping revealed the presence of two SelU–tRNA complexes in the asymmetric unit.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 2","pages":"35-40"},"PeriodicalIF":1.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142942400","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}
引用次数: 0
IF 1.1 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-01-13
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 2","pages":"41-46"},"PeriodicalIF":1.1,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143114729","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}
引用次数: 0
IF 1.1 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-01-03
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 1","pages":"19-29"},"PeriodicalIF":1.1,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143111466","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}
引用次数: 0
Crystallization and preliminary X-ray crystallographic studies of AfeH from Acimetobacter sp. DL-2 acmetobacter sp. DL-2中AfeH的结晶及x射线晶体学初步研究。
IF 1.1 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-01-03 DOI: 10.1107/S2053230X24012275
Huiling Tang, XiaoRan Zhang, Yajuan Duan, Yan Huang
{"title":"Crystallization and preliminary X-ray crystallographic studies of AfeH from Acimetobacter sp. DL-2","authors":"Huiling Tang,&nbsp;XiaoRan Zhang,&nbsp;Yajuan Duan,&nbsp;Yan Huang","doi":"10.1107/S2053230X24012275","DOIUrl":"10.1107/S2053230X24012275","url":null,"abstract":"<p>Fenoxaprop-P-ethyl (FE) is widely applied as a post-emergence aryloxyphenoxy propionate (AOPP) herbicide in agriculture. A novel FE hydrolase esterase from <i>Acinetobacter</i> sp. DL-2 (AfeH) was identified which belongs to the family IV carboxylesterases and shows less than 30% identity to other reported homologues with known structure. In order to understand the catalytic mechanism, recombinant AfeH was prepared in <i>Escherichia coli</i> and crystallized using the sitting-drop vapor-diffusion method. X-ray diffraction data were collected to 1.9 Å resolution. The crystal belonged to space group <i>P</i>12<sub>1</sub>1, with unit-cell parameters <i>a</i> = 84.27, <i>b</i> = 46.74, <i>c</i> = 258.68 Å. The Matthews coefficient (<i>V</i><sub>M</sub>) was calculated to be 2.43 Å<sup>3</sup> Da<sup>−1</sup>, which corresponds to a solvent content of 49.4%, suggesting the presence of three monomers in the crystallographic asymmetric unit. The crystal was assessed to be suitable for further structural determination, which is currently in progress.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 1","pages":"30-34"},"PeriodicalIF":1.1,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142881041","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}
引用次数: 0
Structure of Plasmodium vivaxN-myristoyltransferase with inhibitor IMP-1088: exploring an NMT inhibitor for antimalarial therapy. 间日疟原虫肉豆浆酰基转移酶抑制剂IMP-1088的结构：探索用于抗疟疾治疗的NMT抑制剂。
IF 1.1 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-01-01 DOI: 10.1107/S2053230X24011348
Alex Mendez, Cydni Bolling, Shane Taylor, Stanley Makumire, Bart Staker, Alexandra Reers, Brad Hammerson, Stephen J Mayclin, Jan Abendroth, Donald D Lorimer, Thomas E Edwards, Edward W Tate, Sandhya Subramanian, Andrew S Bell, Peter J Myler, Oluwatoyin A Asojo, Graham Chakafana
{"title":"Structure of Plasmodium vivaxN-myristoyltransferase with inhibitor IMP-1088: exploring an NMT inhibitor for antimalarial therapy.","authors":"Alex Mendez, Cydni Bolling, Shane Taylor, Stanley Makumire, Bart Staker, Alexandra Reers, Brad Hammerson, Stephen J Mayclin, Jan Abendroth, Donald D Lorimer, Thomas E Edwards, Edward W Tate, Sandhya Subramanian, Andrew S Bell, Peter J Myler, Oluwatoyin A Asojo, Graham Chakafana","doi":"10.1107/S2053230X24011348","DOIUrl":"10.1107/S2053230X24011348","url":null,"abstract":"<p><p>Plasmodium vivax, a significant contributor to global malaria cases, poses an escalating health burden on a substantial portion of the world's population. The increasing spread of P. vivax because of climate change underscores the development of new and rational drug-discovery approaches. The Seattle Structural Genomics Center for Infectious Diseases is taking a structure-based approach by investigating essential enzymes such as N-myristoyltransferase (NMT). P. vivax N-myristoyltransferase (PvNMT) is a promising target for the development of novel malaria treatments unlike current drugs, which target only the erythrocytic stages of the parasite. Here, the 1.8 Å resolution ternary structure of PvNMT in complex with myristoyl-CoA and IMP-1088, a validated NMT inhibitor, is reported. IMP-1088 is a validated nonpeptidic inhibitor and a ternary complex structure with human NMT has previously been reported. IMP-1088 binds similarly to PvNMT as to human NMT.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"1-10"},"PeriodicalIF":1.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11701927/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142798930","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}
引用次数: 0
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