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

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Structural and biochemical characterization of the M405S variant of Desulfovibrio vulgaris formate dehydrogenase. 低俗脱硫弧菌甲酸脱氢酶 M405S 变体的结构和生物化学特征。
IF 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-05-01 DOI: 10.1107/S2053230X24003911
Guilherme Vilela-Alves, Rita Rebelo Manuel, Neide Pedrosa, Inês A Cardoso Pereira, Maria João Romão, Cristiano Mota
{"title":"Structural and biochemical characterization of the M405S variant of Desulfovibrio vulgaris formate dehydrogenase.","authors":"Guilherme Vilela-Alves, Rita Rebelo Manuel, Neide Pedrosa, Inês A Cardoso Pereira, Maria João Romão, Cristiano Mota","doi":"10.1107/S2053230X24003911","DOIUrl":"10.1107/S2053230X24003911","url":null,"abstract":"<p><p>Molybdenum- or tungsten-dependent formate dehydrogenases have emerged as significant catalysts for the chemical reduction of CO<sub>2</sub> to formate, with biotechnological applications envisaged in climate-change mitigation. The role of Met405 in the active site of Desulfovibrio vulgaris formate dehydrogenase AB (DvFdhAB) has remained elusive. However, its proximity to the metal site and the conformational change that it undergoes between the resting and active forms suggests a functional role. In this work, the M405S variant was engineered, which allowed the active-site geometry in the absence of methionine S<sup>δ</sup> interactions with the metal site to be revealed and the role of Met405 in catalysis to be probed. This variant displayed reduced activity in both formate oxidation and CO<sub>2</sub> reduction, together with an increased sensitivity to oxygen inactivation.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"98-106"},"PeriodicalIF":0.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11134731/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140849963","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
X-ray crystal structure of a designed rigidified imaging scaffold in the ligand-free conformation. 设计的无配体构象刚性成像支架的 X 射线晶体结构。
IF 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-05-01 Epub Date: 2024-05-20 DOI: 10.1107/S2053230X2400414X
Matthew P Agdanowski, Roger Castells-Graells, Michael R Sawaya, Duilio Cascio, Todd O Yeates, Mark A Arbing
{"title":"X-ray crystal structure of a designed rigidified imaging scaffold in the ligand-free conformation.","authors":"Matthew P Agdanowski, Roger Castells-Graells, Michael R Sawaya, Duilio Cascio, Todd O Yeates, Mark A Arbing","doi":"10.1107/S2053230X2400414X","DOIUrl":"10.1107/S2053230X2400414X","url":null,"abstract":"<p><p>Imaging scaffolds composed of designed protein cages fused to designed ankyrin repeat proteins (DARPins) have enabled the structure determination of small proteins by cryogenic electron microscopy (cryo-EM). One particularly well characterized scaffold type is a symmetric tetrahedral assembly composed of 24 subunits, 12 A and 12 B, which has three cargo-binding DARPins positioned on each vertex. Here, the X-ray crystal structure of a representative tetrahedral scaffold in the apo state is reported at 3.8 Å resolution. The X-ray crystal structure complements recent cryo-EM findings on a closely related scaffold, while also suggesting potential utility for crystallographic investigations. As observed in this crystal structure, one of the three DARPins, which serve as modular adaptors for binding diverse `cargo' proteins, present on each of the vertices is oriented towards a large solvent channel. The crystal lattice is unusually porous, suggesting that it may be possible to soak crystals of the scaffold with small (≤30 kDa) protein cargo ligands and subsequently determine cage-cargo structures via X-ray crystallography. The results suggest the possibility that cryo-EM scaffolds may be repurposed for structure determination by X-ray crystallography, thus extending the utility of electron-microscopy scaffold designs for alternative structural biology applications.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"107-115"},"PeriodicalIF":0.9,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11134730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141070264","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
Cryo-EM sample preparation for high-resolution structure studies 用于高分辨率结构研究的低温电子显微镜样品制备。
IF 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-04-30 DOI: 10.1107/S2053230X24002553
Liguo Wang, Christina M. Zimanyi
{"title":"Cryo-EM sample preparation for high-resolution structure studies","authors":"Liguo Wang,&nbsp;Christina M. Zimanyi","doi":"10.1107/S2053230X24002553","DOIUrl":"10.1107/S2053230X24002553","url":null,"abstract":"<p>High-resolution structures of biomolecules can be obtained using single-particle cryo-electron microscopy (SPA cryo-EM), and the rapidly growing number of structures solved by this method is encouraging more researchers to utilize this technique. As with other structural biology methods, sample preparation for an SPA cryo-EM data collection requires some expertise and an understanding of the strengths and limitations of the technique in order to make sensible decisions in the sample-preparation process. In this article, common strategies and pitfalls are described and practical advice is given to increase the chances of success when starting an SPA cryo-EM project.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"80 4","pages":"74-81"},"PeriodicalIF":0.9,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140292470","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
Structural and functional characterization of FabG4 from Mycolicibacterium smegmatis 烟曲霉分枝杆菌 FabG4 的结构和功能表征
IF 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-04-30 DOI: 10.1107/S2053230X2400356X
Xinping Ran, Prashit Parikh, Jan Abendroth, Tracy L. Arakaki, Matthew C. Clifton, Thomas E. Edwards, Donald D. Lorimer, Stephen Mayclin, Bart L. Staker, Peter Myler, Krystle J. McLaughlin
{"title":"Structural and functional characterization of FabG4 from Mycolicibacterium smegmatis","authors":"Xinping Ran,&nbsp;Prashit Parikh,&nbsp;Jan Abendroth,&nbsp;Tracy L. Arakaki,&nbsp;Matthew C. Clifton,&nbsp;Thomas E. Edwards,&nbsp;Donald D. Lorimer,&nbsp;Stephen Mayclin,&nbsp;Bart L. Staker,&nbsp;Peter Myler,&nbsp;Krystle J. McLaughlin","doi":"10.1107/S2053230X2400356X","DOIUrl":"https://doi.org/10.1107/S2053230X2400356X","url":null,"abstract":"<p>The rise in antimicrobial resistance is a global health crisis and necessitates the development of novel strategies to treat infections. For example, in 2022 tuberculosis (TB) was the second leading infectious killer after COVID-19, with multi-drug-resistant strains of TB having an ∼40% fatality rate. Targeting essential biosynthetic pathways in pathogens has proven to be successful for the development of novel antimicrobial treatments. Fatty-acid synthesis (FAS) in bacteria proceeds via the type II pathway, which is substantially different from the type I pathway utilized in animals. This makes bacterial fatty-acid biosynthesis (Fab) enzymes appealing as drug targets. FabG is an essential FASII enzyme, and some bacteria, such as <i>Mycobacterium tuberculosis</i>, the causative agent of TB, harbor multiple homologs. FabG4 is a conserved, high-molecular-weight FabG (HMwFabG) that was first identified in <i>M. tuberculosis</i> and is distinct from the canonical low-molecular-weight FabG. Here, structural and functional analyses of <i>Mycolicibacterium smegmatis</i> FabG4, the third HMwFabG studied to date, are reported. Crystal structures of NAD<sup>+</sup> and apo <i>Ms</i>FabG4, along with kinetic analyses, show that <i>Ms</i>FabG4 preferentially binds and uses NADH when reducing CoA substrates. As <i>M. smegmatis</i> is often used as a model organism for <i>M. tuberculosis</i>, these studies may aid the development of drugs to treat TB and add to the growing body of research that distinguish HMwFabGs from the archetypal low-molecular-weight FabG.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"80 4","pages":"82-91"},"PeriodicalIF":0.9,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140814303","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
Beyond publishing: introducing Interviews with authors 出版之外：介绍作者访谈。
IF 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-04-30 DOI: 10.1107/S2053230X24003339
Maria Cristina Nonato, Mark J. van Raaij, Jon Agirre
{"title":"Beyond publishing: introducing Interviews with authors","authors":"Maria Cristina Nonato,&nbsp;Mark J. van Raaij,&nbsp;Jon Agirre","doi":"10.1107/S2053230X24003339","DOIUrl":"10.1107/S2053230X24003339","url":null,"abstract":"<p>To find out what lies behind the articles published in <i>Acta Cryst. F – Structural Biology Communications</i> the journal now publishes interviews with its authors.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"80 4","pages":"73"},"PeriodicalIF":0.9,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140763979","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
The unbearable burden of peer review? 难以承受的同行评审负担？
IF 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-03-04 DOI: 10.1107/S2053230X24002024
Mark J. van Raaij
{"title":"The unbearable burden of peer review?","authors":"Mark J. van Raaij","doi":"10.1107/S2053230X24002024","DOIUrl":"10.1107/S2053230X24002024","url":null,"abstract":"<p>The current situation of scientific manuscript peer review is discussed, both generally and as applied to A<i>cta Crystallographica F – Biological Research Communications</i>.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"80 3","pages":"52"},"PeriodicalIF":0.9,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140020716","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 biochemical studies of the NYN domain of human KHNYN 人类 KHNYN NYN 结构域的结晶和生化研究。
IF 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-03-04 DOI: 10.1107/S2053230X24000943
Sunho Hong, Jungwoo Choe
{"title":"Crystallization and biochemical studies of the NYN domain of human KHNYN","authors":"Sunho Hong,&nbsp;Jungwoo Choe","doi":"10.1107/S2053230X24000943","DOIUrl":"10.1107/S2053230X24000943","url":null,"abstract":"<p>KHNYN is composed of an N-terminal KH-like RNA-binding domain and a C-terminal PIN/NYN endoribonuclease domain. It forms a complex with zinc-finger antiviral protein (ZAP), leading to the degradation of viral or cellular RNAs depending on the ZAP isoform. Here, the production, crystallization and biochemical analysis of the NYN domain (residues 477–636) of human KHNYN are presented. The NYN domain was crystallized with a heptameric single-stranded RNA from the AU-rich elements of the 3′-UTR of interferon lambda 3. The crystal belonged to space group <i>P</i>4<sub>1</sub>32, with unit-cell parameters <i>a</i> = <i>b</i> = <i>c</i> = 111.3 Å, and diffacted to 1.72 Å resolution. The RNase activity of the NYN domain was demonstrated using different single-stranded RNAs, together with the binding between the NYN domain of KHNYN and the zinc-finger domain of ZAP.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"80 3","pages":"67-72"},"PeriodicalIF":0.9,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139904725","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 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-03-04
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"80 3","pages":"53-58"},"PeriodicalIF":0.9,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140024620","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 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-03-04
{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"80 3","pages":"59-66"},"PeriodicalIF":0.9,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140024621","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 the GDP-bound state of the SRP GTPase FlhF. SRP GTPase FlhF 的 GDP 结合态结构。
IF 0.9 4区 生物学
Acta crystallographica. Section F, Structural biology communications Pub Date : 2024-03-01 Epub Date: 2024-02-20 DOI: 10.1107/S2053230X24000979
Anita Dornes, Christopher Nils Mais, Gert Bange
{"title":"Structure of the GDP-bound state of the SRP GTPase FlhF.","authors":"Anita Dornes, Christopher Nils Mais, Gert Bange","doi":"10.1107/S2053230X24000979","DOIUrl":"10.1107/S2053230X24000979","url":null,"abstract":"<p><p>The GTPase FlhF, a signal recognition particle (SRP)-type enzyme, is pivotal for spatial-numerical control and bacterial flagella assembly across diverse species, including pathogens. This study presents the X-ray structure of FlhF in its GDP-bound state at a resolution of 2.28 Å. The structure exhibits the classical N- and G-domain fold, consistent with related SRP GTPases such as Ffh and FtsY. Comparative analysis with GTP-loaded FlhF elucidates the conformational changes associated with GTP hydrolysis. These topological reconfigurations are similarly evident in Ffh and FtsY, and play a pivotal role in regulating the functions of these hydrolases.</p>","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"53-58"},"PeriodicalIF":0.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10910532/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139904727","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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