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

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IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-03-04
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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 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-03-01 Epub Date: 2024-02-20 DOI: 10.1107/S2053230X24000979
Anita Dornes, Christopher Nils Mais, Gert Bange

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.

GTP酶FlhF是一种信号识别颗粒(SRP)型酶,在包括病原体在内的不同物种的空间-数量控制和细菌鞭毛组装中起着关键作用。本研究以 2.28 Å 的分辨率展示了 FlhF 在 GDP 结合态下的 X 射线结构。该结构表现出经典的 N 和 G 域折叠,与 Ffh 和 FtsY 等相关 SRP GTP 酶一致。与加载了 GTP 的 FlhF 的比较分析阐明了与 GTP 水解相关的构象变化。这些拓扑重组在 Ffh 和 FtsY 中同样明显,并在调节这些水解酶的功能方面发挥了关键作用。
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引用次数: 0
Expression, purification and crystallization of the photosensory module of phytochrome B (phyB) from Sorghum bicolor. 双色高粱植物色素 B (phyB) 光感模块的表达、纯化和结晶。
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-03-01 Epub Date: 2024-02-20 DOI: 10.1107/S2053230X24000827
Sintayehu Manaye Shenkutie, Soshichiro Nagano, Jon Hughes

Sorghum, a short-day tropical plant, has been adapted for temperate grain production, in particular through the selection of variants at the MATURITY loci (Ma1-Ma6) that reduce photoperiod sensitivity. Ma3 encodes phytochrome B (phyB), a red/far-red photochromic biliprotein photoreceptor. The multi-domain gene product, comprising 1178 amino acids, autocatalytically binds the phytochromobilin chromophore to form the photoactive holophytochrome (Sb.phyB). This study describes the development of an efficient heterologous overproduction system which allows the production of large quantities of various holoprotein constructs, along with purification and crystallization procedures. Crystals of the Pr (red-light-absorbing) forms of NPGP, PGP and PG (residues 1-655, 114-655 and 114-458, respectively), each C-terminally tagged with His6, were successfully produced. While NPGP crystals did not diffract, those of PGP and PG diffracted to 6 and 2.1 Å resolution, respectively. Moving the tag to the N-terminus and replacing phytochromobilin with phycocyanobilin as the ligand produced PG crystals that diffracted to 1.8 Å resolution. These results demonstrate that the diffraction quality of challenging protein crystals can be improved by removing flexible regions, shifting fusion tags and altering small-molecule ligands.

高粱是一种短日照热带植物,已适应温带谷物生产,特别是通过在成熟度基因座(Ma1-Ma6)上选择变体,降低了对光周期的敏感性。Ma3 编码植物色素 B(phyB),它是一种红/远红光色素双蛋白光感受器。该多域基因产物由 1178 个氨基酸组成,能自动催化与植物色素的发色团结合,形成具有光活性的全植物色素(Sb.phyB)。本研究描述了一种高效异源过量生产系统的开发过程,该系统可大量生产各种整体蛋白构建体,以及纯化和结晶过程。我们成功制备出了 NPGP、PGP 和 PG 的 Pr(吸收红光)形式晶体(残基分别为 1-655、114-655 和 114-458),每种晶体都在 C 端用 His6 标记。NPGP 晶体没有衍射,而 PGP 和 PG 晶体的衍射分辨率分别为 6 Å 和 2.1 Å。将标签移至 N 端,并用藻蓝蛋白取代藻蓝蛋白作为配体,制备出的 PG 晶体衍射分辨率为 1.8 Å。这些结果表明,通过移除柔性区域、移动融合标签和改变小分子配体,可以提高具有挑战性的蛋白质晶体的衍射质量。
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引用次数: 0
Private glycan investigations and public video content 私人聚糖调查和公共视频内容
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-02-02 DOI: 10.1107/S2053230X2400102X
Mark J. van Raaij

Acta Cryst. F – Structural Biology Communications plans to introduce more video content to articles and Dialpuri et al. [(2024). Acta Cryst. F80, 30–35] provide an early example.

Acta Cryst.F - 结构生物学通讯》计划在文章中引入更多视频内容,Dialpuri 等人的文章[(2024). Acta Cryst. F80, 30-35]提供了一个早期范例。
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引用次数: 0
Crystal structure and biophysical characterization of IspD from Burkholderia thailandensis and Mycobacterium paratuberculosis 泰国伯克霍尔德菌和副结核分枝杆菌 IspD 的晶体结构和生物物理特征
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-02-02 DOI: 10.1107/S2053230X24000621
Phillip G. Pierce, Brian E. Hartnett, Tosha M. Laughlin, Joy M. Blain, Stephen J. Mayclin, Madison J. Bolejack, Janette B. Myers, Tate W. Higgins, David M. Dranow, Amy Sullivan, Donald D. Lorimer, Thomas E. Edwards, Timothy J. Hagen, James R. Horn, Peter J. Myler

The methylerythritol phosphate (MEP) pathway is a metabolic pathway that produces the isoprenoids isopentyl pyrophosphate and dimethylallyl pyrophosphate. Notably, the MEP pathway is present in bacteria and not in mammals, which makes the enzymes of the MEP pathway attractive targets for discovering new anti-infective agents due to the reduced chances of off-target interactions leading to side effects. There are seven enzymes in the MEP pathway, the third of which is IspD. Two crystal structures of Burkholderia thailandensis IspD (BtIspD) were determined: an apo structure and that of a complex with cytidine triphosphate (CTP). Comparison of the CTP-bound BtIspD structure with the apo structure revealed that CTP binding stabilizes the loop composed of residues 13–19. The apo structure of Mycobacterium paratuberculosis IspD (MpIspD) is also reported. The melting temperatures of MpIspD and BtIspD were evaluated by circular dichroism. The moderate Tm values suggest that a thermal shift assay may be feasible for future inhibitor screening. Finally, the binding affinity of CTP for BtIspD was evaluated by isothermal titration calorimetry. These structural and biophysical data will aid in the discovery of IspD inhibitors.

季戊四醇磷酸甲酯(MEP)途径是产生焦磷酸异戊酯和焦磷酸二甲基烯丙基酯的代谢途径。值得注意的是,MEP 途径存在于细菌中,而不存在于哺乳动物中,这使得 MEP 途径的酶成为发现新的抗感染药物的有吸引力的靶点,因为它们减少了脱靶相互作用导致副作用的机会。MEP 途径中有七种酶,其中第三种是 IspD。我们测定了泰国伯克霍尔德氏菌 IspD(BtIspD)的两种晶体结构:一种是apo结构,另一种是与三磷酸胞苷(CTP)的复合物结构。将与 CTP 结合的 BtIspD 结构与 apo 结构进行比较后发现,与 CTP 结合可稳定由残基 13-19 组成的环路。此外,还报告了副结核分枝杆菌 IspD(MpIspD)的 apo 结构。通过圆二色性评估了 MpIspD 和 BtIspD 的熔化温度。适中的 Tm 值表明,在未来的抑制剂筛选中,热转移测定可能是可行的。最后,通过等温滴定量热法评估了 CTP 与 BtIspD 的结合亲和力。这些结构和生物物理数据将有助于发现 IspD 抑制剂。
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引用次数: 0
Crystal structure of the RNA-recognition motif of Drosophila melanogaster tRNA (uracil-5-)-methyltransferase homolog A. 黑腹果蝇 tRNA(尿嘧啶-5-)甲基转移酶同源物 A 的 RNA 识别基团晶体结构。
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-02-01 Epub Date: 2024-01-25 DOI: 10.1107/S2053230X24000645
Monika Witzenberger, Robert Janowski, Dierk Niessing

Human tRNA (uracil-5-)-methyltransferase 2 homolog A (TRMT2A) is the dedicated enzyme for the methylation of uridine 54 in transfer RNA (tRNA). Human TRMT2A has also been described as a modifier of polyglutamine (polyQ)-derived neuronal toxicity. The corresponding human polyQ pathologies include Huntington's disease and constitute a family of devastating neurodegenerative diseases. A polyQ tract in the corresponding disease-linked protein causes neuronal death and symptoms such as impaired motor function, as well as cognitive impairment. In polyQ disease models, silencing of TRMT2A reduced polyQ-associated cell death and polyQ protein aggregation, suggesting this protein as a valid drug target against this class of disorders. In this paper, the 1.6 Å resolution crystal structure of the RNA-recognition motif (RRM) from Drosophila melanogaster, which is a homolog of human TRMT2A, is described and analysed.

人类 tRNA(尿嘧啶-5-)甲基转移酶 2 同源物 A(TRMT2A)是转移核糖核酸(tRNA)中尿嘧啶 54 甲基化的专用酶。人类 TRMT2A 也被描述为聚谷氨酰胺(polyQ)引起的神经元毒性的调节剂。相应的人类多聚 Q 病症包括亨廷顿氏病,并构成了一个破坏性神经退行性疾病家族。与疾病相关的蛋白质中的 polyQ 道会导致神经元死亡和运动功能受损以及认知障碍等症状。在多Q疾病模型中,沉默TRMT2A可减少与多Q相关的细胞死亡和多Q蛋白聚集,这表明该蛋白是治疗这类疾病的有效药物靶点。本文描述并分析了来自黑腹果蝇的 RNA 识别基序(RRM)的 1.6 Å 分辨率晶体结构,它是人类 TRMT2A 的同源物。
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引用次数: 0
Online carbohydrate 3D structure validation with the Privateer web app. 利用 Privateer 网络应用程序在线验证碳水化合物的三维结构。
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-02-01 Epub Date: 2024-01-24 DOI: 10.1107/S2053230X24000359
Jordan S Dialpuri, Haroldas Bagdonas, Lucy C Schofield, Phuong Thao Pham, Lou Holland, Paul S Bond, Filomeno Sánchez Rodríguez, Stuart J McNicholas, Jon Agirre

Owing to the difficulties associated with working with carbohydrates, validating glycan 3D structures prior to deposition into the Protein Data Bank has become a staple of the structure-solution pipeline. The Privateer software provides integrative methods for the validation, analysis, refinement and graphical representation of 3D atomic structures of glycans, both as ligands and as protein modifiers. While Privateer is free software, it requires users to install any of the structural biology software suites that support it or to build it from source code. Here, the Privateer web app is presented, which is always up to date and available to be used online (https://privateer.york.ac.uk) without installation. This self-updating tool, which runs locally on the user's machine, will allow structural biologists to simply and quickly analyse carbohydrate ligands and protein glycosylation from a web browser whilst retaining all confidential information on their devices.

由于与碳水化合物相关的工作困难重重,在将聚糖三维结构存入蛋白质数据库之前对其进行验证已成为结构解析管道的主要工作。Privateer 软件提供了验证、分析、完善和以图形表示聚糖三维原子结构的综合方法,既可作为配体,也可作为蛋白质修饰物。虽然 Privateer 是免费软件,但它要求用户安装任何支持它的结构生物学软件套件,或从源代码中构建它。这里介绍的 Privateer 网络应用程序始终是最新的,无需安装即可在线使用(https://privateer.york.ac.uk)。这种在用户机器上本地运行的自我更新工具,将使结构生物学家能够通过网络浏览器简单快速地分析碳水化合物配体和蛋白质糖基化,同时将所有机密信息保留在他们的设备上。
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引用次数: 0
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-25
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引用次数: 0
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-24
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引用次数: 0
IF 0.9 4区 生物学 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-11
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引用次数: 0
期刊
Acta crystallographica. Section F, Structural biology communications
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