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Acta Crystallographica. Section F, Structural Biology Communications

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https://www.readbyqxmd.com/read/30605128/atnpr4-from-arabidopsis-thaliana-expression-purification-crystallization-and-crystallographic-analysis
#1
Qingzhan Yang, Mengze Zhang, Jimin Zheng, Zongchao Jia
Salicylic acid (SA) is an important phytohormone that is involved in the regulation of plant defence, growth and development. A large number of proteins have been shown to have the ability to interact with SA, and NPR4 has been demonstrated to be a receptor of SA that plays significant roles in the innate immune response of plants. In this study, Spodoptera frugiperda (Sf9) cells were used to express full-length AtNPR4 from Arabidopsis thaliana. To facilitate crystallization, T4 lysozyme (T4L) was added to the N-terminus of the AtNPR4 protein...
January 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30605127/the-redefined-dna-binding-domain-of-human-xeroderma-pigmentosum-complementation-group-a-production-crystallization-and-structure-solution
#2
Fu Ming Lian, Xiangwei Yang, Wancai Yang, Yong Liang Jiang, Chengmin Qian
Human xeroderma pigmentosum complementation group A (XPA) is a scaffold protein that plays significant roles in DNA-damage verification and in recruiting downstream endonucleases to facilitate the repair of DNA lesions in nucleotide-excision repair. XPA98-219 (residues 98-219) has been identified as a DNA-binding domain and has been extensively studied in the last two decades. However, the most recent studies have redefined the DNA-binding domain as XPA98-239 (residues 98-239); it exerts a remarkably higher DNA-binding affinity than XPA98-219 and has a binding affinity that is quite similar to that of the full-length protein...
January 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30605126/the-structure-and-activity-of-the-glutathione-reductase-from-streptococcus-pneumoniae
#3
Mwilye Sikanyika, David Aragão, Christopher A McDevitt, Megan J Maher
The glutathione reductase (GR) from Streptococcus pneumoniae is a flavoenzyme that catalyzes the reduction of oxidized glutathione (GSSG) to its reduced form (GSH) in the cytoplasm of this bacterium. The maintenance of an intracellular pool of GSH is critical for the detoxification of reactive oxygen and nitrogen species and for intracellular metal tolerance to ions such as zinc. Here, S. pneumoniae GR (SpGR) was overexpressed and purified and its crystal structure determined at 2.56 Å resolution. SpGR shows overall structural similarity to other characterized GRs, with a dimeric structure that includes an antiparallel β-sheet at the dimer interface...
January 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30605125/the-x-ray-crystal-structure-of-human-endothelin-1-a-polypeptide-hormone-regulator-of-blood-pressure
#4
Alexander McPherson, Steven B Larson
Human endothelin is a 21-amino-acid polypeptide, constrained by two intra-chain disulfide bridges, that is made by endothelial cells. It is the most potent vasoconstrictor in the body and is crucially important in the regulation of blood pressure. It plays a major role in a host of medical conditions, including hypertension, diabetes, stroke and cancer. Endothelin was crystallized 28 years ago in the putative space group P61 22, but the structure was never successfully solved by X-ray diffraction. Using X-ray diffraction data from 1992, the structure has now been solved...
January 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30605124/never-too-late-for-endothelin
#5
Robyn L Stanfield
No abstract text is available yet for this article.
January 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30605123/single-particle-reconstruction-statistics-a-diagnostic-tool-in-solving-biomolecular-structures-by-cryo-em
#6
J Bernard Heymann
In single-particle analysis (SPA), the aim is to obtain a 3D reconstruction of a biological molecule from 2D electron micrographs to the highest level of detail or resolution as possible. Current practice is to collect large volumes of data, hoping to reach high-resolution maps through sheer numbers. However, adding more particles from a specific data set eventually leads to diminishing improvements in resolution. Understanding what these resolution limits are and how to deal with them are important in optimization and automation of SPA...
January 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30605122/survey-of-the-analysis-of-continuous-conformational-variability-of-biological-macromolecules-by-electron-microscopy
#7
C O S Sorzano, A Jiménez, J Mota, J L Vilas, D Maluenda, M Martínez, E Ramírez-Aportela, T Majtner, J Segura, R Sánchez-García, Y Rancel, L Del Caño, P Conesa, R Melero, S Jonic, J Vargas, F Cazals, Z Freyberg, J Krieger, I Bahar, R Marabini, J M Carazo
Single-particle analysis by electron microscopy is a well established technique for analyzing the three-dimensional structures of biological macromolecules. Besides its ability to produce high-resolution structures, it also provides insights into the dynamic behavior of the structures by elucidating their conformational variability. Here, the different image-processing methods currently available to study continuous conformational changes are reviewed.
January 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30605121/on-cross-correlations-averages-and-noise-in-electron-microscopy
#8
Michael Radermacher, Teresa Ruiz
Biological samples are radiation-sensitive and require imaging under low-dose conditions to minimize damage. As a result, images contain a high level of noise and exhibit signal-to-noise ratios that are typically significantly smaller than 1. Averaging techniques, either implicit or explicit, are used to overcome the limitations imposed by the high level of noise. Averaging of 2D images showing the same molecule in the same orientation results in highly significant projections. A high-resolution structure can be obtained by combining the information from many single-particle images to determine a 3D structure...
January 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30605120/visualization-of-biological-macromolecules-at-near-atomic-resolution-cryo-electron-microscopy-comes-of-age
#9
Alok K Mitra
Structural biology is going through a revolution as a result of transformational advances in the field of cryo-electron microscopy (cryo-EM) driven by the development of direct electron detectors and ultrastable electron microscopes. High-resolution cryo-EM images of isolated biomolecules (single particles) suspended in a thin layer of vitrified buffer are subjected to powerful image-processing algorithms, enabling near-atomic resolution structures to be determined in unprecedented numbers. Prior to these advances, electron crystallography of two-dimensional crystals and helical assemblies of proteins had established the feasibility of atomic resolution structure determination using cryo-EM...
January 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30605119/acta-crystallographica-section-f-another-home-for-cryo-electron-microscopy-contributions
#10
Alok K Mitra, Mark van Raaij
No abstract text is available yet for this article.
January 1, 2019: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30511677/the-structure-of-sds22-provides-insights-into-the-mechanism-of-heterodimer-formation-with-pp1
#11
Meng S Choy, Nicolas Bolik-Coulon, Tara L Archuleta, Wolfgang Peti, Rebecca Page
Protein phosphatase 1 (PP1) dephosphorylates hundreds of key biological targets by associating with nearly 200 regulatory proteins to form highly specific holoenzymes. The vast majority of regulators are intrinsically disordered proteins (IDPs) and bind PP1 via short linear motifs within their intrinsically disordered regions. One of the most ancient PP1 regulators is SDS22, a protein that is conserved from yeast to mammals. Sequence analysis of SDS22 revealed that it is a leucine-rich repeat (LRR) protein, suggesting that SDS22, unlike nearly every other known PP1 regulator, is not an IDP but instead is fully structured...
December 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30511676/crystal-structure-of-the-agrobacterium-tumefaciens-type-vi-effector-immunity-complex
#12
Satoshi Fukuhara, Takanori Nakane, Keitaro Yamashita, Ryohei Ishii, Ryuichiro Ishitani, Osamu Nureki
The type VI secretion system (T6SS) comprises needle-shaped multisubunit complexes that play a role in the microbial defense systems of Gram-negative bacteria. Some Gram-negative bacteria harboring a T6SS deliver toxic effector proteins into the cytoplasm or periplasm of competing bacteria in order to lyse and kill them. To avoid self-cell disruption, these bacteria have cognate immunity proteins that inhibit their toxic effector proteins. T6SS amidase effector protein 4 (Tae4) and T6SS amidase immunity protein 4 (Tai4) are a representative of the toxic effector-immunity pairs of the T6SS...
December 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30511675/the-crystal-structure-of-mycobacterium-tuberculosis-high-temperature-requirement-a-protein-reveals-an-autoregulatory-mechanism
#13
Arvind Kumar Gupta, Debashree Behera, Balasubramanian Gopal
The crystal structure of Mycobacterium tuberculosis high-temperature requirement A (HtrA) protein was determined at 1.83 Å resolution. This membrane-associated protease is essential for the survival of M. tuberculosis. The crystal structure reveals that interactions between the PDZ domain and the catalytic domain in HtrA lead to an inactive conformation. This finding is consistent with its proposed role as a regulatory protease that is conditionally activated upon appropriate environmental triggers. The structure provides a basis for directed studies to evaluate the role of this essential protein and the regulatory pathways that are influenced by this protease...
December 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30511674/an-inexpensive-system-for-imaging-the-contents-of-multi-well-plates
#14
Andrew Bohm
An inexpensive system for automated imaging of the contents of 12-, 24- and 96-well plates has been built. The xyz stage is constructed from parts from a light-duty computer numerical control wood-carving/engraving machine, and the Arduino-based board was wired so that it can trigger still images or movies though a microscope-mounted digital camera. The translation stage provides reproducible three-dimensional movement of the sample over a volume of 160 mm in x, 100 mm in y and 40 mm in z. A Python script generates the G-code command file that scans the plate and collects a series of z-stacked images of each sample...
December 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30511673/structural-studies-of-a-glycoside-hydrolase-family-3-%C3%AE-glucosidase-from-the-model-fungus-neurospora-crassa
#15
Saeid Karkehabadi, Henrik Hansson, Nils Egil Mikkelsen, Steve Kim, Thijs Kaper, Mats Sandgren, Mikael Gudmundsson
The glycoside hydrolase family 3 (GH3) β-glucosidases are a structurally diverse family of enzymes. Cel3A from Neurospora crassa (NcCel3A) belongs to a subfamily of key enzymes that are crucial for industrial biomass degradation. β-Glucosidases hydrolyse the β-1,4 bond at the nonreducing end of cellodextrins. The hydrolysis of cellobiose is of special importance as its accumulation inhibits other cellulases acting on crystalline cellulose. Here, the crystal structure of the biologically relevant dimeric form of NcCel3A is reported...
December 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30511672/crystal-structure-of-the-dimethylsulfide-monooxygenase-dmoa-from-hyphomicrobium-sulfonivorans
#16
Hai Yan Cao, Peng Wang, Ming Peng, Xuan Shao, Xiu Lan Chen, Chun Yang Li
DmoA is a monooxygenase which uses dioxygen (O2 ) and reduced flavin mononucleotide (FMNH2 ) to catalyze the oxidation of dimethylsulfide (DMS). Although it has been characterized, the structure of DmoA remains unknown. Here, the crystal structure of DmoA was determined to a resolution of 2.28 Å and was compared with those of its homologues LadA and BdsA. The results showed that their overall structures are similar: they all share a conserved TIM-barrel fold which is composed of eight α-helices and eight β-strands...
December 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30511671/structures-of-endo-1-5-%C3%AE-l-arabinanase-mutants-from-bacillus-thermodenitrificans-ts-3-in-complex-with-arabino-oligosaccharides
#17
Asako Yamaguchi, Yuri Sogabe, Satomi Fukuoka, Takuo Sakai, Toshiji Tada
The thermostable endo-1,5-α-L-arabinanase from Bacillus thermodenitrificans TS-3 (ABN-TS) hydrolyzes the α-1,5-L-arabinofuranoside linkages of arabinan. In this study, the crystal structures of inactive ABN-TS mutants, D27A and D147N, were determined in complex with arabino-oligosaccharides. The crystal structures revealed that ABN-TS has at least six subsites in the deep V-shaped cleft formed across one face of the propeller structure. The structural features indicate that substrate recognition is profoundly influenced by the remote subsites as well as by the subsites surrounding the active center...
December 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30511670/x-ray-crystallographic-analysis-of-the-catalytic-domain-of-%C3%AE-1-3-glucanase-fh1-from-paenibacillus-glycanilyticus-overexpressed-in-brevibacillus-choshinensis
#18
Rattanaporn Intuy, Takafumi Itoh, Wasana Suyotha, Junji Hayashi, Shigekazu Yano, Koki Makabe, Mamoru Wakayama, Takao Hibi
α-1,3-Glucanase hydrolyzes α-1,3-glucan, an insoluble linear α-1,3-linked homopolymer of glucose that is found in the extracellular polysaccharides produced by oral streptococci in dental plaque and in fungal cell walls. This enzyme could be of application in dental care and the development of fungal cell-wall lytic enzymes, but its three-dimensional structure has not been available to date. In this study, the recombinant catalytic domain of α-1,3-glucanase FH1 from Paenibacillus glycanilyticus FH11, which is classified into glycoside hydrolase family 87, was prepared using a Brevibacillus choshinensis expression system and purified in a soluble form...
December 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30511669/structure-of-undecaprenyl-pyrophosphate-synthase-from-acinetobacter-baumannii
#19
Tzu Ping Ko, Chi Hung Huang, Shu Jung Lai, Yeh Chen
Undecaprenyl pyrophosphate (UPP) is an important carrier of the oligosaccharide component in peptidoglycan synthesis. Inhibition of UPP synthase (UPPS) may be an effective strategy in combating the pathogen Acinetobacter baumannii, which has evolved to be multidrug-resistant. Here, A. baumannii UPPS (AbUPPS) was cloned, expressed, purified and crystallized, and its structure was determined by X-ray diffraction. Each chain of the dimeric protein folds into a central β-sheet with several surrounding α-helices, including one at the C-terminus...
December 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30511668/neutron-and-x-ray-crystal-structures-of-lactobacillus-brevis-alcohol-dehydrogenase-reveal-new-insights-into-hydrogen-bonding-pathways
#20
Johannes Hermann, Phillip Nowotny, Tobias E Schrader, Philipp Biggel, Dariusch Hekmat, Dirk Weuster-Botz
Lactobacillus brevis alcohol dehydrogenase (LbADH) is a well studied homotetrameric enzyme which catalyzes the enantioselective reduction of prochiral ketones to the corresponding secondary alcohols. LbADH is stable and enzymatically active at elevated temperatures and accepts a broad range of substrates, making it a valuable tool in industrial biocatalysis. Here, the expression, purification and crystallization of LbADH to generate large, single crystals with a volume of up to 1 mm3 suitable for neutron diffraction studies are described...
December 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
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