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Acta Crystallographica. Section F, Structural Biology Communications

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https://www.readbyqxmd.com/read/27834791/natural-and-non-natural-amino-acid-side-chain-substitutions-affinity-and-diffraction-studies-of-meditope-fab-complexes
#1
Krzysztof P Bzymek, Kendra A Avery, Yuelong Ma, David A Horne, John C Williams
Herein, multiple crystal structures of meditope peptide derivatives incorporating natural and unnatural amino acids bound to the cetuximab Fab domain are presented. The affinity of each derivative was determined by surface plasmon resonance and correlated to the atomic structure. Overall, it was observed that the hydrophobic residues in the meditope peptide, Phe3, Leu5 and Leu10, could accommodate a number of moderate substitutions, but these invariably reduced the overall affinity and half-life of the interaction...
November 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27834790/the-structure-of-the-metallo-%C3%AE-lactamase-vim-2-in-complex-with-a-triazolylthioacetamide-inhibitor
#2
Tony Christopeit, Ke Wu Yang, Shao Kang Yang, Hanna Kirsti S Leiros
The increasing number of pathogens expressing metallo-β-lactamases (MBLs), and in this way achieving resistance to β-lactam antibiotics, is a significant threat to global public health. A promising strategy to treat such resistant pathogens is the co-administration of MBL inhibitors together with β-lactam antibiotics. However, an MBL inhibitor suitable for clinical use has not yet been identified. Verona integron-encoded metallo-β-lactamase 2 (VIM-2) is a widespread MBL with a broad substrate spectrum and hence is an interesting drug target for the treatment of β-lactam-resistant infections...
November 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27827356/structural-characterization-of-the-thermostable-bradyrhizobium-japonicumd-sorbitol-dehydrogenase
#3
Folmer Fredslund, Harm Otten, Sabrina Gemperlein, Jens Christian N Poulsen, Yvonne Carius, Gert Wieland Kohring, Leila Lo Leggio
Bradyrhizobium japonicum sorbitol dehydrogenase is NADH-dependent and is active at elevated temperatures. The best substrate is D-glucitol (a synonym for D-sorbitol), although L-glucitol is also accepted, giving it particular potential in industrial applications. Crystallization led to a hexagonal crystal form, with crystals diffracting to 2.9 Å resolution. In attempts to phase the data, a molecular-replacement solution based upon PDB entry 4nbu (33% identical in sequence to the target) was found. The solution contained one molecule in the asymmetric unit, but a tetramer similar to that found in other short-chain dehydrogenases, including the search model, could be reconstructed by applying crystallographic symmetry operations...
November 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27827355/development-of-a-high-throughput-crystal-structure-determination-platform-for-jak1-using-a-novel-metal-chelator-soaking-system
#4
Nicole L Caspers, Seungil Han, Francis Rajamohan, Lise R Hoth, Kieran F Geoghegan, Timothy A Subashi, Michael L Vazquez, Neelu Kaila, Ciarán N Cronin, Eric Johnson, Ravi G Kurumbail
Crystals of phosphorylated JAK1 kinase domain were initially generated in complex with nucleotide (ADP) and magnesium. The tightly bound Mg(2+)-ADP at the ATP-binding site proved recalcitrant to ligand displacement. Addition of a molar excess of EDTA helped to dislodge the divalent metal ion, promoting the release of ADP and allowing facile exchange with ATP-competitive small-molecule ligands. Many kinases require the presence of a stabilizing ligand in the ATP site for crystallization. This procedure could be useful for developing co-crystallization systems with an exchangeable ligand to enable structure-based drug design of other protein kinases...
November 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27827354/crystal-structure-of-fuculose-aldolase-from-the-antarctic-psychrophilic-yeast-glaciozyma-antarctica-pi12
#5
Nardiah Rizwana Jaafar, Dene Littler, Travis Beddoe, Jamie Rossjohn, Rosli Md Illias, Nor Muhammad Mahadi, Mukram Mohamed Mackeen, Abdul Munir Abdul Murad, Farah Diba Abu Bakar
Fuculose-1-phosphate aldolase (FucA) catalyses the reversible cleavage of L-fuculose 1-phosphate to dihydroxyacetone phosphate (DHAP) and L-lactaldehyde. This enzyme from mesophiles and thermophiles has been extensively studied; however, there is no report on this enzyme from a psychrophile. In this study, the gene encoding FucA from Glaciozyma antarctica PI12 (GaFucA) was cloned and the enzyme was overexpressed in Escherichia coli, purified and crystallized. The tetrameric structure of GaFucA was determined to 1...
November 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27827353/crystal-structure-of-a-phosphoribosyl-anthranilate-isomerase-from-the-hyperthermophilic-archaeon-thermococcus-kodakaraensis
#6
Sumera Perveen, Naeem Rashid, Anastassios C Papageorgiou
A phosphoribosyl anthranilate isomerase, TkTrpF, from Thermococcus kodakaraensis was expressed in Escherichia coli and purified to homogeneity. TkTrpF was crystallized and its structure was determined by molecular replacement in two different space groups (C2 and P1) using data to 1.85 and 1.75 Å resolution, respectively. TkTrpF belongs to the class of TIM-barrel proteins. Structural comparison with other phosphoribosyl anthranilate isomerases (TrpFs) showed the highest structural similarity to Pyrococcus furiosus TrpF...
November 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27827352/crystal-structures-of-a-yeast-14-3-3-protein-from-lachancea-thermotolerans-in-the-unliganded-form-and-bound-to-a-human-lipid-kinase-pi4kb-derived-peptide-reveal-high-evolutionary-conservation
#7
Andrea Eisenreichova, Martin Klima, Evzen Boura
14-3-3 proteins bind phosphorylated binding partners to regulate several of their properties, including enzymatic activity, stability and subcellular localization. Here, two crystal structures are presented: the crystal structures of the 14-3-3 protein (also known as Bmh1) from the yeast Lachancea thermotolerans in the unliganded form and bound to a phosphopeptide derived from human PI4KB (phosphatidylinositol 4-kinase B). The structures demonstrate the high evolutionary conservation of ligand recognition by 14-3-3 proteins...
November 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27710946/expression-and-crystallographic-studies-of-the-arabidopsis-thaliana-gdp-d-mannose-pyrophosphorylase-vtc1
#8
Shun Zhao, Lin Liu
GDP-D-mannose pyrophosphorylase catalyzes the production of GDP-D-mannose, an intermediate product in the plant ascorbic acid (AsA) biosynthetic pathway. This enzyme is a key regulatory target in AsA biosynthesis and is encoded by VITAMIN C DEFECTIVE 1 (VTC1) in the Arabidopsis thaliana genome. Here, recombinant VTC1 was expressed, purified and crystallized. Diffraction data were obtained from VTC1 crystals grown in the absence and presence of substrate using X-rays. The ligand-free VTC1 crystal diffracted X-rays to 3...
October 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27710945/biochemical-spectroscopic-and-x-ray-structural-analysis-of-deuterated-multicopper-oxidase-cueo-prepared-from-a-new-expression-construct-for-neutron-crystallography
#9
Mahfuza Akter, Chika Inoue, Hirofumi Komori, Nana Matsuda, Takeshi Sakurai, Kunishige Kataoka, Yoshiki Higuchi, Naoki Shibata
Multicopper oxidases oxidize various phenolic and nonphenolic compounds by using molecular oxygen as an electron acceptor to produce water. A multicopper oxidase protein, CueO, from Escherichia coli is involved in copper homeostasis in the bacterial cell. Although X-ray crystallographic studies have been conducted, the reduction mechanism of oxygen and the proton-transfer pathway remain unclear owing to the difficulty in identifying H atoms from X-ray diffraction data alone. To elucidate the reaction mechanism using neutron crystallography, a preparation system for obtaining large, high-quality single crystals of deuterated CueO was developed...
October 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27710944/x-ray-crystallographic-studies-of-the-extracellular-domain-of-the-first-plant-atp-receptor-dorn1-and-the-orthologous-protein-from-camelina-sativa
#10
Zhijie Li, Sayan Chakraborty, Guozhou Xu
Does not respond to nucleotides 1 (DORN1) has recently been identified as the first membrane-integral plant ATP receptor, which is required for ATP-induced calcium response, mitogen-activated protein kinase activation and defense responses in Arabidopsis thaliana. In order to understand DORN1-mediated ATP sensing and signal transduction, crystallization and preliminary X-ray studies were conducted on the extracellular domain of DORN1 (atDORN1-ECD) and that of an orthologous protein, Camelina sativa lectin receptor kinase I...
October 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27710943/crystallographic-study-of-the-2-thioribothymidine-synthetic-complex-ttua-ttub-from-thermus-thermophilus
#11
Minghao Chen, Shun Narai, Naoki Omura, Naoki Shigi, Sarin Chimnaronk, Yoshikazu Tanaka, Min Yao
The ubiquitin-like protein TtuB is a sulfur carrier for the biosynthesis of 2-thioribothymidine (s(2)T) at position 54 in some thermophilic bacterial tRNAs. TtuB captures a S atom at its C-terminus as a thiocarboxylate and transfers it to tRNA by the transferase activity of TtuA. TtuB also functions to suppress s(2)T formation by forming a covalent bond with TtuA. To explore how TtuB interacts with TtuA and switches between these two different functions, high-resolution structure analysis of the TtuA-TtuB complex is required...
October 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27710942/crystal-structure-of-rofecoxib-bound-to-human-cyclooxygenase-2
#12
Benjamin J Orlando, Michael G Malkowski
Rofecoxib (Vioxx) was one of the first selective cyclooxygenase-2 (COX-2) inhibitors (coxibs) to be approved for use in humans. Within five years after its release to the public, Vioxx was withdrawn from the market owing to the adverse cardiovascular effects of the drug. Despite the widespread knowledge of the development and withdrawal of Vioxx, relatively little is known at the molecular level about how the inhibitor binds to COX-2. Vioxx is unique in that the inhibitor contains a methyl sulfone moiety in place of the sulfonamide moiety found in other coxibs such as celecoxib and valdecoxib...
October 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27710941/comparative-analysis-of-anti-polyglutamine-fab-crystals-grown-on-earth-and-in-microgravity
#13
Gwen E Owens, Danielle M New, Alejandra I Olvera, Julia Ashlyn Manzella, Brittney L Macon, Joshua C Dunn, David A Cooper, Robyn L Rouleau, Daniel S Connor, Pamela J Bjorkman
Huntington's disease is one of nine neurodegenerative diseases caused by a polyglutamine (polyQ)-repeat expansion. An anti-polyQ antigen-binding fragment, MW1 Fab, was crystallized both on Earth and on the International Space Station, a microgravity environment where convection is limited. Once the crystals returned to Earth, the number, size and morphology of all crystals were recorded, and X-ray data were collected from representative crystals. The results generally agreed with previous microgravity crystallization studies...
October 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27710940/the-structure-of-a-glycoside-hydrolase-29-family-member-from-a-rumen-bacterium-reveals-unique-dual-carbohydrate-binding-domains
#14
Emma L Summers, Christina D Moon, Renee Atua, Vickery L Arcus
Glycoside hydrolase (GH) family 29 consists solely of α-L-fucosidases. These enzymes catalyse the hydrolysis of glycosidic bonds. Here, the structure of GH29_0940, a protein cloned from metagenomic DNA from the rumen of a cow, has been solved, which reveals a multi-domain arrangement that has only recently been identified in bacterial GH29 enzymes. The microbial species that provided the source of this enzyme is unknown. This enzyme contains a second carbohydrate-binding domain at its C-terminal end in addition to the typical N-terminal catalytic domain and carbohydrate-binding domain arrangement of GH29-family proteins...
October 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27710939/crystal-and-solution-structural-studies-of-mouse-phospholipid-hydroperoxide-glutathione-peroxidase-4
#15
Robert Janowski, Sandra Scanu, Dierk Niessing, Tobias Madl
The mammalian glutathione peroxidase (GPx) family is a key component of the cellular antioxidative defence system. Within this family, GPx4 has unique features as it accepts a large class of hydroperoxy lipid substrates and has a plethora of biological functions, including sperm maturation, regulation of apoptosis and cerebral embryogenesis. In this paper, the structure of the cytoplasmic isoform of mouse phospholipid hydroperoxide glutathione peroxidase (O70325-2 GPx4) with selenocysteine 46 mutated to cysteine is reported solved at 1...
October 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27710938/arabidopsis-receptor-like-cytoplasmic-kinase-bik1-purification-crystallization-and-x-ray-diffraction-analysis
#16
Neeraj K Lal, Andrew J Fisher, Savithramma P Dinesh-Kumar
Receptor-like cytoplasmic kinases (RLCKs) in Arabidopsis play a central role in the integration of signaling input from various growth and immune signaling pathways. BOTRYTIS-INDUCED KINASE 1 (BIK1), belonging to the RLCK family, is an important player in defense against bacterial and fungal pathogens and in ethylene and brassinosteroid hormone signaling. In this study, the purification and crystallization of a first member of the class VI family of RLCK proteins, BIK1, are reported. BIK1 was crystallized using the microbatch-under-oil method...
October 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27710937/crystal-structure-of-yeast-monothiol-glutaredoxin-grx6-in-complex-with-a-glutathione-coordinated-2fe-2s-cluster
#17
Mohnad Abdalla, Ya Nan Dai, Chang Biao Chi, Wang Cheng, Dong Dong Cao, Kang Zhou, Wafa Ali, Yuxing Chen, Cong Zhao Zhou
Glutaredoxins (Grxs) constitute a superfamily of proteins that perform diverse biological functions. The Saccharomyces cerevisiae glutaredoxin Grx6 not only serves as a glutathione (GSH)-dependent oxidoreductase and as a GSH transferase, but also as an essential [2Fe-2S]-binding protein. Here, the dimeric structure of the C-terminal domain of Grx6 (holo Grx6C), bridged by one [2Fe-2S] cluster coordinated by the active-site Cys136 and two external GSH molecules, is reported. Structural comparison combined with multiple-sequence alignment demonstrated that holo Grx6C is similar to the [2Fe-2S] cluster-incorporated dithiol Grxs, which share a highly conserved [2Fe-2S] cluster-binding pattern and dimeric conformation that is distinct from the previously identified [2Fe-2S] cluster-ligated monothiol Grxs...
October 1, 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27599865/1-65%C3%A2-%C3%A3-resolution-structure-of-the-arac-family-transcriptional-activator-toxt-from-vibrio-cholerae
#18
Jiaqin Li, Graham Wehmeyer, Scott Lovell, Kevin P Battaile, Susan M Egan
ToxT is an AraC-family transcriptional activator protein that controls the expression of key virulence factors in Vibrio cholerae, the causative agent of cholera. ToxT directly activates the expression of the genes that encode the toxin-coregulated pilus and cholera toxin, and also positively auto-regulates its own expression from the tcp promoter. The crystal structure of ToxT has previously been solved at 1.9 Å resolution (PDB entry 3gbg). In this study, a crystal structure of ToxT at 1.65 Å resolution with a similar overall structure to the previously determined structure is reported...
September 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27599864/crystal-structure-of-the-yajq-family-protein-xc_3703-from-xanthomonas-campestris-pv-campestris
#19
Zhixin Zhao, Zhen Wu, Jun Zhang
As an important bacterial second messenger, bis-(3',5')-cyclic diguanylate (cyclic di-GMP or c-di-GMP) has been implicated in numerous biological activities, including biofilm formation, motility, survival and virulence. These processes are manipulated by the binding of c-di-GMP to its receptors. XC_3703 from the plant pathogen Xanthomonas campestris pv. campestris, which belongs to the YajQ family of proteins, has recently been identified as a potential c-di-GMP receptor. XC_3703, together with XC_2801, functions as a transcription factor activating virulence-related genes, which can be reversed by the binding of c-di-GMP to XC_3703...
September 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27599863/crystallization-of-and-selenomethionine-phasing-strategy-for-a-setmar-dna-complex
#20
Qiujia Chen, Millie Georgiadis
Transposable elements have played a critical role in the creation of new genes in all higher eukaryotes, including humans. Although the chimeric fusion protein SETMAR is no longer active as a transposase, it contains both the DNA-binding domain (DBD) and catalytic domain of the Hsmar1 transposase. The amino-acid sequence of the DBD has been virtually unchanged in 50 million years and, as a consequence, SETMAR retains its sequence-specific binding to the ancestral Hsmar1 terminal inverted repeat (TIR) sequence...
September 2016: Acta Crystallographica. Section F, Structural Biology Communications
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