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Acta Crystallographica. Section F, Structural Biology Communications

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https://www.readbyqxmd.com/read/29969107/crystal-structures-and-kinetic-analyses-of-n-acetylmannosamine-6-phosphate-2-epimerases-from-fusobacterium-nucleatum-and-vibrio-cholerae
#1
Lavanyaa Manjunath, Sai Rohit Guntupalli, Michael J Currie, Rachel A North, Renwick C J Dobson, Vinod Nayak, Ramaswamy Subramanian
Sialic acids are nine-carbon sugars that are found abundantly on the cell surfaces of mammals as glycoprotein or glycolipid complexes. Several Gram-negative and Gram-positive bacteria have the ability to scavenge and catabolize sialic acids to use as a carbon source. This gives them an advantage in colonizing sialic acid-rich environments. The genes of the sialic acid catabolic pathway are generally present as the operon nanAKE. The third gene in the operon encodes the enzyme N-acetylmannosamine-6-phosphate 2-epimerase (NanE), which catalyzes the conversion of N-acetylmannosamine 6-phosphate to N-acetylglucosamine 6-phosphate, thus committing it to enter glycolysis...
July 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29969106/crystal-structure-of-human-anterior-gradient-protein-3
#2
Van Dat Nguyen, Ekaterina Biterova, Mikko Salin, Rik K Wierenga, Lloyd W Ruddock
Oxidative protein folding in the endoplasmic reticulum is catalyzed by the protein disulfide isomerase family of proteins. Of the 20 recognized human family members, the structures of eight have been deposited in the PDB along with domains from six more. Three members of this family, ERp18, anterior gradient protein 2 (AGR2) and anterior gradient protein 3 (AGR3), are single-domain proteins which share sequence similarity. While ERp18 has a canonical active-site motif and is involved in native disulfide-bond formation, AGR2 and AGR3 lack elements of the active-site motif found in other family members and may both interact with mucins...
July 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29969105/a-novel-bacterial-class-v-dye-decolourizing-peroxidase-from-the-extremophile-deinococcus-radiodurans-cloning-expression-optimization-purification-crystallization-initial-characterization-and-x-ray-diffraction-analysis
#3
Kelly Stefany Tuna Frade, Andreia Cecília Pimenta Fernandes, Celia Marisa Silveira, Carlos Frazão, Elin Moe
Deinococcus radiodurans is a bacterium with extreme resistance to desiccation and radiation. The resistance mechanism is unknown, but an efficient reactive oxygen species (ROS) scavenging system and DNA-repair and DNA-protection mechanisms are believed to play important roles. Here, the cloning and small- and medium-scale expression tests of a novel dye-decolourizing peroxidase from D. radiodurans (DrDyP) using three different Escherichia coli strains and three different temperatures in order to identify the optimum conditions for the expression of recombinant DrDyP are presented...
July 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29969104/cinder-keeping-crystallographers-app-y
#4
Nicholas Rosa, Marko Ristic, Bevan Marshall, Janet Newman
The process of producing suitable crystals for X-ray diffraction analysis most often involves the setting up of hundreds (or thousands) of individual crystallization trials, each of which must be repeatedly examined for crystals or hints of crystallinity. Currently, the only real way to address this bottleneck is to use an automated imager to capture images of the trials. However, the images still need to be assessed for crystals or other outcomes. Ideally, there would exist some rapid and reliable machine-analysis tool to translate the images into a quantitative result...
July 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29969103/crystal-structure-of-escherichia-coli-purine-nucleoside-phosphorylase-complexed-with-acyclovir
#5
Vladimir I Timofeev, Nadezhda E Zhukhlistova, Yuliya A Abramchik, Tatiana I Muravieva, Roman S Esipov, Inna P Kuranova
Escherichia coli purine nucleoside phosphorylase (PNP), which catalyzes the reversible phosphorolysis of purine ribonucleosides, belongs to the family I hexameric PNPs. Owing to their key role in the purine salvage pathway, PNPs are attractive targets for drug design against some pathogens. Acyclovir (ACV) is an acyclic derivative of the PNP substrate guanosine and is used as an antiviral drug for the treatment of some human viral infections. The crystalline complex of E. coli PNP with acyclovir was prepared by co-crystallization in microgravity using counter-diffusion through a gel layer in a capillary...
July 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29969102/crystallization-and-x-ray-analysis-of-all-of-the-players-in-the-autoregulation-of-the-atart-toxin-antitoxin-system
#6
Dukas Jurėnas, Laurence Van Melderen, Abel Garcia-Pino
The ataRT operon from enteropathogenic Escherichia coli encodes a toxin-antitoxin (TA) module with a recently discovered novel toxin activity. This new type II TA module targets translation initiation for cell-growth arrest. Virtually nothing is known regarding the molecular mechanisms of neutralization, toxin catalytic action or translation autoregulation. Here, the production, biochemical analysis and crystallization of the intrinsically disordered antitoxin AtaR, the toxin AtaT, the AtaR-AtaT complex and the complex of AtaR-AtaT with a double-stranded DNA fragment of the operator region of the promoter are reported...
July 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29969101/structural-polymorphism-of-the-escherichia-coli-poly-%C3%AE-l-glutamate-synthetase-rimk
#7
Yasuhiro Arimura, Tomonori Kono, Kuniki Kino, Hitoshi Kurumizaka
Bacterial RimK is an enzyme that catalyzes the polyglutamylation of the C-terminus of ribosomal protein S6 and the synthesis of poly-α-L-glutamate peptides using L-glutamic acid. In the present study, the crystal structure of the Escherichia coli RimK protein complexed with the ATP analogue AMP-PNP was determined at 2.05 Å resolution. Two different conformations of RimK, closed and open forms, were observed in the crystals. The structural polymorphism revealed in this study provided important information to understand the mechanism by which RimK catalyzes the synthesis of poly-α-L-glutamate peptides and the polyglutamylation of ribosomal protein S6...
July 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29870023/structure-and-analysis-of-nucleoside-diphosphate-kinase-from-borrelia-burgdorferi-prepared-in-a-transition-state-complex-with-adp-and-vanadate-moieties
#8
Mitchell Dumais, Douglas R Davies, Tao Lin, Bart L Staker, Peter J Myler, Wesley C Van Voorhis
Nucleoside diphosphate kinases (NDKs) are implicated in a wide variety of cellular functions owing to their enzymatic conversion of NDP to NTP. NDK from Borrelia burgdorferi (BbNDK) was selected for functional and structural analysis to determine whether its activity is required for infection and to assess its potential for therapeutic inhibition. The Seattle Structural Genomics Center for Infectious Diseases (SSGCID) expressed recombinant BbNDK protein. The protein was crystallized and structures were solved of both the apoenzyme and a liganded form with ADP and vanadate ligands...
June 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29870022/psest3-a-new-psychrophilic-esterase-from-the-arctic-bacterium-paenibacillus-sp-r4-crystallization-and-x-ray-crystallographic-analysis
#9
Hyun Kim, Ae Kyung Park, Jun Hyuck Lee, Seung Chul Shin, Hyun Park, Han Woo Kim
Esterases are very useful biocatalysts in industry: they hydrolyze esters and split them into a carboxylic acid and an alcohol. The psychrophilic esterase PsEst3 was obtained from Paenibacillus sp. R4, which was isolated from the active layer of the permafrost in Council, Alaska. PsEst3 was successfully overexpressed using a psychrophilic chaperonin co-expression system and was purified by nickel-affinity and size-exclusion chromatography. Recombinant PsEst3 was crystallized at 290 K using the hanging-drop vapour-diffusion method...
June 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29870021/picw2-from-picea-wilsonii-preparation-purification-crystallization-and-x-ray-diffraction-analysis
#10
Bei Zhang, Gangxing Guo, Fang Lu, Ying Song, Yong Liu, JiChen Xu, Wei Gao
Low temperature is a major limiting factor for plant growth and development. Dehydrin proteins are generally induced in response to low-temperature stress. In previous research, a full-length dehydrin gene, PicW2, was isolated from Picea wilsonii and its expression was associated with hardiness to cold. In order to gain insight into the mechanism of low-temperature tolerance by studying its three-dimensional crystal structure, prokaryotically expressed PicW2 dehydrin protein was purified using chitosan-affinity chromatography and gel filtration, and crystallized using the vapour-diffusion method...
June 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29870020/crystal-structure-of-escherichia-coli-purine-nucleoside-phosphorylase-in-complex-with-7-deazahypoxanthine
#11
Vladimir I Timofeev, Nadezhda E Zhukhlistova, Yuliya A Abramchik, Ilya I Fateev, Maria A Kostromina, Tatiana I Muravieva, Roman S Esipov, Inna P Kuranova
Purine nucleoside phosphorylases (EC 2.4.2.1; PNPs) reversibly catalyze the phosphorolytic cleavage of glycosidic bonds in purine nucleosides to generate ribose 1-phosphate and a free purine base, and are key enzymes in the salvage pathway of purine biosynthesis. They also catalyze the transfer of pentosyl groups between purine bases (the transglycosylation reaction) and are widely used for the synthesis of biologically important analogues of natural nucleosides, including a number of anticancer and antiviral drugs...
June 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29870019/crystallographic-analysis-of-the-staphylococcus-epidermidis-lipase-involved-in-esterification-in-aqueous-solution
#12
Cheng Huan Liu, Yu Ting Chen, Ming Hon Hou, Nien Jen Hu, Chin Shuh Chen, Jei Fu Shaw
The Staphylococcus epidermidis lipase (SeLip, GehC) can be used in flavour-compound production via esterification in aqueous solution. This study reports the crystallization and crystallographic analysis of recombinant GehC (rGehC; Lys303-Lys688) with a molecular weight of 43 kDa. rGehC was crystallized at 293 K using PEG 10 000 as a precipitant, and a 99.9% complete native data set was collected from a cooled crystal at 77 K to a resolution of 1.9 Å with an overall Rmerge value of 7.3%. The crystals were orthorhombic and belonged to space group P21 21 21 , with unit-cell parameters a = 42...
June 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29870018/perfect-merohedral-twinning-combined-with-noncrystallographic-symmetry-potentially-causes-the-failure-of-molecular-replacement-with-low-homology-search-models-for-the-flavin-dependent-halogenase-halx-from-xanthomonas-campestris
#13
Maren Buss, Christina Geerds, Thomas Patschkowski, Karsten Niehaus, Hartmut H Niemann
Flavin-dependent halogenases can be used as biocatalysts because they regioselectively halogenate their substrates under mild reaction conditions. New halogenases with novel substrate specificities will add to the toolbox of enzymes available to organic chemists. HalX, the product of the xcc-b100_4193 gene, is a putative flavin-dependent halogenase from Xanthomonas campestris. The enzyme was recombinantly expressed and crystallized in order to aid in identifying its hitherto unknown substrate. Native data collected to a resolution of 2...
June 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29870017/t4-lysozyme-facilitated-crystallization-of-the-human-molybdenum-cofactor-dependent-enzyme-marc
#14
Christian Kubitza, Carsten Ginsel, Florian Bittner, Antje Havemeyer, Bernd Clement, Axel J Scheidig
The human mitochondrial amidoxime reducing component (hmARC) is a molybdenum cofactor-dependent enzyme that is involved in the reduction of a diverse range of N-hydroxylated compounds of either physiological or xenobiotic origin. In this study, the use of a fusion-protein approach with T4 lysozyme (T4L) to determine the structure of this hitherto noncrystallizable enzyme by X-ray crystallography is described. A set of four different hmARC-T4L fusion proteins were designed. Two of them contained either an N-terminal or a C-terminal T4L moiety fused to hmARC, while the other two contained T4L as an internal fusion partner tethered to the hmARC enzyme between two predicted secondary-structure elements...
June 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29870016/crystal-structure-of-an-inactive-variant-of-the-quorum-sensing-master-regulator-hapr-from-the-protease-deficient-non-o1-non-o139-vibrio-cholerae-strain-v2
#15
Justin Cruite, Patrick Succo, Saumya Raychaudhuri, F Jon Kull
HapR is a TetR-family transcriptional regulator that controls quorum sensing in Vibrio cholerae, the causative agent of cholera. HapR regulates the expression of hemagglutinin protease, virulence and biofilm genes. The crystal structure of wild-type HapR from V. cholerae strain O1 El Tor C6706 has previously been solved. In this study, the structure of a DNA-binding-deficient variant of HapR (HapRV2 ) derived from the protease-deficient V. cholerae serotype O37 strain V2 is reported. The structure reveals no structural differences compared with wild-type HapR...
June 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29870015/carbonic-anhydrase-ii-microcrystals-suitable-for-xfel-studies
#16
Carrie L Lomelino, Jin Kyun Kim, Cheol Lee, Seon Woo Lim, Jacob T Andring, Brian P Mahon, Moses Chung, Chae Un Kim, Robert McKenna
Recent advances in X-ray free-electron laser (XFEL) sources have permitted the study of protein dynamics. Femtosecond X-ray pulses have allowed the visualization of intermediate states in enzyme catalysis. In this study, the growth of carbonic anhydrase II microcrystals (40-80 µm in length) suitable for the collection of XFEL diffraction data at the Pohang Accelerator Laboratory is demonstrated. The crystals diffracted to 1.7 Å resolution and were indexed in space group P21 , with unit-cell parameters a = 42...
June 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29718001/the-cd163-long-range-scavenger-receptor-cysteine-rich-repeat-expression-purification-and-x-ray-crystallographic-characterization
#17
Rui Li, Hongfang Ma, Longguang Jiang, Songlin Qiao, Yubao Zhi, Mingdong Huang, Ruiguang Deng, Gaiping Zhang
Scavenger receptors (SRs) play critical roles in various physiological and pathological pathways. One of them, CD163, is a multifunctional endocytic receptor and is characterized by a long-range scavenger receptor cysteine-rich (SRCR) repeat. However, the structural and functional details of this long-range SRCR repeat have not yet been elucidated. In this study, the CD163 long-range SRCR repeat was expressed in Drosophila Schneider 2 cells. The recombinant protein was homogeneous after purification by metal-affinity, cation-exchange and size-exclusion chromatography...
May 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29718000/structure-of-the-tandem-px-ph-domains-of-bem3-from-saccharomyces-cerevisiae
#18
Imtiaz Ali, Sungmin Eu, Daniel Koch, Nathalie Bleimling, Roger S Goody, Matthias P Müller
The structure of the tandem lipid-binding PX and pleckstrin-homology (PH) domains of the Cdc42 GTPase-activating protein Bem3 from Saccharomyces cerevisiae (strain S288c) has been determined to a resolution of 2.2 Å (Rwork = 21.1%, Rfree = 23.4%). It shows that the domains adopt a relative orientation that enables them to simultaneously bind to a membrane and suggests possible cooperativity in membrane binding.
May 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29717999/improved-protein-crystal-identification-by-using-2-2-2-trichloroethanol-as-a-fluorescence-enhancer
#19
Christian Pichlo, Christine Toelzer, Konrad Chojnacki, Sinan Öcal, Matthias Uthoff, Sabine Ruegenberg, Thomas Hermanns, Magdalena Schacherl, Martin S Denzel, Kay Hofmann, Karsten Niefind, Ulrich Baumann
The identification of initial lead conditions for successful protein crystallization is crucial for structural studies using X-ray crystallography. In order to reduce the number of false-negative conditions, an emerging number of fluorescence-based methods have been developed which allow more efficient identification of protein crystals and help to distinguish them from salt crystals. Detection of the native tryptophan fluorescence of protein crystals is one of the most widely used methods. However, this method can fail owing to the properties of the crystallized protein or the chemical composition of the crystallization trials...
May 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29717998/in-situ-proteolysis-of-an-n-terminal-his-tag-with-thrombin-improves-the-diffraction-quality-of-human-aldo-keto-reductase-1c3-crystals
#20
Jovana J Plavša, Pavlína Řezáčová, Michael Kugler, Petr Pachl, Jiří Brynda, Zdeněk Voburka, Anđelka Ćelić, Edward T Petri, Jana Škerlová
Human aldo-keto reductase 1C3 (AKR1C3) stereospecifically reduces steroids and prostaglandins and is involved in the biotransformation of xenobiotics. Its role in various cancers makes it a potential therapeutic target for the development of inhibitors. Recombinant AKR1C3 with a thrombin-cleavable N-terminal His6 tag was expressed from a pET-28(+) vector for structural studies of enzyme-inhibitor complexes. A modified in situ proteolysis approach was applied to specifically remove the His tag by thrombin cleavage during crystallization screening trials...
May 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
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