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Acta Crystallographica. Section F, Structural Biology Communications

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https://www.readbyqxmd.com/read/29095158/biochemical-and-structural-studies-of-mutants-indicate-concerted-movement-of-the-dimer-interface-and-ligand-binding-region-of-mycobacterium-tuberculosis-pantothenate-kinase
#1
A Paul, P Kumar, A Surolia, M Vijayan
Two point mutants and the corresponding double mutant of Mycobacterium tuberculosis pantothenate kinase have been prepared and biochemically and structurally characterized. The mutants were designed to weaken the affinity of the enzyme for the feedback inhibitor CoA. The mutants exhibit reduced activity, which can be explained in terms of their structures. The crystals of the mutants are not isomorphous to any of the previously analysed crystals of the wild-type enzyme or its complexes. The mycobacterial enzyme and its homologous Escherichia coli enzyme exhibit structural differences in their nucleotide complexes in the dimer interface and the ligand-binding region...
November 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29095157/pteridine-glycosyltransferase-from-chlorobium-tepidum-crystallization-and-x-ray-analysis
#2
Asaithambi Killivalavan, Young Shik Park, Kon Ho Lee
The pteridine glycosyltransferase (PGT) found in Chlorobium tepidum (CtPGT) catalyzes the conversion of L-threo-tetrahydrobiopterin to 1-O-(L-threo-biopterin-2'-yl)-β-N-acetylglucosamine using UDP-N-acetylglucosamine. The gene for CtPGT was cloned, and selenomethionine-derivatized protein was overexpressed and purified using various chromatographic techniques. The protein was crystallized by the hanging-drop vapour-diffusion method using 0.24 M triammonium citrate pH 7.0, 14%(w/v) PEG 3350 as a reservoir solution...
November 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29095156/structure-of-the-bacillus-anthracis-dtdp-l-rhamnose-biosynthetic-enzyme-glucose-1-phosphate-thymidylyltransferase-rfba
#3
Jackson Baumgartner, Jesi Lee, Andrei S Halavaty, George Minasov, Wayne F Anderson, Misty L Kuhn
L-Rhamnose is a ubiquitous bacterial cell-wall component. The biosynthetic pathway for its precursor dTDP-L-rhamnose is not present in humans, which makes the enzymes of the pathway potential drug targets. In this study, the three-dimensional structure of the first protein of this pathway, glucose-1-phosphate thymidylyltransferase (RfbA), from Bacillus anthracis was determined. In other organisms this enzyme is referred to as RmlA. RfbA was co-crystallized with the products of the enzymatic reaction, dTDP-α-D-glucose and pyrophosphate, and its structure was determined at 2...
November 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29095155/structural-studies-of-domain-movement-in-active-site-mutants-of-porphobilinogen-deaminase-from-bacillus-megaterium
#4
Jingxu Guo, Peter Erskine, Alun R Coker, Steve P Wood, Jonathan B Cooper
The enzyme porphobilinogen deaminase (PBGD) is one of the key enzymes in tetrapyrrole biosynthesis. It catalyses the formation of a linear tetrapyrrole from four molecules of the substrate porphobilinogen (PBG). It has a dipyrromethane cofactor (DPM) in the active site which is covalently linked to a conserved cysteine residue through a thioether bridge. The substrate molecules are linked to the cofactor in a stepwise head-to-tail manner during the reaction, which is catalysed by a conserved aspartate residue: Asp82 in the B...
November 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29095154/crystallization-and-x-ray-diffraction-analysis-of-native-and-selenomethionine-substituted-phyh-di-from-bacillus-sp-hjb17
#5
Fang Lu, Bei Zhang, Yong Liu, Ying Song, Gangxing Guo, Duo Feng, Huoqing Huang, Peilong Yang, Wei Gao, Sujuan Guo, Bin Yao
Phytases are phosphatases that hydrolyze phytates to less phosphorylated myo-inositol derivatives and inorganic phosphate. β-Propeller phytases, which are very diverse phytases with improved thermostability that are active at neutral and alkaline pH and have absolute substrate specificity, are ideal substitutes for other commercial phytases. PhyH-DI, a β-propeller phytase from Bacillus sp. HJB17, was found to act synergistically with other single-domain phytases and can increase their efficiency in the hydrolysis of phytate...
November 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29095153/periplasmic-form-of-dipeptidyl-aminopeptidase-iv-from-pseudoxanthomonas-mexicana-wo24-purification-kinetic-characterization-crystallization-and-x-ray-crystallographic-analysis
#6
Saori Roppongi, Chika Tateoka, Mayu Fujimoto, Ippei Iizuka, Saori Morisawa, Akihiro Nakamura, Nobuyuki Honma, Yoshiyuki Suzuki, Yosuke Shida, Wataru Ogasawara, Nobutada Tanaka, Yasumitsu Sakamoto, Takamasa Nonaka
Dipeptidyl aminopeptidase IV (DAP IV or DPP IV) from Pseudoxanthomonas mexicana WO24 (PmDAP IV) preferentially cleaves substrate peptides with Pro or Ala at the P1 position [NH2-P2-P1(Pro/Ala)-P1'-P2'…]. For crystallographic studies, the periplasmic form of PmDAP IV was overproduced in Escherichia coli, purified and crystallized in complex with the tripeptide Lys-Pro-Tyr using the hanging-drop vapour-diffusion method. Kinetic parameters of the purified enzyme against a synthetic substrate were also determined...
November 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29095152/structure-of-the-staphylococcal-enterotoxin-b-vaccine-candidate-s19-showing-eliminated-superantigen-activity
#7
Woo Hyeon Jeong, Dong Hyun Song, Gyeung Haeng Hur, Seong Tae Jeong
Four mutations (N23A, Y90A, R110A and F177A) were introduced into S19, a vaccine candidate for staphylococcal enterotoxin B (SEB), resulting in a lower binding affinity towards the T-cell receptor beta chain (TCB) and reducing its superantigen activity. The structure of S19 was solved and was superposed on the native or complex structure of SEB. In the superposition model, mutations that were introduced seemed to reduce the number of hydrogen bonds at the SEB-TCB interface. S19 also displayed an unexpected structural change around the flexible-loop region owing to the Y90A mutation...
November 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29095151/the-n253f-mutant-structure-of-trehalose-synthase-from-deinococcus-radiodurans-reveals-an-open-active-site-topology
#8
Sih Yao Chow, Yung Lin Wang, Yu Chiao Hsieh, Guan Chiun Lee, Shwu Huey Liaw
Trehalose synthase (TS) catalyzes the reversible conversion of maltose to trehalose and belongs to glycoside hydrolase family 13 (GH13). Previous mechanistic analysis suggested a rate-limiting protein conformational change, which is probably the opening and closing of the active site. Consistently, crystal structures of Deinococcus radiodurans TS (DrTS) in complex with the inhibitor Tris displayed an enclosed active site for catalysis of the intramoleular isomerization. In this study, the apo structure of the DrTS N253F mutant displays a new open conformation with an empty active site...
November 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28994407/structure-activity-and-thermostability-investigations-of-oxa-163-oxa-181-and-oxa-245-using-biochemical-analysis-crystal-structures-and-differential-scanning-calorimetry-analysis
#9
Bjarte Aarmo Lund, Ane Molden Thomassen, Trine Josefine Olsen Carlsen, Hanna Kirsti S Leiros
The first crystal structures of the class D β-lactamases OXA-181 and OXA-245 were determined to 2.05 and 2.20 Å resolution, respectively; in addition, the structure of a new crystal form of OXA-163 was resolved to 2.07 Å resolution. All of these enzymes are OXA-48-like and have been isolated from different clinical Klebsiella pneumoniae strains and also from other human pathogens such as Pseudomonas aeruginosa and Escherichia coli. Here, enzyme kinetics and thermostability studies are presented, and the new crystal structures are used to explain the observed variations...
October 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28994406/crystallization-via-tubing-microfluidics-permits-both-in-situ-and-ex-situ-x-ray-diffraction
#10
Charline J J Gerard, Gilles Ferry, Laurent M Vuillard, Jean A Boutin, Leonard M G Chavas, Tiphaine Huet, Nathalie Ferte, Romain Grossier, Nadine Candoni, Stéphane Veesler
A microfluidic platform was used to address the problems of obtaining diffraction-quality crystals and crystal handling during transfer to the X-ray diffractometer. Crystallization conditions of a protein of pharmaceutical interest were optimized and X-ray data were collected both in situ and ex situ.
October 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28994405/crystallization-and-x-ray-analysis-of-23%C3%A2-nm-virus-like-particles-from-norovirus-chiba-strain
#11
Kazuya Hasegawa, Yuichi Someya, Hideki Shigematsu, Tomomi Kimura-Someya, Nipawan Nuemket, Takashi Kumasaka
Norovirus is a major causative pathogen of nonbacterial acute gastroenteritis. Despite the sequence similarity among various strains, noroviruses of different genotypes show different antigenicities and different binding profiles to histo-blood group antigens (HBGAs). To reveal the relationships between the structure of the capsid and the diversity in antigenicity and the HBGA-binding profile, virus-like particles (VLPs) of the Chiba strain that belongs to genogroup I, genotype 4 were crystallized for X-ray structural analysis...
October 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28994404/identification-biochemical-characterization-and-crystallization-of-the-central-region-of-human-atg16l1
#12
Archna Archna, Andrea Scrima
ATG16L1 plays a major role in autophagy. It acts as a molecular scaffold which mediates protein-protein interactions essential for autophagosome formation. The ATG12~ATG5-ATG16L1 complex is one of the key complexes involved in autophagosome formation. Human ATG16L1 comprises 607 amino acids with three functional domains named ATG5BD, CCD and WD40, where the C-terminal WD40 domain represents approximately 50% of the full-length protein. Previously, structures of the C-terminal WD40 domain of human ATG16L1 as well as of human ATG12~ATG5 in complex with the ATG5BD of ATG16L1 have been reported...
October 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28994403/large-scale-crystallization-and-neutron-crystallographic-analysis-of-hsp70-in-complex-with-adp
#13
Takeshi Yokoyama, Andreas Ostermann, Tobias E Schrader, Mineyuki Mizuguchi
HSP70 belongs to the heat-shock protein family and binds to unfolded proteins, driven by ATP hydrolysis, in order to prevent aggregation. Previous X-ray crystallographic analyses of HSP70 have shown that HSP70 binds to ADP with internal water molecules. In order to elucidate the role of the water molecules, including their H/D atoms, a neutron diffraction study of the human HSP70 ATPase domain was initiated. Deuterated large crystals of the HSP-ADP complex (1.2-1.8 mm(3)) were successfully grown by large-scale crystallization, and a neutron diffraction experiment at BIODIFF resulted in diffraction to a maximum resolution of 2...
October 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28994402/crystal-structure-of-the-starch-binding-domain-of-glucoamylase-from-aspergillus-niger
#14
Yousuke Suyama, Norifumi Muraki, Masami Kusunoki, Hideo Miyake
Glucoamylases are widely used commercially to produce glucose syrup from starch. The starch-binding domain (SBD) of glucoamylase from Aspergillus niger is a small globular protein containing a disulfide bond. The structure of A. niger SBD has been determined by NMR, but the conformation surrounding the disulfide bond was unclear. Therefore, X-ray crystal structural analysis was used to attempt to clarify the conformation of this region. The SBD was purified from an Escherichia coli-based expression system and crystallized at 293 K...
October 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28994401/crystal-structure-of-type-ii-nadh-quinone-oxidoreductase-from-caldalkalibacillus-thermarum-with-an-improved-resolution-of-2-15%C3%A2-%C3%A3
#15
Yoshio Nakatani, Wanting Jiao, David Aragão, Yosuke Shimaki, Jessica Petri, Emily J Parker, Gregory M Cook
Type II NADH:quinone oxidoreductase (NDH-2) is a respiratory enzyme found in the electron-transport chain of many species, with the exception of mammals. It is a 40-70 kDa single-subunit monotopic membrane protein that catalyses the oxidation of NADH and the reduction of quinone molecules via the cofactor FAD. NDH-2 is a promising new target for drug development given its essential role in many bacterial species and intracellular parasites. Only two bacterial NDH-2 structures have been reported and these structures are at moderate resolution (2...
October 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28876234/production-crystallization-and-structure-determination-of-a-mycobacterial-glucosylglycerate-hydrolase
#16
Tatiana Barros Cereija, Susana Alarico, Nuno Empadinhas, Pedro José Barbosa Pereira
Glucosylglycerate hydrolase is highly conserved among rapidly growing mycobacteria and has been found to be involved in recovery from nitrogen starvation by promoting the rapid mobilization of the glucosylglycerate that accumulates under these conditions. Here, the production, crystallization and structure determination of glucosylglycerate hydrolase from Mycobacterium hassiacum using two-wavelength anomalous diffraction of selenomethionine-substituted crystals are described. The monoclinic (space group P21) crystals diffracted to ∼2...
September 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28876233/ectodomain-of-plasmodesmata-localized-protein-5-in-arabidopsis-expression-purification-crystallization-and-crystallographic-analysis
#17
Xiaocui Wang, Peiyan Zhu, Shanshan Qu, Jie Zhao, Prashant K Singh, Wei Wang
Plasmodesmata-localized protein 5 (PDLP5) is a cysteine-rich receptor-like protein which is localized on the plasmodesmata of Arabidopsis thaliana. Overexpression of PDLP5 can reduce the permeability of the plasmodesmata and further affect the cell-to-cell movement of viruses and macromolecules in plants. The ectodomain of PDLP5 contains two DUF26 domains; however, the function of these domains is still unknown. Here, the ectodomain of PDLP5 from Arabidopsis was cloned and overexpressed using an insect expression system and was then purified and crystallized...
September 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28876232/protein-crystallization-and-initial-neutron-diffraction-studies-of-the-photosystem-ii-subunit-psbo
#18
Martin Bommer, Leighton Coates, Holger Dau, Athina Zouni, Holger Dobbek
The PsbO protein of photosystem II stabilizes the active-site manganese cluster and is thought to act as a proton antenna. To enable neutron diffraction studies, crystals of the β-barrel core of PsbO were grown in capillaries. The crystals were optimized by screening additives in a counter-diffusion setup in which the protein and reservoir solutions were separated by a 1% agarose plug. Crystals were cross-linked with glutaraldehyde. Initial neutron diffraction data were collected from a 0.25 mm(3) crystal at room temperature using the MaNDi single-crystal diffractometer at the Spallation Neutron Source, Oak Ridge National Laboratory...
September 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28876231/the-lrr-roc-cor-module-of-the-chlorobium-tepidum-roco-protein-crystallization-and-x-ray-crystallographic-analysis
#19
Egon Deyaert, Arjan Kortholt, Wim Versées
Roco proteins are characterized by the presence of a Roc-COR supradomain harbouring GTPase activity, which is often preceded by an LRR domain. The most notorious member of the Roco protein family is the Parkinson's disease-associated LRRK2. The Roco protein from the bacterium Chlorobium tepidum has been used as a model system to investigate the structure and mechanism of this class of enzymes. Here, the crystallization and crystallographic analysis of the LRR-Roc-COR construct of the C. tepidum Roco protein is reported...
September 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28876230/characterization-and-crystal-structure-of-a-novel-zearalenone-hydrolase-from-cladophialophora-bantiana
#20
Renjie Hui, Xiangying Hu, Wenting Liu, Weidong Liu, Yingying Zheng, Yun Chen, Rey Ting Guo, Jian Jin, Chun Chi Chen
Zearalenone (ZEN) is a mycotoxin which causes huge economic losses in the food and animal feed industries. The lactonase ZHD101 from Clonostachys rosea, which catalyzes the hydrolytic degradation of ZEN, is the only known ZEN-detoxifying enzyme. Here, a protein homologous to ZHD101, denoted CbZHD, from Cladophialophora batiana was expressed and characterized. Sequence alignment indicates that CbZHD possesses the same catalytic triad and ZEN-interacting residues as found in ZHD101. CbZHD exhibits optimal enzyme activity at 35°C and pH 8, and is sensitive to heat treatment...
September 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
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