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Acta Crystallographica. Section D, Structural Biology

Naoki Saka, Hiroyuki Iwamoto, Dominggus Malle, Nobuyuki Takahashi, Kimihiko Mizutani, Bunzo Mikami
Crystal structures of Klebsiella pneumoniae pullulanase (KPP) in complex with α-cyclodextrin (α-CD), β-cyclodextrin (β-CD) and γ-cyclodextrin (γ-CD) were refined at around 1.98-2.59 Å resolution from data collected at SPring-8. In the structures of the complexes obtained with 1 mM α-CD or γ-CD, one molecule of CD was found at carbohydrate-binding module 41 only (CBM41). In the structures of the complexes obtained with 1 mM β-CD or with 10 mM α-CD or γ-CD, two molecules of CD were found at CBM41 and in the active-site cleft, where the hydrophobic residue of Phe746 occupies the inside cavity of the CD rings...
November 1, 2018: Acta Crystallographica. Section D, Structural Biology
Marian S Vogt, Simon L Völpel, Sonja Verena Albers, Lars Oliver Essen, Ankan Banerjee
The small winged helix-turn-helix (wHTH) proteins of the Lrs14 family are major transcriptional regulators and act as archaeal biofilm regulators (AbfRs) in the crenarchaeote Sulfolobus acidocaldarius. Here, the first crystal structure of an AbfR ortholog, AbfR2, the deletion of which is known to impair biofilm formation, is presented. Like most other wHTH orthologs, AbfR2 is dimeric in solution as well as in its 2.45 Å resolution crystal structure. Given the presence of three independent AbfR2 dimers in the asymmetric unit, the crystal structure shows a considerable degree of conformational variation within the dimer, the antiparallel orientations of which are stabilized by coiled-coil interaction between H4 helices...
November 1, 2018: Acta Crystallographica. Section D, Structural Biology
Maria Cristina Burla, Benedetta Carrozzini, Giovanni Luca Cascarano, Giampiero Polidori, Carmelo Giacovazzo
The program Buccaneer, a well known fast and efficient automatic model-building program, is also a tool for phase refinement: indeed, input phases are used to calculate electron-density maps that are interpreted in terms of a molecular model, from which new phase estimates may be obtained. This specific property is shared by all other automatic model-building programs and allows their cyclic use, as is usually performed in other phase-refinement methods (for example electron-density modification techniques)...
November 1, 2018: Acta Crystallographica. Section D, Structural Biology
Brendan Sullivan, Rick Archibald, Patricia S Langan, Holger Dobbek, Martin Bommer, Robert L McFeeters, Leighton Coates, Xiaoping Wang, Franz Gallmeier, John M Carpenter, Vickie Lynch, Paul Langan
Neutron crystallography is a powerful technique for directly visualizing the locations of H atoms in biological macromolecules. This information has provided key new insights into enzyme mechanisms, ligand binding and hydration. However, despite the importance of this information, the application of neutron crystallography in biology has been limited by the relatively low flux of available neutron beams and the large incoherent neutron scattering from hydrogen, both of which contribute to weak diffraction data with relatively low signal-to-background ratios...
November 1, 2018: Acta Crystallographica. Section D, Structural Biology
Petr Pachl, Jana Škerlová, Daniela Šimčíková, Michael Kotik, Alena Křenková, Pavel Mader, Jiří Brynda, Jana Kapešová, Vladimír Křen, Zbyszek Otwinowski, Pavlína Řezáčová
α-L-Rhamnosidases cleave terminal nonreducing α-L-rhamnosyl residues from many natural rhamnoglycosides. This makes them catalysts of interest for various biotechnological applications. The X-ray structure of the GH78 family α-L-rhamnosidase from Aspergillus terreus has been determined at 1.38 Å resolution using the sulfur single-wavelength anomalous dispersion phasing method. The protein was isolated from its natural source in the native glycosylated form, and the active site contained a glucose molecule, probably from the growth medium...
November 1, 2018: Acta Crystallographica. Section D, Structural Biology
Oleg Borbulevych, Roger I Martin, Lance M Westerhoff
Conventional macromolecular crystallographic refinement relies on often dubious stereochemical restraints, the preparation of which often requires human validation for unusual species, and on rudimentary energy functionals that are devoid of nonbonding effects owing to electrostatics, polarization, charge transfer or even hydrogen bonding. While this approach has served the crystallographic community for decades, as structure-based drug design/discovery (SBDD) has grown in prominence it has become clear that these conventional methods are less rigorous than they need to be in order to produce properly predictive protein-ligand models, and that the human intervention that is required to successfully treat ligands and other unusual chemistries found in SBDD often precludes high-throughput, automated refinement...
November 1, 2018: Acta Crystallographica. Section D, Structural Biology
Wangshu Jiang, Wimal Ubhayasekera, Melanie M Pearson, Stefan D Knight
The important uropathogen Proteus mirabilis encodes a record number of chaperone/usher-pathway adhesive fimbriae. Such fimbriae, which are used for adhesion to cell surfaces/tissues and for biofilm formation, are typically important virulence factors in bacterial pathogenesis. Here, the structures of the receptor-binding domains of the tip-located two-domain adhesins UcaD (1.5 Å resolution) and AtfE (1.58 Å resolution) from two P. mirabilis fimbriae (UCA/NAF and ATF) are presented. The structures of UcaD and AtfE are both similar to the F17G type of tip-located fimbrial receptor-binding domains, and the structures are very similar despite having only limited sequence similarity...
November 1, 2018: Acta Crystallographica. Section D, Structural Biology
Naomine Yano, Taro Yamada, Takaaki Hosoya, Takashi Ohhara, Ichiro Tanaka, Nobuo Niimura, Katsuhiro Kusaka
The STARGazer data-processing software is used for neutron time-of-flight (TOF) single-crystal diffraction data collected using the IBARAKI Biological Crystal Diffractometer (iBIX) at the Japan Proton Accelerator Research Complex (J-PARC). This software creates hkl intensity data from three-dimensional (x, y, TOF) diffraction data. STARGazer is composed of a data-processing component and a data-visualization component. The former is used to calculate the hkl intensity data. The latter displays the three-dimensional diffraction data with searched or predicted peak positions and is used to determine and confirm integration regions...
November 1, 2018: Acta Crystallographica. Section D, Structural Biology
George B Richter-Addo
No abstract text is available yet for this article.
November 1, 2018: Acta Crystallographica. Section D, Structural Biology
Changlin Xie, Chao He, Yiyang Jiang, Hailong Yu, Lin Cheng, Gilbert Nshogoza, Moududee Sayed Ala, Changlin Tian, Jihui Wu, Yunyu Shi, Fudong Li
The FHA domain-containing protein Mek1 is a meiosis-specific kinase that is involved in the regulation of interhomolog recombination in meiosis in Saccharomyces cerevisiae. The recruitment and activation of Mek1 require the phosphorylation of the chromosome axis protein Hop1 at Thr318 (pT318), which is necessary for recognition by the Mek1 FHA domain. Here, crystal structures of the Mek1 FHA domain in the apo state and in complex with the Hop1 pT318 peptide are presented, demonstrating that the hydrophobic residues Phe320 and Val321 at the pT+2 and pT+3 positions in the ligand contribute to the preferential recognition...
October 1, 2018: Acta Crystallographica. Section D, Structural Biology
George T Lountos, Sreejith Raran-Kurussi, Bryan M Zhao, Beverly K Dyas, Terrence R Burke, Robert G Ulrich, David S Waugh
Here, new crystal structures are presented of the isolated membrane-proximal D1 and distal D2 domains of protein tyrosine phosphatase epsilon (PTPℇ), a protein tyrosine phosphatase that has been shown to play a positive role in the survival of human breast cancer cells. A triple mutant of the PTPℇ D2 domain (A455N/V457Y/E597D) was also constructed to reconstitute the residues of the PTPℇ D1 catalytic domain that are important for phosphatase activity, resulting in only a slight increase in the phosphatase activity compared with the native D2 protein...
October 1, 2018: Acta Crystallographica. Section D, Structural Biology
James W Noble, Rehab Almalki, S Mark Roe, Armin Wagner, Ramona Duman, John R Atack
Calbindin-D28K is a widely expressed calcium-buffering cytoplasmic protein that is involved in many physiological processes. It has been shown to interact with other proteins, suggesting a role as a calcium sensor. Many of the targets of calbindin-D28K are of therapeutic interest: for example, inositol monophosphatase, the putative target of lithium therapy in bipolar disorder. Presented here is the first crystal structure of human calbindin-D28K. There are significant deviations in the tertiary structure when compared with the NMR structure of rat calbindin-D28K (PDB entry 2g9b), despite 98% sequence identity...
October 1, 2018: Acta Crystallographica. Section D, Structural Biology
R Bruce Doak, Gabriela Nass Kovacs, Alexander Gorel, Lutz Foucar, Thomas R M Barends, Marie Luise Grünbein, Mario Hilpert, Marco Kloos, Christopher M Roome, Robert L Shoeman, Miriam Stricker, Kensuke Tono, Daehyun You, Kiyoshi Ueda, Darren A Sherrell, Robin L Owen, Ilme Schlichting
Crystallography chips are fixed-target supports consisting of a film (for example Kapton) or wafer (for example silicon) that is processed using semiconductor-microfabrication techniques to yield an array of wells or through-holes in which single microcrystals can be lodged for raster-scan probing. Although relatively expensive to fabricate, chips offer an efficient means of high-throughput sample presentation for serial diffraction data collection at synchrotron or X-ray free-electron laser (XFEL) sources...
October 1, 2018: Acta Crystallographica. Section D, Structural Biology
Yasmin N Samara, Haley M Brennan, Liam McCarthy, Mary T Bollard, Denise Laspina, Jakub M Wlodek, Stefanie L Campos, Ramya Natarajan, Kazimierz Gofron, Sean McSweeney, Alexei S Soares, Ludmila Leroy
Crystal harvesting has proven to be difficult to automate and remains the rate-limiting step for many structure-determination and high-throughput screening projects. This has resulted in crystals being prepared more rapidly than they can be harvested for X-ray data collection. Fourth-generation synchrotrons will support extraordinarily rapid rates of data acquisition, putting further pressure on the crystal-harvesting bottleneck. Here, a simple solution is reported in which crystals can be acoustically harvested from slightly modified MiTeGen In Situ-1 crystallization plates...
October 1, 2018: Acta Crystallographica. Section D, Structural Biology
Yonca Yuzugullu Karakus, Gunce Goc, Sinem Balci, Briony A Yorke, Chi H Trinh, Michael J McPherson, Arwen R Pearson
The catalase from Scytalidium thermophilum is a homotetramer containing a heme d in each active site. Although the enzyme has a classical monofunctional catalase fold, it also possesses oxidase activity towards a number of small organics, including catechol and phenol. In order to further investigate this, the crystal structure of the complex of the catalase with the classical catalase inhibitor 3-amino-1,2,4-triazole (3TR) was determined at 1.95 Å resolution. Surprisingly, no binding to the heme site was observed; instead, 3TR occupies a binding site corresponding to the NADPH-binding pocket in mammalian catalases at the entrance to a lateral channel leading to the heme...
October 1, 2018: Acta Crystallographica. Section D, Structural Biology
Lucas Kraft, S Mark Roe, Raj Gill, John R Atack
Lithium, which is still the gold standard in the treatment of bipolar disorder, has been proposed to inhibit inositol monophosphatase (IMPase) and is hypothesized to exert its therapeutic effects by attenuating phosphatidylinositol (PI) cell signalling. Drug-discovery efforts have focused on small-molecule lithium mimetics that would specifically inhibit IMPase without exhibiting the undesired side effects of lithium. L-690,330 is a potent bisphosphonate substrate-based inhibitor developed by Merck Sharp & Dohme...
October 1, 2018: Acta Crystallographica. Section D, Structural Biology
Andrew P Thompson, Kate L Wegener, Grant W Booker, Steven W Polyak, John B Bruning
Dethiobiotin synthetase from Mycobacterium tuberculosis (MtDTBS) is a promising antituberculosis drug target. Small-molecule inhibitors that target MtDTBS provide a route towards new therapeutics for the treatment of antibiotic-resistant tuberculosis. Adenosine diphosphate (ADP) is an inhibitor of MtDTBS; however, structural studies into its mechanism of inhibition have been unsuccessful owing to competitive binding to the enzyme by crystallographic precipitants such as citrate and sulfate. Here, a crystallographic technique termed precipitant-ligand exchange has been developed to exchange protein-bound precipitants with ligands of interest...
October 1, 2018: Acta Crystallographica. Section D, Structural Biology
Tanvi M Deshpande, Piyusha P Pagare, Mohini S Ghatge, Qiukan Chen, Faik N Musayev, Jurgen Venitz, Yan Zhang, Osheiza Abdulmalik, Martin K Safo
Increasing the affinity of hemoglobin for oxygen represents a feasible and promising therapeutic approach for sickle cell disease by mitigating the primary pathophysiological event, i.e. the hypoxia-induced polymerization of sickle hemoglobin (Hb S) and the concomitant erythrocyte sickling. Investigations on a novel synthetic antisickling agent, SAJ-310, with improved and sustained antisickling activity have previously been reported. To further enhance the biological effects of SAJ-310, a structure-based approach was employed to modify this compound to specifically inhibit Hb S polymer formation through interactions which perturb the Hb S polymer-stabilizing αF-helix, in addition to primarily increasing the oxygen affinity of hemoglobin...
October 1, 2018: Acta Crystallographica. Section D, Structural Biology
Claire A Fowler, Glyn R Hemsworth, Fiona Cuskin, Sam Hart, Johan Turkenburg, Harry J Gilbert, Paul H Walton, Gideon J Davies
The biological conversion of lignocellulosic matter into high-value chemicals or biofuels is of increasing industrial importance as the sector slowly transitions away from nonrenewable sources. Many industrial processes involve the use of cellulolytic enzyme cocktails - a selection of glycoside hydrolases and, increasingly, polysaccharide oxygenases - to break down recalcitrant plant polysaccharides. ORFs from the genome of Teredinibacter turnerae, a symbiont hosted within the gills of marine shipworms, were identified in order to search for enzymes with desirable traits...
October 1, 2018: Acta Crystallographica. Section D, Structural Biology
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