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Acta Crystallographica. Section F, Structural Biology Communications

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https://www.readbyqxmd.com/read/28471363/crystallization-and-biochemical-characterization-of-an-archaeal-lectin-from-methanococcus-voltae-a3
#1
N Sivaji, K V Abhinav, M Vijayan
A lectin from Methanococcus voltae A3 has been cloned, expressed, purified and characterized. The lectin appears to be specific for complex sugars. The protein crystallized in a tetragonal space group, with around 16 subunits in the asymmetric unit. Sequence comparisons indicate the lectin to have a β-prism I fold, with poor homology to lectins of known three-dimensional structure.
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28471362/crystal-structure-of-cd27-in-complex-with-a-neutralizing-noncompeting-antibody
#2
Alexey Teplyakov, Galina Obmolova, Thomas J Malia, Gary L Gilliland
CD27 is a T-cell and B-cell co-stimulatory glycoprotein of the tumor necrosis factor (TNF) receptor superfamily that is dependent on the availability of the TNF-like ligand CD70. Therapeutic approaches to treating autoimmune diseases and cancers with antagonistic and agonistic anti-CD27 monoclonal antibodies (mAbs), respectively, have recently been developed. Mouse anti-human CD27 mAb 2177 shows potency in neutralizing CD70-induced signaling; however, it does not block the binding of soluble CD70. To provide insight into the mechanism of action of the mAb, the crystal structure of the CD27 extracellular domain in complex with the Fab fragment of mAb 2177 was determined at 1...
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28471361/camelid-nanobodies-used-as-crystallization-chaperones-for-different-constructs-of-porm-a-component-of-the-type-ix-secretion-system-from-porphyromonas-gingivalis
#3
Yoan Duhoo, Jennifer Roche, Thi Trang Nhung Trinh, Aline Desmyter, Anaïs Gaubert, Christine Kellenberger, Christian Cambillau, Alain Roussel, Philippe Leone
PorM is a membrane protein that is involved in the assembly of the type IX secretion system (T9SS) in Porphyromonas gingivalis, a major bacterial pathogen that is responsible for periodontal disease in humans. In the context of structural studies of PorM to better understand T9SS assembly, four camelid nanobodies were selected, produced and purified, and their specific interaction with the N-terminal or C-terminal part of the periplasmic domain of PorM was investigated. Diffracting crystals were also obtained, and the structures of the four nanobodies were solved by molecular replacement...
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28471360/transcription-factor-rv0081-from-mycobacterium-tuberculosis-purification-crystallization-and-initial-crystallographic-analysis
#4
Shishang Dong, Zhenzhen Ding, Yu Wang, Yan Yang, Yonghong Mao, Ying Wang
Because of its high infectivity and pathogenicity, Mycobacterium tuberculosis is a serious threat to human health. While the transcription-regulatory system of M. tuberculosis remains incompletely understood, Rv0081, an essential regulatory hub, is known to mediate the initial response to hypoxia in the long-term survival of M. tuberculosis. Here, the production, crystallization and initial X-ray crystallographic analysis of Rv0081 are reported. The crystals of Rv0081 belonged to space group P62, with unit-cell parameters a = 67...
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28471359/crystal-structure-of-the-rna-2-3-cyclic-phosphodiesterase-from-deinococcus-radiodurans
#5
Wanchun Han, Jiahui Cheng, Congli Zhou, Yuejin Hua, Ye Zhao
2',3'-Cyclic phosphodiesterase (CPDase) homologues have been found in all domains of life and are involved in diverse RNA and nucleotide metabolisms. The CPDase from Deinococcus radiodurans was crystallized and the crystals diffracted to 1.6 Å resolution, which is the highest resolution currently known for a CPDase structure. Structural comparisons revealed that the enzyme is in an open conformation in the absence of substrate. Nevertheless, the active site is well formed, and the representative motifs interact with sulfate ion, which suggests a conserved catalytic mechanism...
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28471358/structural-insights-into-the-mechanism-of-the-drastic-changes-in-enzymatic-activity-of-the-cytochrome-p450-vitamin-d3-hydroxylase-cyp107br1-caused-by-a-mutation-distant-from-the-active-site
#6
Yoshiaki Yasutake, Tomoshi Kameda, Tomohiro Tamura
Cytochromes P450 (P450s) are haem-containing enzymes that catalyze medically and industrially important oxidative reactions, and many P450s have been subjected to directed evolution and site-directed mutagenesis to improve their activity and substrate specificity. Nonetheless, in most cases the mechanism that leads to drastic changes in specific activity after the introduction of an amino-acid substitution distant from the active-site pocket is unclear. Here, two crystal structures of inactive mutants of the P450 vitamin D3 hydroxylase (Vdh), Vdh-F106V and Vdh-L348M, which were obtained in the course of protein-engineering experiments on Vdh, are reported...
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28471357/crystal-structure-of-d-ccggggtaccccgg-2-at-1-4%C3%A2-%C3%A3-resolution
#7
Selvam Karthik, Arunachalam Thirugnanasambandam, Pradeep Kumar Mandal, Namasivayam Gautham
The X-ray crystal structure of the DNA tetradecamer sequence d(CCGGGGTACCCCGG)2 is reported at 1.4 Å resolution in the tetragonal space group P41212. The sequence was designed to fold as a four-way junction. However, it forms an A-type double helix in the presence of barium chloride. The metal ion could not be identified in the electron-density map. The crystallographic asymmetric unit consists of one A-type double helix with 12 base pairs per turn, in contrast to 11 base pairs per turn for canonical A-DNA...
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28471356/increasing-the-soluble-expression-and-crystallization-of-the-escherichia-coli-quorum-sensing-protein-lsrk
#8
Jung Hye Ha, Yumi Eo, Hee Chul Ahn, Kyoung Seok Ryu
LsrK is one of the key components of the luxS-regulated (lsr) operon in Escherichia coli and plays an important role during the quorum-sensing (QS) process mediated by autoinducer-2 (AI-2). The AI-2 molecule is imported into the cell by the LsrACB transporter and is subsequently phosphorylated (to AI-2-P) by LsrK. AI-2-P binds to the repressor protein of the lsr operon (LsrR) and triggers various cellular responses related to QS by dissociating LsrR from the DNA. Although a large amount of purified LsrK is required for structural studies, recombinant GST-LsrK was mostly expressed in an insoluble form...
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28471355/structure-of-nadp-bound-7%C3%AE-hydroxysteroid-dehydrogenase-reveals-two-cofactor-binding-modes
#9
Rui Wang, Jiaquan Wu, David Kin Jin, Yali Chen, Zhijia Lv, Qian Chen, Qiwei Miao, Xiaoyu Huo, Feng Wang
In mammals, bile acids/salts and their glycine and taurine conjugates are effectively recycled through enterohepatic circulation. 7β-Hydroxysteroid dehydrogenases (7β-HSDHs; EC 1.1.1.201), including that from the intestinal microbe Collinsella aerofaciens, catalyse the NADPH-dependent reversible oxidation of secondary bile-acid products to avoid potential toxicity. Here, the first structure of NADP(+) bound to dimeric 7β-HSDH is presented. In one active site, NADP(+) adopts a conventional binding mode similar to that displayed in related enzyme structures...
May 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28368284/x-ray-diffraction-analysis-and-in-vitro-characterization-of-the-uam2-protein-from-oryza-sativa
#10
Ditte Hededam Welner, Alex Yi Lin Tsai, Andy M DeGiovanni, Henrik Vibe Scheller, Paul D Adams
The role of seemingly non-enzymatic proteins in complexes interconverting UDP-arabinopyranose and UDP-arabinofuranose (UDP-arabinosemutases; UAMs) in the plant cytosol remains unknown. To shed light on their function, crystallographic and functional studies of the seemingly non-enzymatic UAM2 protein from Oryza sativa (OsUAM2) were undertaken. Here, X-ray diffraction data are reported, as well as analysis of the oligomeric state in the crystal and in solution. OsUAM2 crystallizes readily but forms highly radiation-sensitive crystals with limited diffraction power, requiring careful low-dose vector data acquisition...
April 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28368283/preliminary-neutron-diffraction-analysis-of-challenging-human-manganese-superoxide-dismutase-crystals
#11
Jahaun Azadmanesh, Scott R Trickel, Kevin L Weiss, Leighton Coates, Gloria E O Borgstahl
Superoxide dismutases (SODs) are enzymes that protect against oxidative stress by dismutation of superoxide into oxygen and hydrogen peroxide through cyclic reduction and oxidation of the active-site metal. The complete enzymatic mechanisms of SODs are unknown since data on the positions of hydrogen are limited. Here, methods are presented for large crystal growth and neutron data collection of human manganese SOD (MnSOD) using perdeuteration and the MaNDi beamline at Oak Ridge National Laboratory. The crystal from which the human MnSOD data set was obtained is the crystal with the largest unit-cell edge (240 Å) from which data have been collected via neutron diffraction to sufficient resolution (2...
April 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28368282/crystal-structure-of-enolase-from-drosophila-melanogaster
#12
Congcong Sun, Baokui Xu, Xueyan Liu, Zhen Zhang, Zhongliang Su
Enolase is an important enzyme in glycolysis and various biological processes. Its dysfunction is closely associated with diseases. Here, the enolase from Drosophila melanogaster (DmENO) was purified and crystallized. A crystal of DmENO diffracted to 2.0 Å resolution and belonged to space group R32. The structure was solved by molecular replacement. Like most enolases, DmENO forms a homodimer with conserved residues in the dimer interface. DmENO possesses an open conformation in this structure and contains conserved elements for catalytic activity...
April 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28368281/crystal-structure-of-a-small-heat-shock-protein-from-xylella-fastidiosa-reveals-a-distinct-high-order-structure
#13
Emanuella Maria Barreto Fonseca, Valéria Scorsato, Marcelo Leite Dos Santos, Atilio Tomazini Júnior, Susely Ferraz Siqueira Tada, Clelton Aparecido Dos Santos, Marcelo Augusto Szymanski de Toledo, Anete Pereira de Souza, Igor Polikarpov, Ricardo Aparicio
Citrus variegated chlorosis is a disease that attacks economically important citrus plantations and is caused by the plant-pathogenic bacterium Xylella fastidiosa. In this work, the structure of a small heat-shock protein from X. fastidiosa (XfsHSP17.9) is reported. The high-order structures of small heat-shock proteins from other organisms are arranged in the forms of double-disc, hollow-sphere or spherical assemblies. Unexpectedly, the structure reported here reveals a high-order architecture forming a nearly square cavity...
April 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28368280/x-ray-crystal-structure-of-human-calcium-bound-s100a1
#14
Zephan Melville, Ehson Aligholizadeh, Laura E McKnight, Dylan J Weber, Edwin Pozharski, David J Weber
S100A1 is a member of the S100 family of Ca(2+)-binding proteins and regulates several cellular processes, including those involved in Ca(2+) signaling and cardiac and skeletal muscle function. In Alzheimer's disease, brain S100A1 is overexpressed and gives rise to disease pathologies, making it a potential therapeutic target. The 2.25 Å resolution crystal structure of Ca(2+)-S100A1 is solved here and is compared with the structures of other S100 proteins, most notably S100B, which is a highly homologous S100-family member that is implicated in the progression of malignant melanoma...
April 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28368279/crystal-structure-of-the-human-heterogeneous-ribonucleoprotein-a18-rna-recognition-motif
#15
Katherine Coburn, Zephan Melville, Ehson Aligholizadeh, Braden M Roth, Kristen M Varney, France Carrier, Edwin Pozharski, David J Weber
The heterogeneous ribonucleoprotein A18 (hnRNP A18) is upregulated in hypoxic regions of various solid tumors and promotes tumor growth via the coordination of mRNA transcripts associated with pro-survival genes. Thus, hnRNP A18 represents an important therapeutic target in tumor cells. Presented here is the first X-ray crystal structure to be reported for the RNA-recognition motif of hnRNP A18. By comparing this structure with those of homologous RNA-binding proteins (i.e. hnRNP A1), three residues on one face of an antiparallel β-sheet (Arg48, Phe50 and Phe52) and one residue in an unstructured loop (Arg41) were identified as likely to be involved in protein-nucleic acid interactions...
April 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28368278/crystallization-and-x-ray-analysis-of-the-extracellular-adhesion-domain-of-helicobacter-pylori-adhesin-a-the-significance-of-the-cation-composition-in-the-crystallization-precipitant
#16
Ling Guo, Jinyong Zhang, Liwei Cui, Dong Liu, Bo Ma, Shufeng Wang, Haibo Li, Yuzhang Wu, Wei Liu
Adherence to host cells is a crucial step in the process of bacterial infection, which is usually mediated by a number of outer membrane proteins identified as adhesins. Helicobacter pylori adhesin A (HpaA) is a member of the adhesin family that mediates the adherence of Helicobacter pylori to gastric epithelial cells, and consequently assists the bacteria in becoming a life-long colonizer of the human stomach. In this study, two constructs were made for the production of truncated HpaA proteins comprising residues 31-260 and 53-260, respectively...
April 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28368277/structure-of-the-complex-of-phosphorylated-liver-kinase-b1-and-14-3-3%C3%AE
#17
Yongjian Lu, Sheng Ding, Ruiqing Zhou, Jianyong Wu
The serine/threonine protein kinase liver kinase B1 (LKB1) is a tumour suppressor and plays important roles in development and metabolism. It phosphorylates AMPK and AMPK-related kinases to regulate multiple physiological processes. Mutations in LKB1 often occur in multiple cancers. LKB1 can be suppressed by 14-3-3 proteins in a phosphorylation-dependent manner. Previously, the structure of a 14-3-3ζ-LKB1 fusion protein has been reported, revealing a phosphorylation-independent binding mode of LKB1 to 14-3-3 proteins...
April 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28368276/the-hidden-treasure-in-your-data-phasing-with-unexpected-weak-anomalous-scatterers-from-routine-data-sets
#18
Raghurama P Hegde, Alexander A Fedorov, J Michael Sauder, Stephen K Burley, Steven C Almo, Udupi A Ramagopal
Single-wavelength anomalous dispersion (SAD) utilizing anomalous signal from native S atoms, or other atoms with Z ≤ 20, generally requires highly redundant data collected using relatively long-wavelength X-rays. Here, the results from two proteins are presented where the anomalous signal from serendipitously acquired surface-bound Ca atoms with an anomalous data multiplicity of around 10 was utilized to drive de novo structure determination. In both cases, the Ca atoms were acquired from the crystallization solution, and the data-collection strategy was not optimized to exploit the anomalous signal from these scatterers...
April 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28368275/cryo-electron-microscopy-and-x-ray-crystallography-complementary-approaches-to-structural-biology-and-drug-discovery
#19
Catherine Vénien-Bryan, Zhuolun Li, Laurent Vuillard, Jean Albert Boutin
The invention of the electron microscope has greatly enhanced the view scientists have of small structural details. Since its implementation, this technology has undergone considerable evolution and the resolution that can be obtained for biological objects has been extended. In addition, the latest generation of cryo-electron microscopes equipped with direct electron detectors and software for the automated collection of images, in combination with the use of advanced image-analysis methods, has dramatically improved the performance of this technique in terms of resolution...
April 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28291753/crystal-structure-of-the-type-iv-secretion-system-component-cagx-from-helicobacter-pylori
#20
Jin Zhang, Fei Fan, Yanhe Zhao, Lifang Sun, Yadan Liu, Ronan M Keegan, Michail N Isupov, Yunkun Wu
Helicobacter pylori, a Gram-negative bacterial pathogen prevalent in the human population, is the causative agent of severe gastric diseases. An H. pylori type IV secretion (T4S) system encoded by the cytotoxin-associated gene pathogenicity island (cagPAI) is responsible for communication with host cells. As a component of the cagPAI T4S system core complex, CagX plays an important role in virulence-protein translocation into the host cells. In this work, the crystal structure of the C-terminal domain of CagX (CagXct), which is a homologue of the VirB9 protein from the VirB/D4 T4S system, is presented...
March 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
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