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Acta Crystallographica. Section F, Structural Biology Communications

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https://www.readbyqxmd.com/read/29718001/the-cd163-long-range-scavenger-receptor-cysteine-rich-repeat-expression-purification-and-x-ray-crystallographic-characterization
#1
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
#2
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
#3
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
#4
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
https://www.readbyqxmd.com/read/29717997/crystal-structure-of-chorismate-mutase-from-burkholderia-thailandensis
#5
Oluwatoyin A Asojo, David M Dranow, Dmitry Serbzhinskiy, Sandhya Subramanian, Bart Staker, Thomas E Edwards, Peter J Myler
Burkholderia thailandensis is often used as a model for more virulent members of this genus of proteobacteria that are highly antibiotic-resistant and are potential agents of biological warfare that are infective by inhalation. As part of ongoing efforts to identify potential targets for the development of rational therapeutics, the structures of enzymes that are absent in humans, including that of chorismate mutase from B. thailandensis, have been determined by the Seattle Structural Genomics Center for Infectious Disease...
May 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29717996/crystal-structures-of-human-ck2%C3%AE-2-in-new-crystal-forms-arising-from-a-subtle-difference-in-salt-concentration
#6
Masato Tsuyuguchi, Tetsuko Nakaniwa, Takayoshi Kinoshita
The catalytic subunits of protein kinase CK2 are classified into two subtypes: CK2α1 and CK2α2. CK2α1 is an attractive drug-discovery target for various diseases such as cancers and nephritis. CK2α2 is defined as an off-target of CK2α1 and is a potential target in the development of male contraceptive drugs. High-resolution crystal structures of both isozymes are likely to provide crucial clues for the design of selective inhibitors of CK2α1 and/or CK2α2. To date, several crystal structures of CK2α1 have been solved at high resolutions of beyond 1...
May 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29717995/the-putative-siderophore-interacting-protein-from-vibrio-anguillarum-protein-production-analysis-crystallization-and-x-ray-crystallographic-studies
#7
Yu Han, Kun Zang, Changshui Liu, Yingjie Li, Qingjun Ma
Siderophore-interacting proteins (SIPs) play an important role in iron acquisition in many bacteria. SIPs release iron from the internalized ferric siderophore complex by reducing ferric iron to ferrous iron, but how the iron is reduced is not well understood. Here, a sip gene was identified in the genome of Vibrio anguillarum 775. To further understand the catalytic mechanism of the protein, the SIP was overexpressed in Escherichia coli Rosetta (DE3) cells, purified and crystallized for X-ray diffraction analysis...
May 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29717994/a-cryoprotectant-induces-conformational-change-in-glyceraldehyde-3-phosphate-dehydrogenase
#8
Yong Ju Kim
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a glycolytic enzyme, catalyses the conversion of D-glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate. While mammalian and yeast GAPDHs are multifunctional proteins that have additional functions beyond those involved in glycolysis, including reactions related to nuclear RNA transport, DNA replication/repair, membrane fusion and cellular apoptosis, Escherichia coli GAPDH (ecGAPDH) has only been reported to function in glycolysis. The S-loop of GAPDH is required for interaction with its cofactor and with other proteins...
May 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29717993/crystal-structure-of-the-mouse-innate-immunity-factor-bacterial-permeability-increasing-family-member-a1
#9
Michael S Little, Matthew R Redinbo
Bacterial permeability-increasing family member A1 (BPIFA1) is an innate immunity factor and one of the most abundantly secreted proteins in the upper airways. BPIFA1 is multifunctional, with antimicrobial, surfactant and lipopolysaccharide-binding activities, as well as established roles in lung hydration. Here, the 2.5 Å resolution crystal structure of BPIFA1 from Mus musculus (mBPIFA1) is presented and compared with those of human BPIFA1 (hBPIFA1) and structural homologs. Structural distinctions between mBPIFA1 and hBPIFA1 suggest potential differences in biological function, including the regulation of a key pulmonary ion channel...
May 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29633975/crystallization-of-the-rice-immune-receptor-rga5a_s-with-the-rice-blast-fungus-effector-avr1-co39-prepared-via-mixture-and-tandem-strategies
#10
Liwei Guo, Yikun Zhang, Mengqi Ma, Qiang Liu, Yanan Zhang, Youliang Peng, Junfeng Liu
RGA5 is a component of the Pia resistance-protein pair (RGA4/RGA5) from Oryza sativa L. japonica. It acts as an immune receptor that directly recognizes the effector AVR1-CO39 from Magnaporthe oryzae via a C-terminal non-LRR domain (RGA5A_S). The interaction between RGA5A_S and AVR1-CO39 relieves the repression of RGA4, leading to effector-independent cell death. To determine the structure of the complex of RGA5A_S and AVR1-CO39 and to understand the details of this interaction, the complex was prepared by fusing the proteins together, by mixing them in vitro or by co-expressing them in one host cell...
April 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29633974/structural-view-of-the-2a-protease-from-human-rhinovirus-c15
#11
Hui Ling, Pan Yang, Hai Hou, Yao Sun
The majority of outbreaks of the common cold are caused by rhinoviruses. The 2A protease (2Apro ) of human rhinoviruses (HRVs) is known to play important roles in the propagation of the virus and the modulation of host signal pathways to facilitate viral replication. The 2Apro from human rhinovirus C15 (HRV-C15) has been expressed in Escherichia coli and purified by affinity chromatography, ion-exchange chromatography and gel-filtration chromatography. The crystals diffracted to 2.6 Å resolution. The structure was solved by molecular replacement using the structure of 2Apro from coxsackievirus A16 (CVA16) as the search model...
April 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29633973/the-crystal-structure-of-the-drug-target-mycobacterium-tuberculosis-methionyl-trna-synthetase-in-complex-with-a-catalytic-intermediate
#12
Ximena Barros-Álvarez, Stewart Turley, Ranae M Ranade, J Robert Gillespie, Nicole A Duster, Christophe L M J Verlinde, Erkang Fan, Frederick S Buckner, Wim G J Hol
Mycobacterium tuberculosis is a pathogenic bacterial infectious agent that is responsible for approximately 1.5 million human deaths annually. Current treatment requires the long-term administration of multiple medicines with substantial side effects. Lack of compliance, together with other factors, has resulted in a worrisome increase in resistance. New treatment options are therefore urgently needed. Here, the crystal structure of methionyl-tRNA synthetase (MetRS), an enzyme critical for protein biosynthesis and therefore a drug target, in complex with its catalytic intermediate methionyl adenylate is reported...
April 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29633972/high-resolution-crystal-structure-of-streptococcus-agalactiae-glyceraldehyde-3-phosphate-dehydrogenase
#13
Kang Zhou, Xiaojiao Fan, Yuelong Li, Caiying Zhang, Tengchuan Jin
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a multifunctional enzyme that plays critical roles in bacterial pathogenesis in some pathogenic bacteria. In this study, the crystal structure of group B streptococcus GAPDH was determined at 1.36 Å resolution. The structure contained an asymmetric mixed holo tetramer, with two NAD ligands bound to two protomers. Further structural analysis identified interesting phosphate ion-binding sites, which shed light on its catalytic mechanism.
April 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29633971/the-putative-compatible-solute-binding-protein-prox-from-mycobacterium-tuberculosis-h37rv-biochemical-characterization-and-crystallographic-data
#14
Jian Hong Zhao, Jiang Huai Chen, Yong Wang, Zhi Ping Wang, Yong Xing He
In Mycobacterium tuberculosis, the proX gene encodes a putative compatible solute-binding protein (MtProX). However, it was found through sequence alignment that the MtProX protein has very different ligand-binding residues compared with other compatible solute-binding proteins, implying that MtProX may bind to ligands that are as yet uncharacterized. In this work, it was demonstrated that MtProX binds to polyphenols such as phloretin, monoacetylphloroglucinol and 2,4-dihydroxyacetophloroglucinol with dissociation constants between 20 and 70 µM...
April 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29633970/crystal-structure-of-recr-a-member-of-the-recfor-dna-repair-pathway-from-pseudomonas-aeruginosa-pao1
#15
Shiyou Che, Yujing Chen, Yakun Liang, Qionglin Zhang, Mark Bartlam
DNA damage is usually lethal to all organisms. Homologous recombination plays an important role in the DNA damage-repair process in prokaryotic organisms. Two pathways are responsible for homologous recombination in Pseudomonas aeruginosa: the RecBCD pathway and the RecFOR pathway. RecR is an important regulator in the RecFOR homologous recombination pathway in P. aeruginosa. It forms complexes with RecF and RecO that can facilitate the loading of RecA onto ssDNA in the RecFOR pathway. Here, the crystal structure of RecR from P...
April 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29633969/structure-of-proliferating-cell-nuclear-antigen-pcna-bound-to-an-apim-peptide-reveals-the-universality-of-pcna-interaction
#16
Kodai Hara, Masayuki Uchida, Risa Tagata, Hideshi Yokoyama, Yoshinobu Ishikawa, Asami Hishiki, Hiroshi Hashimoto
Proliferating cell nuclear antigen (PCNA) provides a molecular platform for numerous protein-protein interactions in DNA metabolism. A large number of proteins associated with PCNA have a well characterized sequence termed the PCNA-interacting protein box motif (PIPM). Another PCNA-interacting sequence termed the AlkB homologue 2 PCNA-interacting motif (APIM), comprising the five consensus residues (K/R)-(F/Y/W)-(L/I/V/A)-(L/I/V/A)-(K/R), has also been identified in various proteins. In contrast to that with PIPM, the PCNA-APIM interaction is less well understood...
April 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29633968/structural-view-of-the-helicase-reveals-that-zika-virus-uses-a-conserved-mechanism-for-unwinding-rna
#17
Lei Li, Jin Wang, Zhihui Jia, Neil Shaw
Recent studies suggest a link between infection by Zika virus (ZIKV) and the development of neurological complications. The lack of ZIKV-specific therapeutics has alarmed healthcare professionals worldwide. Here, crystal structures of apo and AMPPNP- and Mn2+ -bound forms of the essential helicase of ZIKV refined to 1.78 and 1.3 Å resolution, respectively, are reported. The structures reveal a conserved trimodular topology of the helicase. ATP and Mn2+ are tethered between two RecA-like domains by conserved hydrogen-bonding interactions...
April 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29633967/bacteriophage-n4-large-terminase-expression-purification-and-x-ray-crystallographic-analysis
#18
Jigme Wangchuk, Prem Prakash, Prasenjit Bhaumik, Kiran Kondabagil
Genome packaging is a critical step in the assembly of dsDNA bacteriophages and is carried out by a powerful molecular motor known as the large terminase. To date, wild-type structures of only two large terminase proteins are available, and more structural information is needed to understand the genome-packaging mechanism. Towards this goal, the large and small terminase proteins from bacteriophage N4, which infects the Escherichia coli K12 strain, have been cloned, expressed and purified. The purified putative large terminase protein hydrolyzes ATP, and this is enhanced in the presence of the small terminase...
April 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29633966/crystal-structure-of-pyrimidine-nucleoside-phosphorylase-from-bacillus-subtilis-in-complex-with-imidazole-and-sulfate
#19
V V Balaev, I I Prokofev, A G Gabdoulkhakov, C Betzel, A A Lashkov
Pyrimidine-nucleoside phosphorylase catalyzes the phosphorolytic cleavage of thymidine and uridine with equal activity. Investigation of this protein is essential for anticancer drug design. Here, the structure of this protein from Bacillus subtilis in complex with imidazole and sulfate is reported at 1.9 Å resolution, which is an improvement on the previously reported structure at 2.6 Å resolution. The localization and position of imidazole in the nucleoside-binding site reflects the possible binding of ligands that possess an imidazole ring...
April 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29633965/crystal-structure-of-chorismate-mutase-from-burkholderia-phymatum
#20
Oluwatoyin A Asojo, Sandhya Subramanian, Jan Abendroth, Ilyssa Exley, Donald D Lorimer, Thomas E Edwards, Peter J Myler
The bacterium Burkholderia phymatum is a promiscuous symbiotic nitrogen-fixating bacterium that belongs to one of the largest groups of Betaproteobacteria. Other Burkholderia species are known to cause disease in plants and animals, and some are potential agents for biological warfare. Structural genomics efforts include characterizing the structures of enzymes from pathways that can be targeted for drug development. As part of these efforts, chorismate mutase from B. phymatum was produced and crystallized, and a 1...
April 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
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