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Acta Crystallographica. Section F, Structural Biology Communications

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https://www.readbyqxmd.com/read/28876234/production-crystallization-and-structure-determination-of-a-mycobacterial-glucosylglycerate-hydrolase
#1
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
#2
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
#3
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
#4
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
#5
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
https://www.readbyqxmd.com/read/28876229/3-6-anhydro-l-galactonate-cycloisomerase-from-vibrio-sp-strain-ejy3-crystallization-and-x-ray-crystallographic-analysis
#6
Saeyoung Lee, Eun Ju Yun, Kyoung Heon Kim, Hye Yeon Kim, In Geol Choi
3,6-Anhydro-L-galactonate cycloisomerase (ACI), which is found in the marine bacterium Vibrio sp. strain EJY3, converts 3,6-anhydro-L-galactonate into 2-keto-3-deoxygalactonate. ACI is a key enzyme in the metabolic pathway of 3,6-anhydro-L-galactose (AHG). Study of AHG metabolism is important for the efficient fermentation of agar and biofuel production, because AHG is a sugar that is non-fermentable by commercial microorganisms. The aci gene from Vibrio sp. strain EJY3 was cloned, and the recombinant protein was overexpressed and crystallized in order to determine the structure and understand the function of the protein...
September 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28876228/hicab-toxin-antitoxin-complex-from-escherichia-coli-expression-and-crystallization
#7
Jingsi Yang, Bingshuang Xu, Zengqiang Gao, Ke Zhou, Peng Liu, Yuhui Dong, Jianjun Zhang, Quansheng Liu
Toxin-antitoxin (TA) systems are widespread in both bacteria and archaea, where they enable cells to adapt to environmental cues. TA systems play crucial roles in various cellular processes, such as programmed cell death, cell growth, persistence and virulence. Here, two distinct forms of the type II toxin-antitoxin complex HicAB were identified and characterized in Escherichia coli K-12, and both were successfully overexpressed and purified. The two proposed forms, HicAB(L) and HicAB(S), differed in the presence or absence of a seven-amino-acid segment at the N-terminus in the antitoxin HicB...
September 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28876227/crystal-structure-of-the-dna-sequence-d-cgtgaattcacg-2-with-dapi
#8
Hristina I Sbirkova-Dimitrova, Boris Shivachev
The structure of 4',6-diamidine-2-phenylindole (DAPI) bound to the synthetic B-DNA oligonucleotide d(CGTGAATTCACG) has been solved in space group P212121 by single-crystal X-ray diffraction at a resolution of 2.2 Å. The structure is nearly isomorphous to that of the previously reported crystal structure of the oligonucleotide d(CGTGAATTCACG) alone. The adjustments in crystal packing between the native DNA molecule and the DNA-DAPI complex are described. DAPI lies in the narrow minor groove near the centre of the B-DNA fragment, positioned over the A-T base pairs...
September 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28777094/in-crystallo-activity-tests-with-latent-apple-tyrosinase-and-two-mutants-reveal-the-importance-of-the-mutated-sites-for-polyphenol-oxidase-activity
#9
Ioannis Kampatsikas, Aleksandar Bijelic, Matthias Pretzler, Annette Rompel
Tyrosinases are type 3 copper enzymes that belong to the polyphenol oxidase (PPO) family and are able to catalyze both the ortho-hydroxylation of monophenols and their subsequent oxidation to o-quinones, which are precursors for the biosynthesis of colouring substances such as melanin. The first plant pro-tyrosinase from Malus domestica (MdPPO1) was recombinantly expressed in its latent form (56.4 kDa) and mutated at four positions around the catalytic pocket which are believed to influence the activity of the enzyme...
August 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28777093/expression-and-crystallographic-studies-of-the-d1d2-domains-of-c4-4a-a-homologous-protein-to-the-urokinase-receptor
#10
Shanli Chen, Lin Lin, Cai Yuan, Henrik Gårdsvoll, Mette C Kriegbaum, Michael Ploug, Mingdong Huang
C4.4A is a glycosylphosphatidylinositol-anchored membrane protein comprised of two LU domains (Ly6/uPAR-like domains) and an extensively O-glycosylated C-terminal Ser/Thr/Pro-rich region. C4.4A is a novel biomarker for squamous epithelial differentiation. Its expression is dysregulated under various pathological conditions and it is a robust biomarker for poor prognosis in various malignant conditions such as pulmonary adenocarcinoma. To facilitate crystallization, the two LU domains were excised from intact C4...
August 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28777092/filament-like-drep4-cide-domain-characterization-and-preliminary-x-ray-crystallographic-studies
#11
Hyun Ho Park
DREP4 is a nuclease from fruit fly that is involved in apoptotic DNA fragmentation. DREP4 contains a conserved CIDE domain that acts as a protein-interaction module and is critical for its function. In this study, it was found that DREP4 CIDE domains form filament-like structures in solution. The length of the highly ordered filament-like structure is dependent on the salt concentration. By adjusting the salt concentration the DREP4 CIDE domain could be crystallized, and X-ray diffraction data were collected to a resolution of 1...
August 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28777091/the-quorum-quenching-lactonase-from-alicyclobacter-acidoterrestris-purification-kinetic-characterization-crystallization-and-crystallographic-analysis
#12
Celine Bergonzi, Michael Schwab, Eric Chabriere, Mikael Elias
Lactonases comprise a class of enzymes that hydrolyze lactones, including acyl-homoserine lactones (AHLs); the latter are used as chemical signaling molecules by numerous Gram-negative bacteria. Lactonases have therefore been demonstrated to quench AHL-based bacterial communication. In particular, lactonases are capable of inhibiting bacterial behaviors that depend on these chemicals, such as the formation of biofilms or the expression of virulence factors. A novel representative from the metallo-β-lactamase superfamily, named AaL, was isolated from the thermoacidophilic bacterium Alicyclobacter acidoterrestris...
August 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28777090/high-resolution-structure-of-a-kazal-type-serine-protease-inhibitor-from-the-dengue-vector-aedes-aegypti
#13
Ricardo J S Torquato, Stephen Lu, Nadia Helena Martins, Aparecida S Tanaka, Pedro José Barbosa Pereira
Blood-feeding exoparasites are rich sources of protease inhibitors, and the mosquito Aedes aegypti, which is a vector of Dengue virus, Yellow fever virus, Chikungunya virus and Zika virus, is no exception. AaTI is a single-domain, noncanonical Kazal-type serine proteinase inhibitor from A. aegypti that recognizes both digestive trypsin-like serine proteinases and the central protease in blood clotting, thrombin, albeit with an affinity that is three orders of magnitude lower. Here, the 1.4 Å resolution crystal structure of AaTI is reported from extremely tightly packed crystals (∼22% solvent content), revealing the structural determinants for the observed inhibitory profile of this molecule...
August 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28777089/crystal-structure-of-the-putative-cytoplasmic-protein-stm0279-hcp2-from-salmonella-typhimurium
#14
Qing Peng Lin, Zeng Qiang Gao, Zhi Geng, Heng Zhang, Yu Hui Dong
STM0279 is a putative cytoplasmic protein from Salmonella typhimurium and was recently renamed haemolysin co-regulated protein 2 (Hcp2), with the neighbouring STM0276 being Hcp1. Both of them are encoded by the type VI secretion system (T6SS) of the Salmonella pathogenicity island 6 (SPI-6) locus and have high sequence identity. The Hcp proteins may function as a vital component of the T6SS nanotube and as a transporter and chaperone of diverse effectors from the bacterial T6SS. In this study, the crystal structure and the oligomeric state in solution of Hcp2 from S...
August 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28777088/production-biophysical-characterization-and-crystallization-of-pseudomonas-putida-graa-and-its-complexes-with-grat-and-the-grata-operator
#15
Ariel Talavera, Hedvig Tamman, Andres Ainelo, San Hadǽi, Abel Garcia-Pino, Rita Hõrak, Albert Konijnenberg, Remy Loris
The graTA operon from Pseudomonas putida encodes a toxin-antitoxin module with an unusually moderate toxin. Here, the production, SAXS analysis and crystallization of the antitoxin GraA, the GraTA complex and the complex of GraA with a 33 bp operator fragment are reported. GraA forms a homodimer in solution and crystallizes in space group P21, with unit-cell parameters a = 66.9, b = 48.9, c = 62.7 Å, β = 92.6°. The crystals are likely to contain two GraA dimers in the asymmetric unit and diffract to 1...
August 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28777087/methylation-crystallization-and-sad-phasing-of-the-csu-pilus-csuc-csue-chaperone-adhesin-subunit-pre-assembly-complex-from-acinetobacter-baumannii
#16
Natalia Pakharukova, Minna Tuittila, Sari Paavilainen, Anton Zavialov
Acinetobacter baumannii is one of the most difficult Gram-negative bacteria to control and treat. This pathogen forms biofilms on hospital surfaces and medical devices using Csu pili assembled via the archaic chaperone-usher pathway. To uncover the mechanism of bacterial attachment to abiotic surfaces, it was aimed to determine the crystal structure of the pilus tip adhesin CsuE. The CsuC-CsuE chaperone-subunit pre-assembly complex was purified from the periplasm of Escherichia coli overexpressing CsuC and CsuE...
August 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28777086/1-12%C3%A2-%C3%A3-resolution-crystal-structure-of-the-catalytic-domain-of-the-plasmid-mediated-colistin-resistance-determinant-mcr-2
#17
Katie Coates, Timothy R Walsh, James Spencer, Philip Hinchliffe
MCR-2 confers resistance to colistin, a `last-line' antibiotic against extensively resistant Gram-negative pathogens. It is a plasmid-encoded phosphoethanolamine transferase that is closely related to MCR-1. To understand the diversity in the MCR family, the 1.12 Å resolution crystal structure of the catalytic domain of MCR-2 was determined. Variable amino acids are located distant from both the di-zinc active site and the membrane-proximal face. The exceptionally high resolution will provide an accurate starting model for further mechanistic studies...
August 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28695854/the-putative-polyketide-cyclase-msmeg_0129-from-mycobacterium-smegmatis-purification-crystallization-and-x-ray-crystallographic-analysis
#18
Shuping Zheng, Ying Zhou, Joy Fleming, Yafeng Zhou, Wei Liu, Lijun Bi
Mycobacterium tuberculosis Rv0164 has previously been identified as a human T-cell antigen that induces significant production of IFN-γ in human peripheral blood mononuclear cells. M. smegmatis MSMEG_0129 shares 59% sequence identity with Rv0164. Based on sequence alignment, both proteins are predicted to be members of the cyclase/dehydrase family, which is part of a large group of enzymes referred to as type II polyketide synthases (PKSs). In biosynthetic pathways mediated by type II PKSs, cyclases catalyze the conversion of linear poly-β-ketones to cyclized intermediates...
July 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28695853/crystal-structure-of-the-n-terminal-domain-of-vqsr-from-pseudomonas-aeruginosa-at-2-1%C3%A2-%C3%A3-resolution
#19
Qing He, Kang Wang, Tiantian Su, Feng Wang, Lichuan Gu, Sujuan Xu
VqsR is a quorum-sensing (QS) transcriptional regulator which controls QS systems (las, rhl and pqs) by directly downregulating the expression of qscR in Pseudomonas aeruginosa. As a member of the LuxR family of proteins, VqsR shares the common motif of a helix-turn-helix (HTH)-type DNA-binding domain at the C-terminus, while the function of its N-terminal domain remains obscure. Here, the crystal structure of the N-terminal domain of VqsR (VqsR-N; residues 1-193) was determined at a resolution of 2.1 Å...
July 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28695852/the-multidrug-resistance-transporter-mdfa-from-escherichia-coli-crystallization-and-x-ray-diffraction-analysis
#20
Kumar Nagarathinam, Frank Jaenecke, Yoshiko Nakada-Nakura, Yunhon Hotta, Kehong Liu, So Iwata, Milton T Stubbs, Norimichi Nomura, Mikio Tanabe
The active efflux of antibiotics by multidrug-resistance (MDR) transporters is a major pathway of drug resistance and complicates the clinical treatment of bacterial infections. MdfA is a member of the major facilitator superfamily (MFS) from Escherichia coli and provides resistance to a wide variety of dissimilar toxic compounds, including neutral, cationic and zwitterionic substances. The 12-transmembrane-helix MdfA was expressed as a GFP-octahistidine fusion protein with a TEV protease cleavage site. Following tag removal, MdfA was purified using two chromatographic steps, complexed with a Fab fragment and further purified using size-exclusion chromatography...
July 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
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