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Acta Crystallographica. Section F, Structural Biology Communications

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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/28695851/structure-of-bovine-cytochrome-c-oxidase-crystallized-at-a-neutral-ph-using-a-fluorinated-detergent
#13
Fangjia Luo, Kyoko Shinzawa-Itoh, Kaede Hagimoto, Atsuhiro Shimada, Satoru Shimada, Eiki Yamashita, Shinya Yoshikawa, Tomitake Tsukihara
Cytochrome c oxidase (CcO) couples proton pumping to O2 reduction. Its enzymatic activity depends sensitively on pH over a wide range. However, owing to difficulty in crystallizing this protein, X-ray structure analyses of bovine CcO aimed at understanding its reaction mechanism have been conducted using crystals prepared at pH 5.7, which is significantly lower than that in the cell. Here, oxidized CcO at pH 7.3 was crystallized using a fluorinated octyl-maltoside derivative, and the structure was determined at 1...
July 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28695850/assembly-of-francisella-novicida-cpf1-endonuclease-in-complex-with-guide-rna-and-target-dna
#14
Pablo Alcón, Guillermo Montoya, Stefano Stella
Bacteria and archaea use the CRISPR-Cas system as an adaptive response against infection by foreign nucleic acids. Owing to its remarkable flexibility, this mechanism has been harnessed and adopted as a powerful tool for genome editing. The CRISPR-Cas system includes two classes that are subdivided into six types and 19 subtypes according to conservation of the cas gene and loci organization. Recently, a new protein with endonuclease activity belonging to class 2 type V has been identified. This endonuclease, termed Cpf1, in complex with a single CRISPR RNA (crRNA) is able to recognize and cleave a target DNA preceded by a 5'-TTN-3' protospacer-adjacent motif (PAM) complementary to the RNA guide...
July 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28695849/full-length-nisin-immunity-protein-nisi-from-lactococcus-lactis-in-a-lipid-free-form-crystallization-and-x-ray-analysis
#15
Jin Hee Jeong, Sung Chul Ha
NisI is a lantibiotic-binding lipoprotein that is specific for nisin. Nisin-producing microorganisms use NisI as an immunity protein for self-protection against nisin. Here, the purification, crystallization and preliminary X-ray diffraction of full-length NisI from Lactobacillus lactis in a lipid-free form (NisI22-C) are reported. Importantly, reductive methylation of the lysine residues in NisI22-C was essential for initial crystallization. Only methylated NisI22-C crystallized. The optimized crystals of methylated NisI22-C were grown in 30-40 mM ammonium sulfate, 0...
July 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28695848/crystal-structure-of-a-family-6-cellobiohydrolase-from-the-basidiomycete-phanerochaete-chrysosporium
#16
Mikako Tachioka, Akihiko Nakamura, Takuya Ishida, Kiyohiko Igarashi, Masahiro Samejima
Cellobiohydrolases belonging to glycoside hydrolase family 6 (CBH II, Cel6A) play key roles in the hydrolysis of crystalline cellulose. CBH II from the white-rot fungus Phanerochaete chrysosporium (PcCel6A) consists of a catalytic domain (CD) and a carbohydrate-binding module connected by a linker peptide, like other known fungal cellobiohydrolases. In the present study, the CD of PcCel6A was crystallized without ligands, and p-nitrophenyl β-D-cellotrioside (pNPG3) was soaked into the crystals. The determined structures of the ligand-free and pNPG3-soaked crystals revealed that binding of cellobiose at substrate subsites +1 and +2 induces a conformational change of the N-terminal and C-terminal loops, switching the tunnel-shaped active site from the open to the closed form...
July 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28695847/dna-binding-domain-of-myelin-gene-regulatory-factor-purification-crystallization-and-x-ray-analysis
#17
WenYu Wu, Xiangkai Zhen, Ning Shi
The myelin sheath, which envelops axons in the vertebrate central nervous system, is crucial for the rapid conduction of action potentials. Myelin-gene regulatory factor (MRF) is a recently identified transcription factor that is required for myelin-sheath formation. Loss of MRF leads to demyelinating diseases and motor learning deficiency. MRF is a membrane-bound transcription factor that undergoes autocleavage from the endoplasmic reticulum membrane. The N-terminus of MRF contains a DNA-binding domain (DBD) that functions as a homotrimer...
July 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28695846/crystal-structure-of-a-%C3%AE-aminopeptidase-from-an-australian-burkholderia-sp
#18
Marietta John-White, Geoff J Dumsday, Priscilla Johanesen, Dena Lyras, Nyssa Drinkwater, Sheena McGowan
β-Aminopeptidases are a unique group of enzymes that have the unusual capability to hydrolyze N-terminal β-amino acids from synthetic β-peptides. β-Peptides can form secondary structures mimicking α-peptide-like structures that are resistant to degradation by most known proteases and peptidases. These characteristics of β-peptides give them great potential as peptidomimetics. Here, the X-ray crystal structure of BcA5-BapA, a β-aminopeptidase from a Gram-negative Burkholderia sp. that was isolated from activated sludge from a wastewater-treatment plant in Australia, is reported...
July 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28695845/recombinant-acht1-from-arabidopsis-thaliana-crystallization-and-x-ray-crystallographic-analysis
#19
Weimin Pan, Junchao Wang, Ye Yang, Lin Liu, Min Zhang
Thioredoxins (Trxs) play important roles in chloroplasts by linking photosynthetic light reactions to a series of plastid functions. They execute their function by regulating the oxidation and reduction of disulfide bonds. ACHT1 (atypical cysteine/histidine-rich Trx1) is a thylakoid-associated thioredoxin-type protein found in the Arabidopsis thaliana chloroplast. Recombinant ACHT1 protein was overexpressed in Escherichia coli, purified and crystallized by the vapour-diffusion method. The crystal diffracted to 1...
July 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28695844/the-structure-of-a-complex-of-the-lactonohydrolase-zearalenone-hydrolase-with-the-hydrolysis-product-of-zearalenone-at-1-60%C3%A2-%C3%A3-resolution
#20
Qi Qi, Wen Jing Yang, Hu Jian Zhou, Deng Ming Ming, Kai Lei Sun, Tian Yu Xu, Xiao Jian Hu, Hong Lv
Zearalenone hydrolase (ZHD) is an α/β-hydrolase that detoxifies and degrades the lactone zearalenone (ZEN), a naturally occurring oestrogenic mycotoxin that contaminates crops. Several apoenzyme and enzyme-substrate complex structures have been reported in the resolution range 2.4-2.6 Å. However, the properties and mechanism of this enzyme are not yet fully understood. Here, a 1.60 Å resolution structure of a ZHD-product complex is reported which was determined from a C-terminally His6-tagged ZHD crystal soaked with 2 mM ZEN for 30 min...
July 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
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