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Acta Crystallographica. Section F, Structural Biology Communications

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https://www.readbyqxmd.com/read/28695854/the-putative-polyketide-cyclase-msmeg_0129-from-mycobacterium-smegmatis-purification-crystallization-and-x-ray-crystallographic-analysis
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/28580926/crystal-structure-of-recombinant-phosphoribosylpyrophosphate-synthetase-2-from-thermus-thermophilus-hb27-complexed-with-adp-and-sulfate-ions
#12
Vladimir I Timofeev, Ekaterina V Sinitsyna, Maria A Kostromina, Tatiana I Muravieva, Dmitry A Makarov, Olga O Mikheeva, Inna P Kuranova, Roman S Esipov
Phosphoribosylpyrophosphate synthetase (PRPPS) from the thermophilic bacterial strain Thermus thermophilus HB27 catalyzes the synthesis of phosphoribosylpyrophosphate from ribose 5-phosphate and ATP, and belongs to the class I PRPPSs. The three-dimensional structure of the recombinant enzyme was solved at 2.2 Å resolution using crystals grown in microgravity from protein solution containing ATP, magnesium and sulfate ions. An ADP molecule was located in the active site of each subunit of the hexameric enzyme molecule and sulfate ions were located in both the active and allosteric sites...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28580925/crystal-structure-of-the-multiple-antibiotic-resistance-regulator-marr-from-clostridium-difficile
#13
J W Peng, H Yuan, X S Tan
Regulators of multiple antibiotic resistance (MarRs) are key players against toxins in prokaryotes. MarR homologues have been identified in many bacterial and archaeal species which pose daunting antibiotic resistance issues that threaten public health. The continuous prevalence of Clostridium difficile infection (CDI) throughout the world is associated with the abuse of antibiotics, and antibiotic treatments of CDI have limited effect. In the genome of C. difficile strain 630, the marR gene (ID 4913953) encodes a MarR protein...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28580924/crystal-structure-of-n-acetylmannosamine-kinase-from-fusobacterium-nucleatum
#14
Rhawnie Caing-Carlsson, Parveen Goyal, Amit Sharma, Swagatha Ghosh, Thanuja Gangi Setty, Rachel A North, Rosmarie Friemann, S Ramaswamy
Sialic acids comprise a varied group of nine-carbon amino sugars that are widely distributed among mammals and higher metazoans. Some human commensals and bacterial pathogens can scavenge sialic acids from their environment and degrade them for use as a carbon and nitrogen source. The enzyme N-acetylmannosamine kinase (NanK; EC 2.7.1.60) belongs to the transcriptional repressors, uncharacterized open reading frames and sugar kinases (ROK) superfamily. NanK catalyzes the second step of the sialic acid catabolic pathway, transferring a phosphate group from adenosine 5'-triphosphate to the C6 position of N-acetylmannosamine to generate N-acetylmannosamine 6-phosphate...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28580923/the-crystal-structure-of-human-deah-box-rna-helicase-15-reveals-a-domain-organization-of-the-mammalian-deah-rha-family
#15
Karin Murakami, Kenji Nakano, Toshiyuki Shimizu, Umeharu Ohto
DEAH-box RNA helicase 15 (DHX15) plays important roles in RNA metabolism, including in splicing and in ribosome biogenesis. In addition, mammalian DHX15 also mediates the innate immune sensing of viral RNA. However, structural information on this protein is not available, although the structure of the fungal orthologue of this protein, Prp43, has been elucidated. Here, the crystal structure of the ADP-bound form of human DHX15 is reported at a resolution of 2.0 Å. This is the first structure to be revealed of a member of the mammalian DEAH-box RNA helicase (DEAH/RHA) family in a nearly complete form, including the catalytic core consisting of the two N-terminal RecA domains and the C-terminal regulatory domains (CTD)...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28580922/phosphate-binding-protein-from-polaromonas-js666-purification-characterization-crystallization-and-sulfur-sad-phasing
#16
Vanessa R Pegos, Louis Hey, Jacob LaMirande, Rachel Pfeffer, Rosalie Lipsh, Moshe Amitay, Daniel Gonzalez, Mikael Elias
Phosphate-binding proteins (PBPs) are key proteins that belong to the bacterial ABC-type phosphate transporters. PBPs are periplasmic (or membrane-anchored) proteins that capture phosphate anions from the environment and release them to the transmembrane transporter. Recent work has suggested that PBPs have evolved for high affinity as well as high selectivity. In particular, a short, unique hydrogen bond between the phosphate anion and an aspartate residue has been shown to be critical for selectivity, yet is not strictly conserved in PBPs...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28580921/crystal-structure-of-the-active-form-of-native-human-thymidylate-synthase-in-the-absence-of-bound-substrates
#17
P Deschamps, S Réty, J Bareille, N Leulliot
Human thymidylate synthase (hTS) provides the sole de novo intracellular source of thymidine 5'-monophosphate (dTMP). hTS is required for DNA replication prior to cell division, making it an attractive target for anticancer chemotherapy and drug discovery. hTS binds 2'-deoxyuridine 5'-monophosphate (dUMP) and the folate co-substrate N(5),N(10)-methylenetetrahydrofolate (meTHF) in a pocket near the catalytic residue Cys195. The catalytic loop, which is composed of amino-acid residues 181-197, can adopt two distinct conformations related by a 180° rotation...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28580920/crystal-structure-of-the-thermoplasma-acidophilum-protein-ta1207
#18
Ganesh Ramnath Pathare, István Nagy, Ágnes Hubert, Dennis R Thomas, Andreas Bracher
The crystal structure of the Ta1207 protein from Thermoplasma acidophilum is reported. Ta1207 was identified in a screen for high-molecular-weight protein complexes in T. acidophilum. In solution, Ta1207 forms homopentamers of 188 kDa. The crystal structure of recombinant Ta1207 solved by Se-MAD at 2.4 Å resolution revealed a complex with fivefold symmetry. In the crystal lattice, calcium ions induce the formation of a nanocage from two pentamers. The Ta1207 protomers comprise two domains with the same novel α/β topology...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28580919/crystallization-and-x-ray-diffraction-analysis-of-spae-a-basal-pilus-protein-from-the-gut-adapted-lactobacillus-rhamnosus-gg
#19
Arjun K Mishra, Abhin Kumar Megta, Airi Palva, Ingemar von Ossowski, Vengadesan Krishnan
SpaE is the predicted basal pilin subunit in the sortase-dependent SpaFED pilus from the gut-adapted and commensal Lactobacillus rhamnosus GG. Thus far, structural characterization of the cell-wall-anchoring basal pilins has remained difficult and has been limited to only a few examples from pathogenic genera and species. To gain a further structural understanding of the molecular mechanisms that are involved in the anchoring and assembly of sortase-dependent pili in less harmful bacteria, L. rhamnosus GG SpaE for crystallization was produced by recombinant expression in Escherichia coli...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28580918/crystal-structure-of-rv1220c-a-sam-dependent-o-methyltransferase-from-mycobacterium-tuberculosis
#20
Qiaoling Yan, Neil Shaw, Lanfang Qian, Dunquan Jiang
Rv1220c from Mycobacterium tuberculosis is annotated as an O-methyltransferase (MtbOMT). Currently, no structural information is available for this protein. Here, the crystal structure of MtbOMT refined to 2.0 Å resolution is described. The structure reveals the presence of a methyltransferase fold and shows clear electron density for one molecule of S-adenosylmethionine (SAM), which was apparently bound by the protein during its production in Escherichia coli. Although the overall structure of MtbOMT resembles the structures of O-methyltransferases from Cornybacterium glutamicum, Coxiella burnetti and Alfa alfa, differences are observed in the residues that make up the active site...
June 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
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