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Acta Crystallographica. Section F, Structural Biology Communications

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https://www.readbyqxmd.com/read/30387781/combining-crystallogenesis-methods-to-produce-diffraction-quality-crystals-of-a-psychrophilic-trna-maturation-enzyme
#1
Raphaël de Wijn, Oliver Hennig, Felix G M Ernst, Bernard Lorber, Heike Betat, Mario Mörl, Claude Sauter
The determination of conditions for the reproducible growth of well diffracting crystals is a critical step in every biocrystallographic study. On the occasion of a new structural biology project, several advanced crystallogenesis approaches were tested in order to increase the success rate of crystallization. These methods included screening by microseed matrix screening, optimization by counter-diffusion and crystal detection by trace fluorescent labeling, and are easily accessible to any laboratory. Their combination proved to be particularly efficient in the case of the target, a 48 kDa CCA-adding enzyme from the psychrophilic bacterium Planococcus halocryophilus...
November 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30387780/crystal-structure-of-glycosyltrehalose-synthase-from-sulfolobus-shibatae-dsm5389
#2
Nobuo Okazaki, Michael Blaber, Ryota Kuroki, Taro Tamada
Glycosyltrehalose synthase (GTSase) converts the glucosidic bond between the last two glucose residues of amylose from an α-1,4 bond to an α-1,1 bond, generating a nonreducing glycosyl trehaloside, in the first step of the biosynthesis of trehalose. To better understand the structural basis of the catalytic mechanism, the crystal structure of GTSase from the hyperthermophilic archaeon Sulfolobus shibatae DSM5389 (5389-GTSase) has been determined to 2.4 Å resolution by X-ray crystallography. The structure of 5389-GTSase can be divided into five domains...
November 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30387779/crystal-structure-and-kinetic-analyses-of-a-hexameric-form-of-s-3-hydroxybutyryl-coa-dehydrogenase-from-clostridium-acetobutylicum
#3
Mihoko Takenoya, Seiichi Taguchi, Shunsuke Yajima
(S)-3-Hydroxybutyryl-CoA dehydrogenase (HBD) has been gaining increased attention recently as it is a key enzyme in the enantiomeric formation of (S)-3-hydroxybutyryl-CoA [(S)-3HB-CoA]. It converts acetoacetyl-CoA to (S)-3HB-CoA in the synthetic metabolic pathway. (S)-3HB-CoA is further modified to form (S)-3-hydroxybutyrate, which is a source of biodegradable polymers. During the course of a study to develop biodegradable polymers, attempts were made to determine the crystal structure of HBD from Clostridium acetobutylicum (CacHBD), and the crystal structures of both apo and NAD+ -bound forms of CacHBD were determined...
November 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30387778/crystal-structures-and-kinetics-of-n-acetylneuraminate-lyase-from-fusobacterium-nucleatum
#4
Jay Prakash Kumar, Harshvardhan Rao, Vinod Nayak, S Ramaswamy
N-Acetyl-D-neuraminic acid lyase (NanA) catalyzes the breakdown of sialic acid (Neu5Ac) to N-acetyl-D-mannosamine (ManNAc) and pyruvate. NanA plays a key role in Neu5Ac catabolism in many pathogenic and bacterial commensals where sialic acid is available as a carbon and nitrogen source. Several pathogens or commensals decorate their surfaces with sialic acids as a strategy to escape host innate immunity. Catabolism of sialic acid is key to a range of host-pathogen interactions. In this study, atomic resolution structures of NanA from Fusobacterium nucleatum (FnNanA) in ligand-free and ligand-bound forms are reported at 2...
November 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30387777/high-resolution-structures-of-inhibitor-complexes-of-human-indoleamine-2-3-dioxygenase-1-in-a-new-crystal-form
#5
Shukun Luo, Ke Xu, Shaoyun Xiang, Jie Chen, Chunyun Chen, Chuangxin Guo, Youzhi Tong, Liang Tong
Human indoleamine 2,3-dioxygenase 1 (IDO1) is a heme-dependent enzyme with important roles in many cellular processes and is a potential target for drug discovery against cancer and other diseases. Crystal structures of IDO1 in complex with various inhibitors have been reported. Many of these crystals belong to the same crystal form and most of the reported structures have resolutions in the range 3.2-2.3 Å. Here, three new crystal forms of human IDO1 obtained by introducing a surface mutation, K116A/K117A, distant from the active site are reported...
November 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30387776/bpeb-a-major-resistance-nodulation-cell-division-transporter-from-burkholderia-cenocepacia-construct-design-crystallization-and-preliminary-structural-analysis
#6
Tomonari Horikawa, Li Wei Hung, Heung Bok Kim, David Shaya, Chang Yub Kim, Thomas C Terwilliger, Eiki Yamashita, Maho Aoki, Ui Okada, Satoshi Murakami
Burkholderia cenocepacia is an opportunistic pathogen that infects cystic fibrosis patients, causing pneumonia and septicemia. B. cenocepacia has intrinsic antibiotic resistance against monobactams, aminoglycosides, chloramphenicol and fluoroquinolones that is contributed by a homologue of BpeB, which is a member of the resistance-nodulation-cell division (RND)-type multidrug-efflux transporters. Here, the cloning, overexpression, purification, construct design for crystallization and preliminary X-ray diffraction analysis of this BpeB homologue from B...
November 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30387775/crystal-structures-of-the-n-terminal-domain-of-the-staphylococcus-aureus-dead-box-rna-helicase-csha-and-its-complex-with-amp
#7
Xiaobao Chen, Chengliang Wang, Xuan Zhang, Tian Tian, Jianye Zang
CshA is a DEAD-box RNA helicase that belongs to the DExD/H-box family of proteins, which generally have an RNA-dependent ATPase activity. In Staphylococcus aureus, CshA was identified as a component of the RNA degradosome and plays important roles in RNA turnover. In this study, the crystal structures of the N-terminal RecA-like domain 1 of S. aureus CshA (SaCshAR1 ) and of its complex with AMP (SaCshAR1 -AMP) are reported at resolutions of 1.5 and 1.8 Å, respectively. SaCshAR1 adopts a conserved α/β RecA-like structure with seven parallel strands surrounded by nine α-helices...
November 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30387774/crystallization-of-ectonucleotide-phosphodiesterase-pyrophosphatase-3-and-orientation-of-the-smb-domains-in-the-full-length-ectodomain
#8
Christoph Döhler, Matthias Zebisch, Dana Krinke, Andrea Robitzki, Norbert Sträter
Ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3, ENPP3) is an ATP-hydrolyzing glycoprotein that is located in the extracellular space. The full-length ectodomain of rat NPP3 was expressed in HEK293S GntI- cells, purified using two chromatographic steps and crystallized. Its structure at 2.77 Å resolution reveals that the active-site zinc ions are missing and a large part of the active site and the surrounding residues are flexible. The SMB-like domains have the same orientation in all four molecules in the asymmetric unit...
November 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30387773/characterization-and-structure-determination-of-a-llama-derived-nanobody-targeting-the-j-base-binding-protein-1
#9
Bart van Beusekom, Tatjana Heidebrecht, Athanassios Adamopoulos, Alexander Fish, Els Pardon, Jan Steyaert, Robbie P Joosten, Anastassis Perrakis
J-base binding protein 1 (JBP1) contributes to the biosynthesis and maintenance of base J (β-D-glucosylhydroxymethyluracil), a modification of thymidine confined to some protozoa. Camelid (llama) single-domain antibody fragments (nanobodies) targeting JBP1 were produced for use as crystallization chaperones. Surface plasmon resonance screening identified Nb6 as a strong binder, recognizing JBP1 with a 1:1 stoichiometry and high affinity (Kd = 30 nM). Crystallization trials of JBP1 in complex with Nb6 yielded crystals that diffracted to 1...
November 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30387772/quo-vadis-acta-crystallographica-f
#10
Mark J van Raaij
No abstract text is available yet for this article.
November 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30279321/redox-manipulation-of-the-manganese-metal-in-human-manganese-superoxide-dismutase-for-neutron-diffraction
#11
Jahaun Azadmanesh, William E Lutz, Kevin L Weiss, Leighton Coates, Gloria E O Borgstahl
Human manganese superoxide dismutase (MnSOD) is one of the most significant enzymes in preventing mitochondrial dysfunction and related diseases by combating reactive oxygen species (ROS) in the mitochondrial matrix. Mitochondria are the source of up to 90% of cellular ROS generation, and MnSOD performs its necessary bioprotective role by converting superoxide into oxygen and hydrogen peroxide. This vital catalytic function is conducted via cyclic redox reactions between the substrate and the active-site manganese using proton-coupled electron transfers...
October 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30279320/x-ray-structure-of-arthrobacter-globiformis-m30-ketose-3-epimerase-for-the-production-of-d-allulose-from-d-fructose
#12
Hiromi Yoshida, Akihide Yoshihara, Pushpa Kiran Gullapalli, Kouhei Ohtani, Kazuya Akimitsu, Ken Izumori, Shigehiro Kamitori
The X-ray structure of ketose 3-epimerase from Arthrobacter globiformis M30, which was previously reported to be a D-allulose 3-epimerase (AgD-AE), was determined at 1.96 Å resolution. The crystal belonged to the hexagonal space group P65 22, with unit-cell parameters a = b = 103.98, c = 256.53 Å. The structure was solved by molecular replacement using the structure of Mesorhizobium loti L-ribulose 3-epimerase (MlL-RE), which has 41% sequence identity, as a search model. A hexagonal crystal contained two molecules in the asymmetric unit, and AgD-AE formed a homotetramer with twofold symmetry...
October 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30279319/re-refinement-of-plasmodium-falciparum-orotidine-5-monophosphate-decarboxylase-provides-a-clearer-picture-of-an-important-malarial-drug-target
#13
Walter R P Novak, Korbin H J West, Lucy M D Kirkman, Gabriel S Brandt
The development of antimalarial drugs remains a public health priority, and the orotidine 5'-monophosphate decarboxylase from Plasmodium falciparum (PfOMPDC) has great potential as a drug target. The crystallization of PfOMPDC with substrate bound represents an important advance for structure-based drug-design efforts [Tokuoka et al. (2008), J. Biochem. 143, 69-78]. The complex of the enzyme bound to the substrate OMP (PDB entry 2za1) would be of particular utility in this regard. However, re-refinement of this structure of the Michaelis complex shows that the bound ligand is the product rather than the substrate...
October 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30279318/comparative-structure-analysis-of-the-etsi-domain-of-erg3-and-its-complex-with-the-e74-promoter-dna-sequence
#14
Ruby Sharma, Shanti P Gangwar, Ajay K Saxena
ERG3 (ETS-related gene) is a member of the ETS (erythroblast transformation-specific) family of transcription factors, which contain a highly conserved DNA-binding domain. The ETS family of transcription factors differ in their binding to promoter DNA sequences, and the mechanism of their DNA-sequence discrimination is little known. In the current study, crystals of the ETSi domain (the ETS domain of ERG3 containing a CID motif) in space group P41 21 2 and of its complex with the E74 DNA sequence (DNA9 ) in space group C2221 were obtained and their structures were determined...
October 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30279317/crystal-structures-of-green-fluorescent-protein-with-the-unnatural-amino-acid-4-nitro-l-phenylalanine
#15
Nicole Maurici, Nicole Savidge, Byung Uk Lee, Scott H Brewer, Christine M Phillips-Piro
The X-ray crystal structures of two superfolder green fluorescent protein (sfGFP) constructs containing a genetically incorporated spectroscopic reporter unnatural amino acid, 4-nitro-L-phenylalanine (pNO2 F), at two unique sites in the protein have been determined. Amber codon-suppression methodology was used to site-specifically incorporate pNO2 F at a solvent-accessible (Asp133) and a partially buried (Asn149) site in sfGFP. The Asp133pNO2 F sfGFP construct crystallized with two molecules per asymmetric unit in space group P32 21 and the crystal structure was refined to 2...
October 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30279316/the-novel-metallo-%C3%AE-lactamase-pngm-1-from-a-deep-sea-sediment-metagenome-crystallization-and-x-ray-crystallographic-analysis
#16
Kwang Seung Park, Myoung Ki Hong, Jin Wan Jeon, Ji Hwan Kim, Jeong Ho Jeon, Jung Hun Lee, Tae Yeong Kim, Asad Mustafa Karim, Sumera Kausar Malik, Lin Woo Kang, Sang Hee Lee
Metallo-β-lactamases (MBLs) are present in major Gram-negative pathogens and environmental species, and pose great health risks because of their ability to hydrolyze the β-lactam rings of antibiotics such as carbapenems. PNGM-1 was the first reported case of a subclass B3 MBL protein that was identified from a metagenomic library from deep-sea sediments that predate the antibiotic era. In this study, PNGM-1 was overexpressed, purified and crystallized. Crystals of native and selenomethionine-substituted PNGM-1 diffracted to 2...
October 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30279315/crystal-structure-of-mutant-carboxypeptidase-t-from-thermoactinomyces-vulgaris-with-an-implanted-s1-subsite-from-pancreatic-carboxypeptidase-b
#17
Valery Kh Akparov, Vladimir I Timofeev, Inna P Kuranova, Tatiana V Rakitina
A site-directed mutagenesis method has been used to obtain the G215S/A251G/T257A/D260G/T262D mutant of carboxypeptidase T from Thermoactinomyces vulgaris (CPT), in which the amino-acid residues of the S1' subsite are substituted by the corresponding residues from pancreatic carboxypeptidase B (CPB). It was shown that the mutant enzyme retained the broad, mainly hydrophobic selectivity of wild-type CPT. The mutant containing the implanted CPB S1' subsite was crystallized and its three-dimensional structure was determined at 1...
October 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30279314/crystal-structure-of-the-ribonuclease-p-protein-subunit-from-staphylococcus-aureus
#18
Lisha Ha, Jennifer Colquhoun, Nicholas Noinaj, Chittaranjan Das, Paul M Dunman, Daniel P Flaherty
Staphylococcus aureus ribonuclease-P-protein subunit (RnpA) is a promising antimicrobial target that is a key protein component for two essential cellular processes, RNA degradation and transfer-RNA (tRNA) maturation. The first crystal structure of RnpA from the pathogenic bacterial species, S. aureus, is reported at 2.0 Å resolution. The structure presented maintains key similarities with previously reported RnpA structures from bacteria and archaea, including the highly conserved RNR-box region and aromatic residues in the precursor-tRNA 5'-leader-binding domain...
October 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30279313/crystal-structure-of-arabidopsis-thaliana-peroxiredoxin-a-c119s-mutant
#19
Ye Yang, Wenguang Cai, Junchao Wang, Weimin Pan, Lin Liu, Mingzhu Wang, Min Zhang
Peroxiredoxins (Prxs), a large family of antioxidant enzymes, are abundant in all living organisms. Peroxiredoxin A (PrxA) from Arabidopsis thaliana belongs to the typical 2-Cys Prx family and is localized in the chloroplast. This article reports the crystal structure of a PrxA C119S mutant refined to 2.6 Å resolution. The protein exists as a decamer both in the crystal structure and in solution. The structure is in the reduced state suitable for the approach of peroxide, though conformational changes are needed for the resolving process...
October 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/30279312/structure-of-glyoxysomal-malate-dehydrogenase-mdh3-from-saccharomyces-cerevisiae
#20
Shu Moriyama, Kazuya Nishio, Tsunehiro Mizushima
Malate dehydrogenase (MDH), a carbohydrate and energy metabolism enzyme in eukaryotes, catalyzes the interconversion of malate to oxaloacetate (OAA) in conjunction with that of nicotinamide adenine dinucleotide (NAD+ ) to NADH. Three isozymes of MDH have been reported in Saccharomyces cerevisiae: MDH1, MDH2 and MDH3. MDH1 is a mitochondrial enzyme and a member of the tricarboxylic acid cycle, whereas MDH2 is a cytosolic enzyme that functions in the glyoxylate cycle. MDH3 is a glyoxysomal enzyme that is involved in the reoxidation of NADH, which is produced during fatty-acid β-oxidation...
October 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
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