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Acta Crystallographica. Section F, Structural Biology Communications

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https://www.readbyqxmd.com/read/29199994/dna-binding-domain-of-myelin-gene-regulatory-factor-purification-crystallization-and-x-ray-analysis-corrigendum
#1
WenYu Wu, Xiangkai Zhen, Ning Shi
An extra affiliation is added for the authors of the article by Wu et al. [(2017), Acta Cryst. F73, 393-397].
December 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29199993/crystal-structure-of-sam-dependent-methyltransferase-from-pyrococcus-horikoshii
#2
K J Pampa, S Madan Kumar, M K Hema, Karthik Kumara, S Naveen, Naoki Kunishima, N K Lokanath
Methyltransferases (MTs) are enzymes involved in methylation that are needed to perform cellular processes such as biosynthesis, metabolism, gene expression, protein trafficking and signal transduction. The cofactor S-adenosyl-L-methionine (SAM) is used for catalysis by SAM-dependent methyltransferases (SAM-MTs). The crystal structure of Pyrococcus horikoshii SAM-MT was determined to a resolution of 2.1 Å using X-ray diffraction. The monomeric structure consists of a Rossmann-like fold (domain I) and a substrate-binding domain (domain II)...
December 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29199992/the-pseudomonas-syringae-pv-actinidiae-chemoreceptor-protein-f-pscf-periplasmic-sensor-domain-cloning-purification-and-x-ray-crystallographic-analysis
#3
Tifany Oulavallickal, Jodi L Brewster, James L O McKellar, Michael J Fairhurst, Nicholas A Tenci, Monica L Gerth
Nitrate- and nitrite-sensing (NIT) domains are found associated with a wide variety of bacterial receptors, including chemoreceptors. However, the structure of a chemoreceptor-associated NIT domain has not yet been characterized. Recently, a chemoreceptor named PscF was identified from the plant pathogen Pseudomonas syringae pv. actinidiae that is predicted to contain a periplasmic NIT domain. The PscF sensor domain (PscF-SD; residues 42-332) was cloned into an appropriate expression vector, recombinantly produced in Escherichia coli BL21-Gold(DE3) cells and purified via immobilized metal-affinity and size-exclusion chromatography...
December 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29199991/crystal-structure-of-the-second-fibronectin-type-iii-fn3-domain-from-human-collagen-%C3%AE-1-type-xx
#4
Jingfeng Zhao, Jixia Ren, Nan Wang, Zhong Cheng, Runmei Yang, Gen Lin, Yi Guo, Dayong Cai, Yong Xie, Xiaohong Zhao
Collagen α1 type XX, which contains fibronectin type III (FN3) repeats involving six FN3 domains (referred to as the FN#1-FN#6 domains), is an unusual member of the fibril-associated collagens with interrupted triple helices (FACIT) subfamily of collagens. The results of standard protein BLAST suggest that the FN3 repeats might contribute to collagen α1 type XX acting as a cytokine receptor. To date, solution NMR structures of the FN#3, FN#4 and FN#6 domains have been determined. To obtain further structural evidence to understand the relationship between the structure and function of the FN3 repeats from collagen α1 type XX, the crystal structure of the FN#2 domain from human collagen α1 type XX (residues Pro386-Pro466; referred to as FN2-HCXX) was solved at 2...
December 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29199990/meditope-fab-interaction-threading-the-hole
#5
Krzysztof P Bzymek, Yuelong Ma, Kendra N Avery, David A Horne, John C Williams
Meditope, a cyclic 12-residue peptide, binds to a unique binding side between the light and heavy chains of the cetuximab Fab. In an effort to improve the affinity of the interaction, it was sought to extend the side chain of Arg8 in the meditope, a residue that is accessible from the other side of the meditope binding site, in order to increase the number of interactions. These modifications included an n-butyl and n-octyl extension as well as hydroxyl, amine and carboxyl substitutions. The atomic structures of the complexes and the binding kinetics for each modified meditope indicated that each extension threaded through the Fab `hole' and that the carboxyethylarginine substitution makes a favorable interaction with the Fab, increasing the half-life of the complex by threefold compared with the unmodified meditope...
December 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29199989/crystal-structure-of-an-anti-idiotype-variable-lymphocyte-receptor
#6
Bernard C Collins, Hiro Nakahara, Sharmistha Acharya, Max D Cooper, Brantley R Herrin, Ian A Wilson
Variable lymphocyte receptors (VLRs), the leucine-rich repeat (LRR)-based antigen receptors of jawless fish, have great utility in a wide variety of biochemical and biological applications, similar to classical Ig-based antibodies. VLR-based reagents may be particularly useful when traditional antibodies are not available. An anti-idiotype lamprey VLR, VLR39, has previously been identified that recognizes the heavy-chain CDR3 of the B-cell receptor (BCR) of a leukemic clone from a patient with chronic lymphocytic leukemia (CLL)...
December 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29199988/swit_4259-an-acetoacetate-decarboxylase-like-enzyme-from-sphingomonas-wittichii-rw1
#7
Lisa S Mydy, Zahra Mashhadi, T William Knight, Tyler Fenske, Trevor Hagemann, Robert W Hoppe, Lanlan Han, Todd R Miller, Alan W Schwabacher, Nicholas R Silvaggi
The Gram-negative bacterium Sphingomonas wittichii RW1 is notable for its ability to metabolize a variety of aromatic hydrocarbons. Not surprisingly, the S. wittichii genome contains a number of putative aromatic hydrocarbon-degrading gene clusters. One of these includes an enzyme of unknown function, Swit_4259, which belongs to the acetoacetate decarboxylase-like superfamily (ADCSF). Here, it is reported that Swit_4259 is a small (28.8 kDa) tetrameric ADCSF enzyme that, unlike the prototypical members of the superfamily, does not have acetoacetate decarboxylase activity...
December 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29199987/structure-of-the-bacillus-anthracis-dtdp-l-rhamnose-biosynthetic-enzyme-dtdp-4-dehydrorhamnose-3-5-epimerase-rfbc
#8
Aleksander Shornikov, Ha Tran, Jennifer Macias, Andrei S Halavaty, George Minasov, Wayne F Anderson, Misty L Kuhn
The exosporium layer of Bacillus anthracis spores is rich in L-rhamnose, a common bacterial cell-wall component, which often contributes to the virulence of pathogens by increasing their adherence and immune evasion. The biosynthetic pathway used to form the activated L-rhamnose donor dTDP-L-rhamnose consists of four enzymes (RfbA, RfbB, RfbC and RfbD) and is an attractive drug target because there are no homologs in mammals. It was found that co-purifying and screening RfbC (dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase) from B...
December 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29199986/a-low-cost-method-for-visible-fluorescence-imaging
#9
Crissy L Tarver, Marc Pusey
A wide variety of crystallization solutions are screened to establish conditions that promote the growth of a diffraction-quality crystal. Screening these conditions requires the assessment of many crystallization plates for the presence of crystals. Automated systems for screening and imaging are very expensive. A simple approach to imaging trace fluorescently labeled protein crystals in crystallization plates has been devised, and can be implemented at a cost as low as $50. The proteins β-lactoglobulin B, trypsin and purified concanavalin A (ConA) were trace fluorescently labeled using three different fluorescent probes: Cascade Yellow (CY), Carboxyrhodamine 6G (CR) and Pacific Blue (PB)...
December 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29199985/crystal-structure-of-a-pyridoxal-5-phosphate-dependent-aspartate-racemase-derived-from-the-bivalve-mollusc-scapharca-broughtonii
#10
Taichi Mizobuchi, Risako Nonaka, Motoki Yoshimura, Katsumasa Abe, Shouji Takahashi, Yoshio Kera, Masaru Goto
Aspartate racemase (AspR) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that is responsible for D-aspartate biosynthesis in vivo. To the best of our knowledge, this is the first study to report an X-ray crystal structure of a PLP-dependent AspR, which was resolved at 1.90 Å resolution. The AspR derived from the bivalve mollusc Scapharca broughtonii (SbAspR) is a type II PLP-dependent enzyme that is similar to serine racemase (SR) in that SbAspR catalyzes both racemization and dehydration. Structural comparison of SbAspR and SR shows a similar arrangement of the active-site residues and nucleotide-binding site, but a different orientation of the metal-binding site...
December 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29199984/structure-of-the-bacillus-anthracis-dtdp-l-rhamnose-biosynthetic-enzyme-dtdp-4-dehydrorhamnose-reductase-rfbd
#11
Ashley Law, Alexander Stergioulis, Andrei S Halavaty, George Minasov, Wayne F Anderson, Misty L Kuhn
Bacillus anthracis is the causative agent of the deadly disease Anthrax. Its use in bioterrorism and its ability to re-emerge have brought renewed interest in this organism. B. anthracis is a Gram-positive bacterium that adds L-rhamnose to its cell-wall polysaccharides using the activated donor dTDP-β-L-rhamnose. The enzymes involved in the biosynthesis of the activated donor are absent in humans, which make them ideal targets for therapeutic development to combat pathogens. Here, the 2.65 Å resolution crystal structure of the fourth enzyme in the dTDP-β-L-rhamnose-biosynthetic pathway from B...
December 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29095158/biochemical-and-structural-studies-of-mutants-indicate-concerted-movement-of-the-dimer-interface-and-ligand-binding-region-of-mycobacterium-tuberculosis-pantothenate-kinase
#12
A Paul, P Kumar, A Surolia, M Vijayan
Two point mutants and the corresponding double mutant of Mycobacterium tuberculosis pantothenate kinase have been prepared and biochemically and structurally characterized. The mutants were designed to weaken the affinity of the enzyme for the feedback inhibitor CoA. The mutants exhibit reduced activity, which can be explained in terms of their structures. The crystals of the mutants are not isomorphous to any of the previously analysed crystals of the wild-type enzyme or its complexes. The mycobacterial enzyme and its homologous Escherichia coli enzyme exhibit structural differences in their nucleotide complexes in the dimer interface and the ligand-binding region...
November 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29095157/pteridine-glycosyltransferase-from-chlorobium-tepidum-crystallization-and-x-ray-analysis
#13
Asaithambi Killivalavan, Young Shik Park, Kon Ho Lee
The pteridine glycosyltransferase (PGT) found in Chlorobium tepidum (CtPGT) catalyzes the conversion of L-threo-tetrahydrobiopterin to 1-O-(L-threo-biopterin-2'-yl)-β-N-acetylglucosamine using UDP-N-acetylglucosamine. The gene for CtPGT was cloned, and selenomethionine-derivatized protein was overexpressed and purified using various chromatographic techniques. The protein was crystallized by the hanging-drop vapour-diffusion method using 0.24 M triammonium citrate pH 7.0, 14%(w/v) PEG 3350 as a reservoir solution...
November 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29095156/structure-of-the-bacillus-anthracis-dtdp-l-rhamnose-biosynthetic-enzyme-glucose-1-phosphate-thymidylyltransferase-rfba
#14
Jackson Baumgartner, Jesi Lee, Andrei S Halavaty, George Minasov, Wayne F Anderson, Misty L Kuhn
L-Rhamnose is a ubiquitous bacterial cell-wall component. The biosynthetic pathway for its precursor dTDP-L-rhamnose is not present in humans, which makes the enzymes of the pathway potential drug targets. In this study, the three-dimensional structure of the first protein of this pathway, glucose-1-phosphate thymidylyltransferase (RfbA), from Bacillus anthracis was determined. In other organisms this enzyme is referred to as RmlA. RfbA was co-crystallized with the products of the enzymatic reaction, dTDP-α-D-glucose and pyrophosphate, and its structure was determined at 2...
November 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29095155/structural-studies-of-domain-movement-in-active-site-mutants-of-porphobilinogen-deaminase-from-bacillus-megaterium
#15
Jingxu Guo, Peter Erskine, Alun R Coker, Steve P Wood, Jonathan B Cooper
The enzyme porphobilinogen deaminase (PBGD) is one of the key enzymes in tetrapyrrole biosynthesis. It catalyses the formation of a linear tetrapyrrole from four molecules of the substrate porphobilinogen (PBG). It has a dipyrromethane cofactor (DPM) in the active site which is covalently linked to a conserved cysteine residue through a thioether bridge. The substrate molecules are linked to the cofactor in a stepwise head-to-tail manner during the reaction, which is catalysed by a conserved aspartate residue: Asp82 in the B...
November 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29095154/crystallization-and-x-ray-diffraction-analysis-of-native-and-selenomethionine-substituted-phyh-di-from-bacillus-sp-hjb17
#16
Fang Lu, Bei Zhang, Yong Liu, Ying Song, Gangxing Guo, Duo Feng, Huoqing Huang, Peilong Yang, Wei Gao, Sujuan Guo, Bin Yao
Phytases are phosphatases that hydrolyze phytates to less phosphorylated myo-inositol derivatives and inorganic phosphate. β-Propeller phytases, which are very diverse phytases with improved thermostability that are active at neutral and alkaline pH and have absolute substrate specificity, are ideal substitutes for other commercial phytases. PhyH-DI, a β-propeller phytase from Bacillus sp. HJB17, was found to act synergistically with other single-domain phytases and can increase their efficiency in the hydrolysis of phytate...
November 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29095153/periplasmic-form-of-dipeptidyl-aminopeptidase-iv-from-pseudoxanthomonas-mexicana-wo24-purification-kinetic-characterization-crystallization-and-x-ray-crystallographic-analysis
#17
Saori Roppongi, Chika Tateoka, Mayu Fujimoto, Ippei Iizuka, Saori Morisawa, Akihiro Nakamura, Nobuyuki Honma, Yoshiyuki Suzuki, Yosuke Shida, Wataru Ogasawara, Nobutada Tanaka, Yasumitsu Sakamoto, Takamasa Nonaka
Dipeptidyl aminopeptidase IV (DAP IV or DPP IV) from Pseudoxanthomonas mexicana WO24 (PmDAP IV) preferentially cleaves substrate peptides with Pro or Ala at the P1 position [NH2-P2-P1(Pro/Ala)-P1'-P2'…]. For crystallographic studies, the periplasmic form of PmDAP IV was overproduced in Escherichia coli, purified and crystallized in complex with the tripeptide Lys-Pro-Tyr using the hanging-drop vapour-diffusion method. Kinetic parameters of the purified enzyme against a synthetic substrate were also determined...
November 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29095152/structure-of-the-staphylococcal-enterotoxin-b-vaccine-candidate-s19-showing-eliminated-superantigen-activity
#18
Woo Hyeon Jeong, Dong Hyun Song, Gyeung Haeng Hur, Seong Tae Jeong
Four mutations (N23A, Y90A, R110A and F177A) were introduced into S19, a vaccine candidate for staphylococcal enterotoxin B (SEB), resulting in a lower binding affinity towards the T-cell receptor beta chain (TCB) and reducing its superantigen activity. The structure of S19 was solved and was superposed on the native or complex structure of SEB. In the superposition model, mutations that were introduced seemed to reduce the number of hydrogen bonds at the SEB-TCB interface. S19 also displayed an unexpected structural change around the flexible-loop region owing to the Y90A mutation...
November 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/29095151/the-n253f-mutant-structure-of-trehalose-synthase-from-deinococcus-radiodurans-reveals-an-open-active-site-topology
#19
Sih Yao Chow, Yung Lin Wang, Yu Chiao Hsieh, Guan Chiun Lee, Shwu Huey Liaw
Trehalose synthase (TS) catalyzes the reversible conversion of maltose to trehalose and belongs to glycoside hydrolase family 13 (GH13). Previous mechanistic analysis suggested a rate-limiting protein conformational change, which is probably the opening and closing of the active site. Consistently, crystal structures of Deinococcus radiodurans TS (DrTS) in complex with the inhibitor Tris displayed an enclosed active site for catalysis of the intramoleular isomerization. In this study, the apo structure of the DrTS N253F mutant displays a new open conformation with an empty active site...
November 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28994407/structure-activity-and-thermostability-investigations-of-oxa-163-oxa-181-and-oxa-245-using-biochemical-analysis-crystal-structures-and-differential-scanning-calorimetry-analysis
#20
Bjarte Aarmo Lund, Ane Molden Thomassen, Trine Josefine Olsen Carlsen, Hanna Kirsti S Leiros
The first crystal structures of the class D β-lactamases OXA-181 and OXA-245 were determined to 2.05 and 2.20 Å resolution, respectively; in addition, the structure of a new crystal form of OXA-163 was resolved to 2.07 Å resolution. All of these enzymes are OXA-48-like and have been isolated from different clinical Klebsiella pneumoniae strains and also from other human pathogens such as Pseudomonas aeruginosa and Escherichia coli. Here, enzyme kinetics and thermostability studies are presented, and the new crystal structures are used to explain the observed variations...
October 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
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