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acid pocket

M Ajitha, K Sundar, S Arul Mugilan, S Arumugam
The advent of whole genome sequencing leads to increasing number of proteins with known amino acid sequences. Despite many efforts, the number of proteins with resolved three dimensional structures is still low. One of the challenging tasks the structural biologists face is the prediction of the interaction of metal ion with any protein for which the structure is unknown. Based on the information available in PDB, a site (METALACTIVE INTERACTION) has been generated which displays information for significant high preferential and low-preferential combination of endogenous ligands for 49 metal ions...
December 13, 2017: Proteins
Hyeoncheol Francis Son, Kyung-Jin Kim
l-lysine is an essential amino acid that is widely used as a food supplement for humans and animals. meso-Diaminopimelic acid decarboxylase (DAPDC) catalyzes the final step in the de novol-lysine biosynthetic pathway by converting meso-diaminopimelic acid (meso-DAP) into l-lysine by decarboxylation reaction. To elucidate its molecular mechanisms, we determined the crystal structure of DAPDC from Corynebacterium glutamicum (CgDAPDC). The PLP cofactor is bound at the center of the barrel domain and forms a Schiff base with the catalytic Lys75 residue...
December 9, 2017: Biochemical and Biophysical Research Communications
Kenjiro Katsu, Rintaro Suzuki, Wataru Tsuchiya, Noritoshi Inagaki, Toshimasa Yamazaki, Tomomi Hisano, Yasuo Yasui, Toshiyuki Komori, Motoyuki Koshio, Seiji Kubota, Amanda R Walker, Kiyoshi Furukawa, Katsuhiro Matsui
BACKGROUND: Dihydroflavonol 4-reductase (DFR) is the key enzyme committed to anthocyanin and proanthocyanidin biosynthesis in the flavonoid biosynthetic pathway. DFR proteins can catalyse mainly the three substrates (dihydrokaempferol, dihydroquercetin, and dihydromyricetin), and show different substrate preferences. Although relationships between the substrate preference and amino acids in the region responsible for substrate specificity have been investigated in several plant species, the molecular basis of the substrate preference of DFR is not yet fully understood...
December 11, 2017: BMC Plant Biology
Concetta De Santi, Osman Absm Gani, Ronny Helland, Adele Williamson
The family 15 carbohydrate esterase (CE15) MZ0003, which derives from a marine Arctic metagenome, has a broader substrate scope than other members of this family. Here we report the crystal structure of MZ0003, which reveals that residues comprising the catalytic triad differ from previously-characterized fungal homologs, and resolves three large loop regions that are unique to this bacterial sub-clade. The catalytic triad of the bacterial CE15, which includes Asp 332 as its third member, closely resembles that of family 1 carbohydrate esterases (CE1), despite the overall lower structural similarity with members of this family...
December 8, 2017: Scientific Reports
Sarah Elizabeth Jones, Lars Olsen, Michael Gajhede
KDM subfamily 6 enzymes KDM6A and KDM6B specifically catalyse demethylation of di-/tri-methylated lysine on Histone 3 lysine 27 (H3K27me3/2) and play an important role in repression of developmental genes. Despite identical amino acid sequence in the immediate surroundings of H3K9me3/2 (ARKS) the enzymes do not catalyse demethylation of this general marker of repression. In order to address this question for KDM6B we used computational methods to identify H3(17-33) derived peptides with improved binding affinity, that would enable co-crystallization with the catalytic core of human KDM6B (ccKDM6B)...
December 8, 2017: Biochemistry
Ying-Yi Huo, Zhen Rong, Shu-Ling Jian, Cao-Di Xu, Jixi Li, Xue-Wei Xu
A novel esterase gene, e69, was cloned from Erythrobacter seohaensis SW-135, which was isolated from a tidal flat sediment of the Yellow Sea in Korea. This gene is 825 bp in length and codes for a 29.54 kDa protein containing 274 amino acids. Phylogenetic analysis showed that E69 is a new member of the bacterial lipolytic enzyme family IV. This enzyme exhibited the highest level of activity toward p-nitrophenyl (NP) butyrate but little or no activity toward the other p-NP esters tested. The optimum temperature and pH of the catalytic activity of E69 were 60°C and pH 10...
2017: Frontiers in Microbiology
Gabriel Macher, Melanie Koehler, Anne Rupprecht, Jürgen Kreiter, Peter Hinterdorfer, Elena E Pohl
Mitochondrial membrane uncoupling protein 3 (UCP3) is not only expressed in skeletal muscle and heart, but also in brown adipose tissue (BAT) alongside UCP1, which facilitates a proton leak to support non-shivering thermogenesis. In contrast to UCP1, the transport function and molecular mechanism of UCP3 regulation are poorly investigated, although it is generally agreed upon that UCP3, analogous to UCP1, transports protons, is activated by free fatty acids (FFAs) and is inhibited by purine nucleotides (PN)...
December 3, 2017: Biochimica et Biophysica Acta
Alexis M Ziemba, Andrea Szabo, David W Pierce, Marian Haburcak, Alex T Stern, Anahita Nourmahnad, Elizabeth S Halpin, Stuart A Forman
BACKGROUND: Neurosteroids like alphaxalone are potent anxiolytics, anticonvulsants, amnestics, and sedative-hypnotics, with effects linked to enhancement of γ-aminobutyric acid type A (GABAA) receptor gating in the central nervous system. Data locating neurosteroid binding sites on synaptic αβγ GABAA receptors are sparse and inconsistent. Some evidence points to outer transmembrane β-α interfacial pockets, near sites that bind the anesthetics etomidate and propofol. Other evidence suggests that steroids bind more intracellularly in β-α interfaces...
November 28, 2017: Anesthesiology
Bittu Saira Koshy, Jaideep Mahendra
Introduction: Lipoprotein associated phospholipase A2 (Lp-PLA2) has been explored as a potential biomarker for Cardiovascular Disease (CVD). The human Lp-PLA2 is a serine-dependent, Ca2+- independent enzyme. It gives way to oxidised free fatty acids and lysophosphatidyl choline by hydrolysing oxidised phospholipids, that leads to smooth muscle cell apoptosis, inflammatory cell chemotaxis and endothelial cell dysfunction in CVD. Owing to its role in inflammation, it may influence the development and progression of periodontitis as well...
September 2017: Journal of Clinical and Diagnostic Research: JCDR
M A Lopez, N Manzulli, A D'Angelo, D Lauritano, R Papalia, V Candotto
It is well known in dentistry that there are numerous chronic conditions that require ongoing and constant management over time, the most noteworthy being periodontal disease, gingivitis and periodontitis. Yet, in recent years, with the increase in the number of implants being placed, mucositis and peri-implantitis have become more and more prevalent pathologies. The results of the statistical analysis demonstrate that there was a slight difference between the pocket depth as measured in the treated sites at time 0 (pre-treatment) and time 1 (15 days post-treatment), although the difference was so small as to render it statistically irrelevant...
December 4, 2017: Journal of Biological Regulators and Homeostatic Agents
M A Lopez, N Manzulli, A D'Angelo, D Lauritano, M Casale, V Candotto
The emollient and restructuring action exerted on the mucous membranes by hyaluronic acid is of particular significance. This is thanks to its reparative (it stimulates angiogenesis) and soothing properties (hyaluronic acid is used in wound care to improve the processes of wound healing), which are effective in treating the symptoms of local inflammation and irritation. The purpose of this clinical trial is to evaluate the potential efficacy of nebulized hyaluronic acid in the management of chronic periodontitis in adults...
December 4, 2017: Journal of Biological Regulators and Homeostatic Agents
M A Lopez, N Manzulli, A D'Angelo, V Candotto, M Casale, D Lauritano
In recent years, with an increase in the number of implants, there has been a related increase in cases of pathologies related to infections around the implant site and on the implant surface i.e. mucositis and peri-implantitis. The purpose of this pilot study is to evaluate the potential efficacy of nebulized hyaluronic acid in the management of mucositis. The results of the statistical analysis demonstrate that there was no difference between the pocket depth as measured in the treated sites at time 0 (pre-treatment) and time 1 (15 days weeks post-treatment)...
December 4, 2017: Journal of Biological Regulators and Homeostatic Agents
M A Lopez, N Manzulli, A D'Angelo, V Candotto, M Casale, D Lauritano
Recently, a specifically designed device was proposed that is able to nebulize particles with a diameter of approximately 16 micrometres to be used mainly in the management of diseases of the upper airway respiratory tract. The purpose of this pilot study is to evaluate the potential efficacy of nebulized hyaluronic acid in the management of gingivitis. The results of the statistical analysis demonstrate that there was no difference between the pocket depth as measured in the treated sites at time 0 (pre-treatment) and time 1 (15 days post-treatment)...
December 4, 2017: Journal of Biological Regulators and Homeostatic Agents
Laura Carzaniga, Gabriele Amari, Andrea Rizzi, Carmelida Capaldi, Renato De Fanti, Eleonora Ghidini, Gino Villetti, Chiara Carnini, Nadia Moretto, Fabrizio Facchinetti, Paola Caruso, Gessica Marchini, Loredana Battipaglia, Riccardo Patacchini, Valentina Cenacchi, Roberta Volta, Francesco Amadei, Alice Pappani, Silvia Capacchi, Valentina Bagnacani, Maurizio Delcanale, Paola Puccini, Silvia Catinella, Maurizio Civelli, Elisabetta Armani
Phosphodiesterase 4 (PDE4) is a key cAMP-metabolising enzyme involved in the pathogenesis of inflammatory disease and its pharmacological inhibition has been shown to exert therapeutic efficacy in chronic obstructive pulmonary disease (COPD). Herein we describe a drug discovery program aiming at the identification of novel classes of potent PDE4 inhibitors suitable for pulmonary administration. Starting from a previous series of benzoic acid esters, we explored the chemical space in the solvent-exposed region of the enzyme catalytic binding pocket...
December 4, 2017: Journal of Medicinal Chemistry
Charles Stewart, Kate Woods, Greg Macias, Andrew C Allan, Roger P Hellens, Joseph P Noel
Biphenyl synthase and benzophenone synthase constitute an evolutionarily distinct clade of type III polyketide synthases (PKSs) that use benzoic acid-derived substrates to produce defense metabolites in plants. The use of benzoyl-CoA as an endogenous substrate is unusual for type III PKSs. Moreover, sequence analyses indicate that the residues responsible for the functional diversification of type III PKSs are mutated in benzoic acid-specific type III PKSs. In order to gain a better understanding of structure-function relationships within the type III PKS family, the crystal structures of biphenyl synthase from Malus × domestica and benzophenone synthase from Hypericum androsaemum were compared with the structure of an archetypal type III PKS: chalcone synthase from Malus × domestica...
December 1, 2017: Acta Crystallographica. Section D, Structural Biology
Sangwoo Kim, Kyung-Jin Kim
Acyl-CoA oxidase (ACOX) plays an important role in fatty acid degradation. The enzyme catalyzes the first reaction in peroxisomal fatty acid β-oxidation by reducing acyl-CoA to 2-trans-enoyl-CoA. The yeast Yarrowia lipolytica is able to utilize fatty acids, fats, and oil as carbon sources to produce valuable bioproducts. We determined the crystal structure of ACOX1 from Y. lipolytica (YlACOX1) at a resolution of 2.5 Å. YlACOX1 forms a homodimer, and the monomeric structure is composed of four domains, the Nα, Nβ, Cα1, and Cα2...
November 30, 2017: Biochemical and Biophysical Research Communications
Ting-Jian Zhang, Song-Ye Li, Wei-Yan Yuan, Yi Zhang, Fan-Hao Meng
A series of N-(9,10-anthraquinone-2-carbonyl)amino acid derivatives (1a-j) was designed and synthesized as novel XO inhibitors. Among them, the L/D-phenylalanine derivatives (1d and 1i) and the L/D-tryptophan derivatives (1e and 1j) were effective with micromolar level potency. In particular, the L-phenylalanine derivative 1d (IC50 = 3.0 μM) and the D-phenylalanine derivative 1i (IC50 = 2.9 μM) presented the highest potency, and were both more potent than the positive control allopurinol (IC50 = 8.1 μM)...
December 1, 2017: Chemical Biology & Drug Design
Tiansheng Li, Mengjie Li, Linlin Hou, Yameng Guo, Lei Wang, Guiqin Sun, Li Chen
All reported α-L-fucosidases catalyze the removal of nonreducing terminal L-fucoses from oligosaccharides or their conjugates, while having no capacity to hydrolyze core fucoses in glycoproteins directly. Here, we identified an α-fucosidase from the bacterium Elizabethkingia meningoseptica with catalytic activity against core α-1,3-fucosylated substrates and named it core fucosidase I (cFase I). Using site-specific mutational analysis, we found that three acidic residues (Asp-242, Glu-302, and Glu-315) in the predicted active pocket are critical for cFase I activity, with Asp-242 and Glu-315 acting as a pair of classic nucleophile and acid/base residues and Glu-302 acting in an as yet undefined role...
December 1, 2017: Journal of Biological Chemistry
Md Yousof Ali, Da Hye Kim, Su Hui Seong, Hyeung-Rak Kim, Hyun Ah Jung, Jae Sue Choi
Sargassum serratifolium C. Agardh (Phaeophyceae, Fucales) is a marine brown alga that belongs to the family Sargassaceae. It is widely distributed throughout coastal areas of Korea and Japan. S. serratifolium has been found to contain high concentrations of plastoquinones, which have strong anti-cancer, anti-inflammatory, antioxidant, and neuroprotective activity. This study aims to investigate the anti-diabetic activity of S. serratifolium and its major constituents through inhibition of protein tyrosine phosphatase 1B (PTP1B), α-glucosidase, and ONOO--mediated albumin nitration...
December 1, 2017: Marine Drugs
Frederick A Jakobiec, Lina Ma, Natalie Wolkow, J Douglas Cameron, Amanda C Maltry
PURPOSE: To analyze three unusual mesenchymal transformations within the eye - adipose or osseous metaplasia of the lens and adipose tissue in the vitreous cavity. DESIGN: Observational case series. METHODS: Re-evaluation of clinico-pathologic diagnoses and histopathologic findings in sections stained with hematoxylin and eosin, periodic acid-Schiff (PAS) reaction and Masson trichrome method. RESULTS: The three cases of mesenchymal transformation occurred in microphthalmic eyes with persistent hyperplastic primary vitreous (more recently termed persistent fetal vasculature)...
November 27, 2017: American Journal of Ophthalmology
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