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catalytic residue

Abdulkadir Kocak, Ismail Erol, Muslum Yildiz, Hatice Can
Developing small compound based drugs targeting the β-secretase (BACE) enzyme is one of the most promising strategies in treatment of the Alzheimer's disease. As the enzyme shows the activity based on the acid-base reaction at a very narrow pH range, the protonation state of aspartic acids with the residue number 32 and 228 (Asp32 and Asp228), which forms the active site dyad, along with the protonation state of the ligand (substrate or inhibitor) play very critical role in interactions between the ligand and enzyme...
October 17, 2016: Journal of Molecular Graphics & Modelling
Sasikala Anbarasan, Ronny Wahlström, Michael Hummel, Heikki Ojamo, Herbert Sixta, Ossi Turunen
Thermophilic Thermopolyspora flexuosa GH10 xylanase (TfXYN10A) was studied in the presence of biomass-dissolving hydrophilic ionic liquids (ILs) [EMIM]OAc, [EMIM]DMP and [DBNH]OAc. The temperature optimum of TfXYN10A with insoluble xylan in the pulp was at 65-70 °C, with solubilised 1 % xylan at 70-75 °C and with 3 % xylan at 75-80 °C. Therefore, the amount of soluble substrate affects the enzyme activity at high temperatures. The experiments with ILs were done with 1 % substrate. TfXYN10A can partially hydrolyse soluble xylan even in the presence of 40 % (v/v) ILs...
October 21, 2016: Applied Microbiology and Biotechnology
Xiangrong Chen, Yijie Luo, Benkun Qi, Jianquan Luo, Yinhua Wan
Ultrasonic probe-assisted enzymolysis technology was developed to improve the hydrolysis efficiency of soy sauce residue (SSR). The effects of enzyme type and enzymatic hydrolysis parameters on the hydrolysis degree of SSR were studied firstly to obtain the optimal enzymatic hydrolysis conditions. Then the effects of ultrasound on protease activity and structure of SSR were investigated to elucidate the acting mechanism of ultrasound. Finally, the ultrasonic-assisted enzymatic hydrolysis modes were designed and compared, and the hydrolysates from SSR were characterized to evaluate their further application...
October 15, 2016: Ultrasonics Sonochemistry
Elena Sugrue, Paul D Carr, Colin Scott, Colin J Jackson
The desolvation of ionizable residues in the active sites of enzymes and the subsequent effects on catalysis and thermostability have been studied in model systems, yet little is known regarding how enzymes can naturally evolve active sites with highly reactive and desolvated charges. Variants of triazine hydrolase (TrzN) with significant differences in their active sites have been isolated from different bacterial strains: TrzN from Nocardioides sp. strain MTD22 contains a catalytic glutamate residue (Glu241) that is surrounded by hydrophobic and aromatic second-shell residues (Pro214, Tyr215), whereas TrzN from Nocardioides sp...
October 21, 2016: Biochemistry
Paola Ferrini, Camila A Rezende, Roberto Rinaldi
Catalytic upstream biorefining (CUB) encompasses processes for plant biomass deconstruction through the early-stage conversion of lignin by the action of a hydrogenation catalyst. CUB processes produce lignin as an extensively depolymerised product (i.e., a viscous lignin oil) and render highly delignified pulps. In this report, we examine CUB from the pulp perspective. Notably, Raney Ni plays an indirect role in the processes that occur within the lignocellulose matrix. As there are negligible points of contact between the poplar wood chips and Raney Ni, the catalyst action is limited to the species leached from the matrix into the liquor...
October 21, 2016: ChemSusChem
Xiaoming Huang, Jiadong Zhu, Tamás I Korányi, Michael D Boot, Emiel J M Hensen
Adding value to lignin, the most complex and recalcitrant fraction in lignocellulosic biomass, is highly relevant to costefficient operation of biorefineries. We report the use of homogeneous metal triflates to rapidly release lignin from biomass. Combined with metal-catalyzed hydrogenolysis, the process separates woody biomass into few lignin-derived alkylmethoxyphenols and cellulose under mild conditions. Model compound studies show the unique catalytic properties of metal triflates in cleaving lignin-carbohydrate interlinkages...
October 21, 2016: ChemSusChem
Beate Schwer, Fahad Khalid, Stewart Shuman
Saccharomyces cerevisiae Dbr1 is a manganese-dependent RNA debranching enzyme that cleaves the 2'-5' phosphodiester bond of the lariat introns formed during pre-mRNA splicing. Dbr1 is a member of the binuclear metallophosphoesterase enzyme superfamily. We showed previously via alanine scanning that RNA debranching in vivo and in vitro depends on conserved active site residues His13, Asp40, Asn85, His86, His179, His231, and His233. Here, by extending the alanine scan, we added Cys11 to the ensemble of essential active site components...
October 7, 2016: RNA
Jong Min Lee, Soo Young Moon, Yu-Ri Kim, Kang Woong Kim, Bong-Joo Lee, In-Soo Kong
The aim of this study was to improve the stability of β-1,3-1,4-glucanase by substituting hydrophobic residue for specific amino acid. The results indicated that the catalytic efficiency, thermostability and halostability were enhanced simultaneously by replacement of Lys48 with Ala (K48A) or Leu (K48L). Comparison of kinetic parameters revealed that catalytic efficiency of mutants is enhanced as a result of the increase in substrate affinity. A great improvement in thermostability and halostability was observed...
October 17, 2016: International Journal of Biological Macromolecules
Meihui Chang, Xiaoyu Chu, Jinzhi Lv, Qingbin Li, Jian Tian, Ningfeng Wu
Pullulanase (EC plays an important role in the specific hydrolysis of branch points in amylopectin. Enhancing its thermostability is required for its industrial application. In this study, rational protein design was used to improve the thermostability of PulB from Bacillus naganoensis (AB231790.1), which has strong enzymatic properties. Three positive single-site mutants (PulB-D328H, PulB-N387D, and PulB-A414P) were selected from six mutants. After incubation at 65°C for 5 min, the residual activities of PulB-D328H, PulB-N387D, and PulB-A414P were 4...
2016: PloS One
Joanna Berlowska, Weronika Cieciura, Sebastian Borowski, Marta Dudkiewicz, Michal Binczarski, Izabela Witonska, Anna Otlewska, Dorota Kregiel
Research into fermentative production of lactic acid from agricultural by-products has recently concentrated on the direct conversion of biomass, whereby pure sugars are replaced with inexpensive feedstock in the process of lactic acid production. In our studies, for the first time, the source of carbon used is sugar beet pulp, generated as a by-product of industrial sugar production. In this paper, we focus on the simultaneous saccharification of lignocellulosic biomass and fermentation of lactic acid, using mixed cultures with complementary assimilation profiles...
October 17, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Hangil Lee, Yeonwoo Kim, Min Ji Kim, Ki-Jeong Kim, Byung-Kwon Kim
In order to compare the catalytic activities of reduced graphene oxide (rGO), graphene oxide (GO), and graphene, we conducted oxidation of 2-aminothiophenol (2-ATP) and reduction of nitrobenzene (NB) in their presence by using high-resolution photoemission spectroscopy (HRPES). In addition, we determined conversion rates of CO to CO2 in the presence of these catalysts by performing a residual gas analyzer (RGA) under a UHV condition, Orange II and methylene blue degradations UV-vis spectrophotometry, and electrochemistry (EC) measurements in an aqueous solution, as well as by obtaining cyclic voltammograms and determining the change of the condition of electrodes before and after the oxidation of 2-ATP...
October 20, 2016: Scientific Reports
Sushant K Sinha, Shubhasish Goswami, Shibashis Das, Supratim Datta
β-glucosidase (EC; BG) cleaves β-glucosidic linkages in disaccharide or glucose-substituted molecules. In an effort towards designing better BGs, we focused on the role of non-conserved residues across an otherwise homologous BG active site tunnel and designed mutants across the aglycone-binding site (V169C) and the gatekeeper residues (I246A) of the active site tunnel. We expressed in Escherichia coli, the Hore_15280 gene encoding a β-glucosidase (BG) in Halothermothrix orenii. The overexpressed and purified wild-type (B8CYA8) has a high specific activity of 345 μmol/min/mg on pNPGlc and a half-life of 1...
October 20, 2016: Applied Microbiology and Biotechnology
Kasper D Tidemand, Hans E M Christensen, Niclas Hoeck, Pernille Harris, Jane Boesen, Günther H Peters
Tryptophan hydroxylase 2 (TPH2) catalyses the initial and rate-limiting step in the biosynthesis of serotonin, which is associated with a variety of disorders such as depression, obsessive compulsive disorder, and schizophrenia. Full-length TPH2 is poorly characterized due to low purification quantities caused by its inherent instability. Three truncated variants of human TPH2 (rch TPH2; regulatory and catalytic domain, NΔ47-rch TPH2; truncation of 47 residues in the N terminus of rch TPH2, and ch TPH2; catalytic domain) were expressed, purified, and examined for changes in transition temperature, inactivation rate, and oligomeric state...
October 2016: FEBS Open Bio
Michael B Lazarus, Rebecca S Levin, Kevan M Shokat
Elongation Factor-2 Kinase (eEF2K) in an unusual mammalian enzyme that has one known substrate, elongation factor-2. It belongs to a class of kinases, called alpha kinases, that has little sequence identity to the >500 conventional protein kinases, but performs the same reaction and has similar catalytic residues. The phosphorylation of eEF2 blocks translation elongation, which is thought to be critical to regulating cellular energy usage. Here we report a system for discovering new substrates of alpha kinases and identify the first new substrates of eEF2K including AMPK and alpha4, and determine a sequence motif for the kinase that shows a requirement for threonine residues as the target of phosphorylation...
October 17, 2016: Cellular Signalling
Andrea Moretti, Jianfeng Li, Stefano Donini, Robert W Sobol, Menico Rizzi, Silvia Garavaglia
The aldehyde dehydrogenase family 1 member A3 (ALDH1A3) catalyzes the oxidation of retinal to the pleiotropic factor retinoic acid using NAD(+). The level of ALDHs enzymatic activity has been used as a cancer stem cell marker and seems to correlate with tumour aggressiveness. Elevated ALDH1A3 expression in mesenchymal glioma stem cells highlights the potential of this isozyme as a prognosis marker and drug target. Here we report the first crystal structure of human ALDH1A3 complexed with NAD(+) and the product all-trans retinoic acid (REA)...
October 19, 2016: Scientific Reports
Yusuke Matsui, Keisuke Shindo, Kayoko Nagata, Noriyoshi Yoshinaga, Kotaro Shirakawa, Masayuki Kobayashi, Akifumi Takaori-Kondo
HIV type 1 overcomes the host restriction factor apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3 (APOBEC3) proteins by organizing an E3 ubiquitin ligase complex together with viral infectivity factor (Vif) and a host transcription cofactor core binding factor β (CBFβ ). CBFβ is essential for Vif to counteract APOBEC3 by enabling the recruitment of cullin 5 to the complex and increasing steady-state level of Vif protein, however, the mechanisms by which CBFβ up-regulates Vif protein remains unclear...
October 7, 2016: Journal of Biological Chemistry
Kelsey S Kalous, Sarah L Wynia-Smith, Michael D Olp, Brian C Smith
The sirtuin family of proteins catalyze the NAD+-dependent deacylation of acyl-lysine residues. Humans encode seven sirtuins (Sirt1-7) and recent studies have suggested that post-translational modification of Sirt1 by cysteine S-nitrosation correlates with increased acetylation of Sirt1 deacetylase substrates. However, the mechanism of Sirt1 inhibition by S-nitrosation was unknown. Here, we show that Sirt1 is transnitrosated and inhibited by the physiologically-relevant nitrosothiol S-nitrosoglutathione (GSNO)...
October 18, 2016: Journal of Biological Chemistry
Liang Dong, Chong Yuan, Benjamin J Orlando, Michael G Malkowski, William L Smith
Prostaglandin endoperoxide H synthase-2 (PGHS-2), also called cyclooxygenase-2 (COX-2), converts arachidonic acid to PGH2. PGHS-2 is a conformational heterodimer comprised of allosteric (Eallo) and catalytic (Ecat) subunits. Fatty acids (FAs) bind to Arg-120 of Eallo increasing to different degrees, depending on the FA, the Vmax of its Ecat partner. We report here that movement of helical residues 120-122 and loop residues 123-129 of Eallo underlie the allosteric effects of FAs and allosteric COX-2 inhibitors including naproxen and flurbiprofen...
October 18, 2016: Journal of Biological Chemistry
Raphael Gasper, Isabelle Effenberger, Piotr Kolesinski, Barbara Terlecka, Eckhard Hofmann, Andreas Schaller
Dirigent proteins impart stereoselectivity to phenoxy radical coupling reactions in plants and thus play an essential role in the biosynthesis of biologically active natural products. This includes the regio- and enantioselective coupling and subsequent cyclization of two coniferyl alcohol radicals to pinoresinol as the committed step of lignan biosynthesis. The reaction is controlled by dirigent proteins which, depending on the species and protein, direct the reaction to either (+)- or (-)-pinoresinol. We present the crystal structure of the (-)-pinoresinol forming Dirigent Protein 6 from Arabidopsis thaliana (AtDIR6) with data to 1...
October 17, 2016: Plant Physiology
Kaleigh Giles, Benjamin Pluvinage, Alisdair B Boraston
The polysaccharide utilization locus in Bacteroides plebeius that confers the ability to catabolize porphyran contains a putative GH50 β-agarase (BACPLE_01683, BpGH50). BpGH50 did not show any clear activity on agarose or on the related algal galactans porphyran and carrageenan. However, the 1.4 Å resolution x-ray crystal structure of BpGH50 confirmed its possession of the core (α/β)8 barrel fold found in GH50 enzymes as well as the structural conservation of the catalytic residues and some substrate binding residues...
October 18, 2016: Proteins
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