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catalytic residue

Adriana Patarroyo Vargas, Yaremis Meriño Cabrera, José Cola Zanuncio, Francelina Rocha, Wellington Garcia Campos, Maria Goreti de Almeida Oliveira
The kinetics of Anticarsia gemmatalis Hübner gut serine proteases with tripeptidyl substrates, and the enzymatic inhibition model using synthetic peptides Gor 3, Gor 4, and Gor 5 are described. The enzymes were purified on p-aminobenzamidine agarose affinity column in an FPLC system using electrophoresis with 12.5% polyacrylamide gel. Michaelis-Menten constants and the inhibition model were determined according to the Dixon methodology and Lineweaver-Burk's double reciprocal. The KM values and catalytic constants of peptide substrates show that A...
September 17, 2017: Protein and Peptide Letters
Chen Song, Leyu Wang, Genlan Ye, Xiaoping Song, Yutong He, Xiaozhong Qiu
Ammonium persulfate (APS), a low molecular weight chemical compound with strong oxidizing properties, should to be totally removed during preparation of nanomaterials due to its cytotoxicity. APS exerts its oxidative stress effects mainly on cell membrane, but its intracellular influence remains unclear. Here, we designed a facile negatively-charged carboxylic gelatin-methyacrylate (carbox-GelMA) nanoparticle (NP) as a cargo-carrier through the catalytic and oxidizing action of APS in W/O system. The formed APS-loaded carbox-GelMA NPs (APS/NPs) were transported into the lysosome in MCF-7 breast cancer cells...
September 18, 2017: Scientific Reports
Ricardo A Zamora, Felipe Gonzalez-Órdenes, Victor Castro-Fernández, Victoria Guixé
The genome of Methanosarcinales organisms presents both ADP-dependent glucokinase and phosphofructokinase genes. However, Methanococcoides burtonii has a truncate glucokinase gene with a large deletion at the C-terminal, where the catalytic GXGD motif is located. Characterization of its phosphofructokinase annotated protein shows that is a bifunctional enzyme able to supply the absence of the glucokinase activity. Moreover, kinetic analyses of the phosphofructokinase annotated enzyme from, Methanohalobium evestigatum demonstrated that this enzyme is also bifunctional...
September 14, 2017: Archives of Biochemistry and Biophysics
Martin Culka, Simona G Huwiler, Matthias Boll, G Matthias Ullmann
Aromatic compounds are environmental pollutants with toxic and carcinogenic properties. Despite the stability of aromatic rings, bacteria are able to degrade the aromatic compounds into simple metabolites and use them as growth substrates under oxic or even under anoxic conditions. In anaerobic microorganisms, most monocyclic aromatic growth substrates are converted to the central intermediate benzoyl-coenzyme A, which is enzymatically reduced to cyclohexa-1,5-dienoyl-CoA. The strcitly anaerobic bacterium \textit{Geobacter metallireducens} uses the class II benzoyl-CoA reductase complex for this reaction...
September 18, 2017: Journal of the American Chemical Society
Giorgio Giardina, Alessandro Paiardini, Riccardo Montioli, Barbara Cellini, Carla Borri Voltattorni, Francesca Cutruzzolà
The alanine:glyoxylate aminotransferase (AGT), a hepatocyte-specific pyridoxal-5'-phosphate (PLP) dependent enzyme, transaminates L-alanine and glyoxylate to glycine and pyruvate, thus detoxifying glyoxylate and preventing pathological oxalate precipitation in tissues. In the widely accepted catalytic mechanism of the aminotransferase family, the lysine binding to PLP acts as a catalyst in the stepwise 1,3-proton transfer, interconverting the external aldimine to ketimine. This step requires protonation by a conserved aspartate of the pyridine nitrogen of PLP to enhance its ability to stabilize the carbanionic intermediate...
September 15, 2017: Scientific Reports
Raman G Kutty, Marat R Talipov, Robert D Bongard, Rachel A Jones Lipinski, Noreena L Sweeney, Daniel S Sem, Rajendra Rathore, Ramani Ramchandran
The mammalian genome contains approximately 200 phosphatases that are responsible for catalytically removing phosphate groups from proteins. In this review, we discuss dual specificity phosphatase 5 (DUSP5). DUSP5 belongs to the dual specificity phosphatase (DUSP) family, so named after the family members' abilities to remove phosphate groups from serine/threonine and tyrosine residues. We provide a comparison of DUSP5's structure to other DUSPs and, using molecular modeling studies, provide an explanation for DUSP5's mechanistic interaction and specificity toward phospho-extracellular regulated kinase, its only known substrate...
September 12, 2017: Comprehensive Physiology
Stefan Kunz, Vreni Balmer, Geert Jan Sterk, Michael P Pollastri, Rob Leurs, Norbert Müller, Andrew Hemphill, Cornelia Spycher
BACKGROUND: Giardiasis is an intestinal infection correlated with poverty and poor drinking water quality, and treatment options are limited. According to the Center for Disease Control and Prevention, Giardia infections afflict nearly 33% of people in developing countries, and 2% of the adult population in the developed world. This study describes the single cyclic nucleotide-specific phosphodiesterase (PDE) of G. lamblia and assesses PDE inhibitors as a new generation of anti-giardial drugs...
September 15, 2017: PLoS Neglected Tropical Diseases
Benjamin R Lichman, Altin Sula, Thomas Pesnot, Helen C Hailes, John Ward, Nicholas H Keep
Norcoclaurine synthase (NCS) is a Pictet-Spenglerase that catalyzes the first key step in plant benzylisoquinoline alkaloid metabolism, a compound family that includes bioactive natural products such as morphine. The enzyme has also shown great potential as a biocata-lyst for the formation of chiral isoquinolines. Here we present new high-resolution X-ray crystallography data describing Thalictrum flavum NCS bound to a mechanism inspired ligand. The structure supports two key features of the NCS 'dopamine-first' mechanism: the binding of dopamine catechol to Lys-122 and the position of the carbonyl substrate binding site at the active site entrance...
September 15, 2017: Biochemistry
Justin M Bradley, Dimitri A Svistunenko, Geoffrey R Moore, Nick E Le Brun
Ferritins are 24meric proteins that overcome problems of toxicity, insolubility and poor bioavailability of iron in all types of cells by storing it in the form of a ferric mineral within their central cavities. In the bacterioferritin (BFR) from Escherichia coli iron mineralization kinetics have been shown to be dependent on an intra-subunit catalytic diiron cofactor site (the ferroxidase centre), three closely located aromatic residues and an inner surface iron site. One of the aromatic residues, Tyr25, is the site of formation of a transient radical, but the roles of the other two residues, Tyr58 and Trp133, are unknown...
September 15, 2017: Metallomics: Integrated Biometal Science
Cristina Oliva, Pedro A Sánchez-Murcia, Eva Rico, Ana Bravo, Margarita Menéndez, Federico Gago, Antonio Jiménez-Ruiz
Mitochondrial endonuclease G from Leishmania infantum (LiEndoG) participates in the degradation of double-stranded DNA (dsDNA) during parasite cell death and is catalytically inactive at a pH of 8.0 or above. The presence, in the primary sequence, of an acidic amino acid-rich insertion exclusive to trypanosomatids and its spatial position in a homology-built model of LiEndoG led us to postulate that this peptide stretch might act as a pH sensor for self-inhibition. We found that a LiEndoG variant lacking residues 145-180 is indeed far more active than its wild-type counterpart at pH values >7...
September 6, 2017: Nucleic Acids Research
Aiswarya Krishnamohan, Jane E Jackman
The tRNA m1G9 methyltransferase (Trm10) is a member of the SpoU-TrmD (SPOUT) superfamily of methyltransferases, and Trm10 homologs are widely conserved throughout Eukarya and Archaea. Despite possessing the trefoil knot characteristic of SPOUT enzymes, Trm10 does not share the same quaternary structure or key sequences with other members of the SPOUT family, suggesting a novel mechanism of catalysis. To investigate the mechanism of m1G9 methylation by Trm10, we performed a biochemical and kinetic analysis of Trm10 and variants with alterations in highly conserved residues, using crystal structures solved in the absence of tRNA as a guide...
September 6, 2017: Nucleic Acids Research
Andrea F Moon, John M Pryor, Dale A Ramsden, Thomas A Kunkel, Katarzyna Bebenek, Lars C Pedersen
While most DNA polymerases discriminate against ribonucleotide triphosphate (rNTP) incorporation very effectively, the Family X member DNA polymerase μ (Pol μ) incorporates rNTPs almost as efficiently as deoxyribonucleotides. To gain insight into how this occurs, here we have used X-ray crystallography to describe the structures of pre- and post-catalytic complexes of Pol μ with a ribonucleotide bound at the active site. These structures reveal that Pol μ binds and incorporates a rNTP with normal active site geometry and no distortion of the DNA substrate or nucleotide...
September 6, 2017: Nucleic Acids Research
Fernanda Mendoza, José M Lluch, Laura Masgrau
Glycosyltransferases are enzymes that catalyze a monosaccharide transfer reaction from a donor to an acceptor substrate with the synthesis of a new glycosidic bond. They are highly substrate specific and regioselective, even though the acceptor substrate often presents multiple reactive groups. Currently, many efforts are dedicated to the development of biocatalysts for glycan synthesis and, therefore, a better understanding of how natural enzymes achieve this goal can be of valuable help. To gain a deeper insight into the catalytic strategies used by retaining glycosyltransferases, the wild type EXTL2 (CAZy family GT64) and four mutant forms (at positions 293 and 246) were studied using QM(DFT)/MM calculations and molecular dynamics simulations...
September 14, 2017: Organic & Biomolecular Chemistry
Jindal Garima, Arieh Warshel
Understanding the origin of the catalytic power of enzymes has both conceptual and practical importance. One of the most important finding from computational studies of enzyme catalysis is that a major part of the catalytic power is due to the preorganization of the enzyme active site. Unfortunately, misunderstanding of the non trivial preorganization idea lead some (e.g. Ref (1) ) to assume that it does not consider the effect of the protein residues. This major confusion reflects a misunderstanding of the statement that the interaction energy of the enzyme group and the transition state is similar to the corresponding interaction between the water molecules and the TS, and that the catalysis is due to the reorganization free energy of the water molecules...
September 14, 2017: Proteins
Toshihiko Kitajima, Yuanling Jia, Akiko Komatsuzaki, Juan Cui, Fumiko Matsuzawa, Sei-Ichi Aikawa, Xiao-Dong Gao, Yasunori Chiba
Endo-β-N-acetylglucosaminidase from the methylotrophic yeast Ogataea minuta (Endo-Om) is a glycoside hydrolase family 85 enzyme that has dual catalytic activity in the hydrolysis and transglycosylation of complex N-glycans, in common with the enzymes from the eukaryotic species. In this study, we have conducted mutagenesis of Endo-Om at Trp295, to determine the effect on hydrolytic activity. Structural modeling predicted that Trp295 forms an important interaction with the α-1,3-linked mannose residue of the trimannosyl N-glycan core, rather than being directly involved in catalytic activity...
September 11, 2017: Journal of Bioscience and Bioengineering
Camilla Camerino Santana, Leandro A Barbosa, Irinaldo Diniz Basílio Júnior, Ticiano Gomes do Nascimento, Camila Braga Dornelas, Luciano A M Grillo
Lipases have key roles in insect lipid acquisition, storage, and mobilization and are also fundamental to many physiological processes in insects. Lipids are an important component of insect diets, where they are hydrolyzed in the midgut lumen, absorbed, and used for the synthesis of complex lipids. The South American palm weevil Rhynchophorus palmarum is one of the most important pests on commercial palm plantations. However, there are few studies about lipid digestion for this insect. In this work, we have described the biochemical characterization of the lipase activity in the posterior midgut of the R...
September 13, 2017: Insects
Riddhi Desai, Kunmo Kim, Hanna C Buechsenschuetz Allan W Chen, Yumin Bi, Mitchell R Mann, Matthew A Turk, Christina Z Chung, Ilka U Heinemann
tRNA(His) guanylyltransferase (Thg1) has unique reverse (3'-5') polymerase activity occurring in all three domains of life. Most eukaryotic Thg1 homologs are essential genes involved in tRNA(His) maturation. These enzymes normally catalyze a single 5' guanylation of tRNA(His) lacking the essential G(-1) identity element required for aminoacylation. Recent studies suggest that archaeal type Thg1, which includes most archaeal and bacterial Thg1 enzymes is phylogenetically distant from eukaryotic Thg1. Thg1 is evolutionarily related to canonical 5'-3' forward polymerases but catalyzes reverse 3'-5'polymerization...
September 13, 2017: RNA Biology
Dima A Sabbah, Bayan Hishmah, Kamal Sweidan, Sanaa Bardaweel, Murad AlDamen, Haizhen A Zhong, Reema Abu Khalaf, Ameerah Hasan Ibrahim, Tariq Al-Qirim, Ghassan Abu Sheikha, Mohammad S Mubarak
BACKGROUND: Oncogenic potential of phosphatidylinositol 3-kinase (PI3Kα) has been highlighted as a therapeutic target for anticancer drug design. OBJECTIVE: Target compounds were designed to address the effect of different substitution patterns at the N atom of the carboxamide moiety on the bioactivity of this series. METHODS: Synthesis of the targeted compounds, crystallography, biological evaluation tests against human colon carcinoma (HCT-116), and Glide docking studies...
September 11, 2017: Anti-cancer Agents in Medicinal Chemistry
Grey S Chen, Siang Wun Siao, Claire R Shen
Iterative ketoacid elongation has been an essential tool in engineering artificial metabolism, in particular the synthetic alcohols. However, precise control of product specificity is still greatly challenged by the substrate promiscuity of the ketoacid decarboxylase, which unselectively hijacks ketoacid intermediates from the elongation cycle along with the target ketoacid. In this work, preferential tuning of the Lactococcus lactis ketoisovalerate decarboxylase (Kivd) specificity toward 1-pentanol synthesis was achieved via saturated mutagenesis of the key residue V461 followed by screening of the resulting alcohol spectrum...
September 12, 2017: Scientific Reports
Henrik Hansson, Saeid Karkehabadi, Nils Mikkelsen, Nicholai R Douglas, Steve Kim, Anna Lam, Thijs Kaper, Brad Kelemen, Katlyn K Meier, Stephen M Jones, Edward I Solomon, Mats Sandgren
For decades, the enzymes of the fungus Hypocrea jecorina have served as a model system for the breakdown of cellulose. Three-dimensional structures for almost all H. jecorina cellulose-degrading enzymes are available, except for HjLPMO9A, belonging to the AA9 family of lytic polysaccharide monooxygenases (LPMOs). These enzymes enhance the hydrolytic activity of cellulases and are essential for cost-efficient conversion of lignocellulosic biomass. Here, using structural and spectroscopic analyses, we found that native HjLPMO9A contains a catalytic domain and a family-1 carbohydrate-binding module (CBM1) connected via a linker sequence...
September 12, 2017: Journal of Biological Chemistry
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