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catalytic residue

Lokesh K Narnoliya, Rajender S Sangwan, Sudhir P Singh
Rose-scented geranium (Pelargonium sp.) is widely known as aromatic and medicinal herb, accumulating specialized metabolites of high economic importance, such as essential oils, ascorbic acid, and tartaric acid. Ascorbic acid and tartaric acid are multifunctional metabolites of human value to be used as vital antioxidants and flavor enhancing agents in food products. No information is available related to the structural and functional properties of the enzymes involved in ascorbic acid and tartaric acid biosynthesis in rose-scented geranium...
March 15, 2018: Molecular Biology Reports
Matthias Bochtler, Danuta Mizgalska, Florian Veillard, Magdalena L Nowak, John Houston, Paul Veith, Eric C Reynolds, Jan Potempa
Bacteroidetes feature prominently in the human microbiome, as major colonizers of the gut and clinically relevant pathogens elsewhere. Here, we reveal a new Bacteroidetes specific feature in the otherwise widely conserved Sec/SPI (Sec translocase/signal peptidase I) pathway. In Bacteroidetes , but not the entire FCB group or related phyla, signal peptide cleavage exposes N-terminal glutamine residues in most SPI substrates. Reanalysis of published mass spectrometry data for five Bacteroidetes species shows that the newly exposed glutamines are cyclized to pyroglutamate (also termed 5-oxoproline) residues...
2018: Frontiers in Microbiology
Tomoko Kubori, Tomoe Kitao, Hiroki Ando, Hiroki Nagai
The intracellular bacterial pathogen Legionella pneumophila establishes the replicative niche as a result of the actions of a large array of effector proteins delivered via the Legionella type IV secretion system (T4SS). Many effector proteins are expected to be involved in biogenesis and regulation of the Legionella-containing vacuole (LCV) that is highly decorated with ubiquitin. Here, we identified a Legionella deubiquitinase (DUB), designated LotA, by carrying out a genome analysis to find proteins resembling the eukaryotic ovarian tumor (OTU) superfamily of cysteine proteases...
March 15, 2018: Cellular Microbiology
Je Min Yoo, Baekwon Park, Sang Jin Kim, Yong Seok Choi, Sungmin Park, Eun Hye Jeong, Hyukjin Lee, Byung Hee Hong
Ferrous ion-based catalysts have been widely employed to oxidatively destruct the major industrial pollutants such as phenolic compounds through advanced oxidation processes (AOPs). These agents, however, inevitably show several drawbacks including the need for pH adjustment and further purification steps to remove residual salts. Here we report the use of a chemical vapour deposition (CVD) graphene film as a novel metal-free catalyst for the AOP-based degradation of phenols in aqueous solution, which does not require additional steps for salt removal nor external energy to activate the process...
March 15, 2018: Nanoscale
María E Errasti, Claudia L Natalucci, Néstor O Caffini, Alejandra E Rotelli, Adriana Brullo, Bruno Maras, Sebastián A Trejo, Laura M I López
The primary structure of macrodontain I, a peptidase from Pseudananas macrodontes fruits, was determined using Edman's degradation. The enzyme is a non-glycosylated peptidase composed by 213 amino acids with a calculated molecular weight of 23,486.18 Da, pI value 6.99, and a molar extinction coefficient at 280 nm of 61,685 M-1  cm-1 . The alignment of the sequence of macrodontain I with those cysteine peptidases from species belonging to the family Bromeliaceae showed the highest identity degree (87.74%) against fruit bromelain...
March 15, 2018: Applied Biochemistry and Biotechnology
Masami Lintuluoto, Juha Mikael Lintuluoto
The inter- and intra-electron and proton transfers in the nitrite reduction of copper-containing nitrite reductase (CuNiR) were investigated by using the QM/MM method with the calculational models containing type 1 (T1) and type 2 (T2) Cu sites. The electron transfer from the outer electron donor protein to the T1 Cu site occurred both before and after nitrite binding, and nitrite binding lowered the reduction potential of the Cu T1 site. The protonation of catalytic His244 subsequent to nitrite binding and T1 Cu reduction induced partial intra-electron transfer from T1 to T2 Cu sites...
March 15, 2018: Metallomics: Integrated Biometal Science
Cody Caba, Hyder Ali Khan, Janeen Auld, Ryo Ushioda, Kazutaka Araki, Kazuhiro Nagata, Bulent Mutus
Despite its study since the 1960's, very little is known about the post-translational regulation of the multiple catalytic activities performed by protein disulfide isomerase (PDI), the primary protein folding catalyst of the cell. This work identifies a functional role for the highly conserved CxxC-flanking residues Lys57 and Lys401 of human PDI in vitro . Mutagenesis studies have revealed these residues as modulating the oxidoreductase activity of PDI in a pH-dependent manner. Non-conservative amino acid substitutions resulted in enzyme variants upwards of 7-fold less efficient...
2018: Frontiers in Molecular Biosciences
Michael V Fiandalo, John J Stocking, Elena A Pop, John H Wilton, Krystin M Mantione, Yun Li, Kristopher M Attwood, Gissou Azabdaftari, Yue Wu, David S Watt, Elizabeth M Wilson, James L Mohler
Androgen deprivation therapy (ADT) is palliative and prostate cancer (CaP) recurs as lethal castration-recurrent/resistant CaP (CRPC). One mechanism that provides CaP resistance to ADT is primary backdoor androgen metabolism, which uses up to four 3α-oxidoreductases to convert 5α-androstane-3α,17β-diol (DIOL) to dihydrotestosterone (DHT). The goal was to determine whether inhibition of 3α-oxidoreductase activity decreased conversion of DIOL to DHT. Protein sequence analysis showed that the four 3α-oxidoreductases have identical catalytic amino acid residues...
February 16, 2018: Oncotarget
Prem Prakash, Narayan S Punekar, Prasenjit Bhaumik
Glutamate dehydrogenase (GDH) is a key enzyme connecting carbon and nitrogen metabolism in all living organisms. Despite extensive studies on GDHs from both prokaryotic and eukaryotic organisms in the last 40 years, the structural basis of the catalytic features of this enzyme remains incomplete. This study reports the structural basis of the GDH catalytic mechanism and allosteric behavior. We determined the first high-resolution crystal structures of glutamate dehydrogenase from the fungus Aspergillus niger (AnGDH), a unique NADP+ -dependent allosteric enzyme that is forward inhibited by the formation of mixed disulfide...
March 14, 2018: Journal of Biological Chemistry
Huanchen Wang, Chunfang Gu, Ronda J Rolfes, Henning J Jessen, Stephen B Shears
Inositol pyrophosphates (PP-InsPs) are 'energetic' intracellular signals that are ubiquitous in animals, plant and fungi; structural and biochemical characterization of PP-InsP metabolic enzymes provides insight into their evolution, reaction mechanisms, and regulation. Here, we describe the 2.35 Å resolution structure of the catalytic core of Siw14, a 5-PP-InsP phosphatase from Saccharomyces cerevisiae, and a member of the protein tyrosinephosphatase (PTP) superfamily. Conclusions that we derive from structural data are supported by extensive site-directed mutagenesis and kinetic analyses, thereby attributing new functional significance to several key residues...
March 14, 2018: Journal of Biological Chemistry
Thomas Germe, Judit Vörös, Frederic Jeannot, Thomas Taillier, Robert A Stavenger, Eric Bacqué, Anthony Maxwell, Benjamin D Bax
Imidazopyrazinones (IPYs) are a new class of compounds that target bacterial topoisomerases as a basis for their antibacterial activity. We have characterized the mechanism of these compounds through structural/mechanistic studies showing they bind and stabilize a cleavage complex between DNA gyrase and DNA ('poisoning') in an analogous fashion to fluoroquinolones, but without the requirement for the water-metal-ion bridge. Biochemical experiments and structural studies of cleavage complexes of IPYs compared with an uncleaved gyrase-DNA complex, reveal conformational transitions coupled to DNA cleavage at the DNA gate...
March 10, 2018: Nucleic Acids Research
Xinxing Zhang, Yuting Wang, David H Perez, Rachel A Jones Lipinski, Rebecca A Butcher
Caenorhabditis elegans produces a complex mixture of ascaroside pheromones to control its development and behavior. Acyl-CoA oxidases, which participate in β-oxidation cycles that shorten the side chains of the ascarosides, regulate the mixture of pheromones produced. Here, we use CRISPR-Cas9 to make specific nonsense and missense mutations in acox genes and determine the effect of these mutations on ascaroside production in vivo. Ascaroside production in acox-1.1 deletion and nonsense strains, as well as a strain with a missense mutation in a catalytic residue, confirms the central importance of ACOX-1...
March 14, 2018: ACS Chemical Biology
Mengzhu Li, Hong Deng, Rui Ma, Huiying Luo, Bin Yao, Xiaoyun Su
Pyranose oxidase (POx) is a homotetrameric flavoprotein that catalyzes the oxidation of pyranose-configured sugars at position C-2 to corresponding 2-ketoaldoses. The wide substrate specificity makes POx potential for application in various biotechnological industries. In the present study we reported the gene cloning and heterologous expression of a POx from the basidiomycete Trametes sp. and functionally expressed the gene in Escherichia coli BL21(DE3). Based on sequence alignment, three residues were chosen for site-directed mutagenesis to obtain two single mutants (K312E and E539K) and two double mutants (T166A/E539K and K312E/E539K)...
March 13, 2018: AMB Express
Palika Abayakoon, James P Lingford, Yi Jin, Christopher Bengt, Gideon J Davies, Shenggen Yao, Ethan D Goddard-Borger, Spencer J Williams
Bacterial sulfoglycolytic pathways catabolise sulfoquinovose (SQ), or glycosides thereof, to generate a three-carbon metabolite for primary cellular metabolism and a three-carbon sulfonate that is expelled from the cell. Sulfoglycolytic operons encoding an Embden-Meyerhof-Parnas (EMP)-like or Entner-Doudoroff (ED)-like pathway harbour an uncharacterized gene ( yihR in Escherichia coli ; PpSQ1_00415 in Pseudomonas putida ) that is upregulated in the presence of SQ and has been annotated as an aldose-1-epimerase and which may encode an SQ mutarotase...
March 13, 2018: Biochemical Journal
Nazan Kaloğlu, İsmail Özdemir, Nevin Gürbüz, Hakan Arslan, Pierre H Dixneuf
A series of new benzimidazolium halides were synthesized in good yields as unsymmetrical N -heterocyclic carbene (NHC) precursors containing the N-CH₂-arene group. The benzimidazolium halides were readily converted into ruthenium(II)-NHC complexes with the general formula [RuCl₂(η⁶,η¹-arene-CH₂-NHC)]. The structures of all new compounds were characterized by ¹H NMR (Nuclear Magnetic Resonance),13 C NMR, FT-IR (Fourier Transform Infrared) spectroscopy and elemental analysis techniques. The single crystal structure of one benzimidazole ruthenium complex, 2b , was determined...
March 13, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Adejoke N Kolawole, Valentine T Akinladejo, Olusola O Elekofehinti, Afolabi C Akinmoladun, Ayodele O Kolawole
Aldehyde dehydrogenases (ALDHs) are a diverse family of enzymes that catalyze the NAD(P)+ -dependent detoxification of toxic aldehyde compounds. ALDHs are also involved in non-enzymatic ligand binding to endobiotics and xenobiotics. Here, the enzyme crucial non-canonical and non-catalytic interaction with kolaflavanone, a component of kolaviron, and a major bioflavonoid isolated from Garcinia kola (Bitter kola) was characterized by various spectroscopic and in silico approaches under stimulated physiological condition...
February 27, 2018: Bioorganic Chemistry
Shui Liu, Yonglin Zhou, Xiaodi Niu, Tingting Wang, Jiyun Li, Zhongjie Liu, Jianfeng Wang, Shusheng Tang, Yang Wang, Xuming Deng
The emergence of plasmid-mediated New Delhi metallo-β-lactamase-1 (NDM-1) in carbapenem-resistant Gram-negative pathogens is an increasing clinical threat. Here we report the discovery of an NDM-1 inhibitor, magnolol, through enzyme inhibition screening. We showed that magnolol significantly inhibited NDM enzyme activity (IC50  = 6.47 µg/mL), and it restored the activity of meropenem against Escherichia coli ZC-YN3, an NDM-1-producing E. coli isolate, in in vitro antibacterial activity assays. Magnolol lacked direct antibacterial activity, but compared with meropenem alone, it reduced the MICs of meropenem against E...
December 2018: Cell Death Discovery
Alicia Del Prado, Elsa Franco-Echevarría, Beatriz González, Luis Blanco, Margarita Salas, Miguel de Vega
Most replicative DNA polymerases (DNAPs) are endowed with a 3'-5' exonuclease activity to proofread the polymerization errors, governed by four universally conserved aspartate residues belonging to the Exo I, Exo II, and Exo III motifs. These residues coordinate the two metal ions responsible for the hydrolysis of the last phosphodiester bond of the primer strand. Structural alignment of the conserved exonuclease domain of DNAPs from families A, B, and C has allowed us to identify an additional and invariant aspartate, located between motifs Exo II and Exo III...
March 12, 2018: Proceedings of the National Academy of Sciences of the United States of America
Haotian Lei, Bruce E Bowler
Structural studies of yeast iso-1-cytochrome c (L.J. McClelland, T.-C. Mou, M.E. Jeakins-Cooley, S.R. Sprang, B.E. Bowler, Proc. Natl. Acad. Sci. U.S.A. 111 (2014) 6648-6653) show that modest movement of Ω-loop D (residues 70-85, average RMSD versus the native structure: 0.81 Å) permits loss of Met80-heme ligation creating an available coordination site to catalyze the peroxidase activity mediated by cytochrome c early in apoptosis. However, Ala81 and Gly83 move significantly (RMSDs of 2.18 and 1.26 Å, respectively)...
February 27, 2018: Journal of Inorganic Biochemistry
Manish Kesherwani, Devadasan Velmurugan
Undecaprenyl phosphate (C55-P) acts as carrier lipid in the synthesis of peptidoglycan, which is de novo synthesized from dephosphorylation of undecaprenyl pyrophosphate (C55-PP). The phosphatidylglycerol phosphate phosphatase B (PgpB) catalyzes the dephosphorylation of C55-PP and forms C55-P. As no structural study has been made regarding the binding of C55-PP to PgpB, in the current study, in silico molecular docking, followed by 150 ns molecular dynamics simulation of the putative binding complex in membrane/solvent environment has been performed to understand conformational dynamics...
March 12, 2018: Journal of Biomolecular Structure & Dynamics
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