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https://www.readbyqxmd.com/read/28448853/a-cluster-of-aspartic-residues-in-the-extracellular-loop-ii-of-par-4-is-important-for-thrombin-interaction-and-activation-of-platelets
#1
Daniel Sánchez Centellas, Sushanth Gudlur, Alejandro Vicente-Carrillo, Sofia Ramström, Tomas L Lindahl
Thrombin activates platelets via proteolytic cleavage of protease-activated receptors (PARs) 1 and 4. The two PARs have distinct but complementary roles. The mechanisms responsible for PAR1 activation by thrombin have been extensively studied. However, much less is known regarding thrombin activation of PAR4, especially the potential involvement of regions of PAR4 other than the N-terminal, which is bound to the catalytic site of thrombin. We have studied PAR4 in S. cerevisiae strain MMY12, an expression system in which the GPCR receptors are connected to a Lac Z reporter gene resulting in increased β-galactosidase activity...
April 13, 2017: Thrombosis Research
https://www.readbyqxmd.com/read/28448625/structural-and-functional-studies-of-ferredoxin-and-oxygenase-components-of-3-nitrotoluene-dioxygenase-from-diaphorobacter-sp-strain-ds2
#2
Archana Kumari, Deepak Singh, S Ramaswamy, Gurunath Ramanathan
3-nitrotoluene dioxygenase (3NTDO) from Diaphorobacter sp. strain DS2 catalyses the conversion of 3-nitrotoluene (3NT) into a mixture of 3- and 4-methylcatechols with release of nitrite. We report here, X-ray crystal structures of oxygenase and ferredoxin components of 3NTDO at 2.9 Å and 2.4 Å, respectively. The residues responsible for nitrite release in 3NTDO were further probed by four single and two double mutations in the catalytic site of α-subunit of the dioxygenase. Modification of Val 350 to Phe, Ile 204 to Ala, and Asn258 to Val by site directed mutagenesis resulted in inactive enzymes revealing the importance of these residues in catalysis...
2017: PloS One
https://www.readbyqxmd.com/read/28446708/structural-and-functional-analysis-of-oceanobacillus-iheyensis-macrodomain-reveals-a-network-of-waters-involved-in-substrate-binding-and-catalysis
#3
Rubén Zapata-Pérez, Fernando Gil-Ortiz, Ana Belén Martínez-Moñino, Antonio Ginés García-Saura, Jordi Juanhuix, Álvaro Sánchez-Ferrer
Macrodomains are ubiquitous conserved domains that bind or transform ADP-ribose (ADPr) metabolites. In humans, they are involved in transcription, X-chromosome inactivation, neurodegeneration and modulating PARP1 signalling, making them potential targets for therapeutic agents. Unfortunately, some aspects related to the substrate binding and catalysis of MacroD-like macrodomains still remain unclear, since mutation of the proposed catalytic aspartate does not completely abolish enzyme activity. Here, we present a functional and structural characterization of a macrodomain from the extremely halotolerant and alkaliphilic bacterium Oceanobacillus iheyensis (OiMacroD), related to hMacroD1/hMacroD2, shedding light on substrate binding and catalysis...
April 2017: Open Biology
https://www.readbyqxmd.com/read/28445031/importance-of-loop-l1-dynamics-for-substrate-capture-and-catalysis-in-pseudomonas-aeruginosa-d-arginine-dehydrogenase
#4
Daniel Ouedraogo, Michael Souffrant, Sheena Vasquez, Donald Hamelberg, Giovanni Gadda
Mobile loops located at the active site entrance in enzymes often participate in conformational changes required to shield the reaction from bulk solvent, to control substrate access to the active site, and to position residues for substrate binding and catalysis. In D-arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) previous crystallographic data suggested that residues 45-47 in the FAD-binding domain and 50-56 in the substrate-binding domain in loop L1 could adopt two distinct conformations. In this study, we have used molecular dynamics, kinetics, and fluorescence spectroscopy on the S45A and A46G enzyme variants of PaDADH to investigate the impact of mutations of loop L1 on the catalytic function of the enzyme...
April 26, 2017: Biochemistry
https://www.readbyqxmd.com/read/28442603/aspergillus-fumigatus-trehalose-regulatory-subunit-homolog-moonlights-to-mediate-cell-wall-homeostasis-through-modulation-of-chitin-synthase-activity
#5
Arsa Thammahong, Alayna K Caffrey-Card, Sourabh Dhingra, Joshua J Obar, Robert A Cramer
Trehalose biosynthesis is found in fungi but not humans. Proteins involved in trehalose biosynthesis are essential for fungal pathogen virulence in humans and plants through multiple mechanisms. Loss of canonical trehalose biosynthesis genes in the human pathogen Aspergillus fumigatus significantly alters cell wall structure and integrity, though the mechanistic link between these virulence-associated pathways remains enigmatic. Here we characterize genes, called tslA and tslB, which encode proteins that contain domains similar to those corresponding to trehalose-6-phosphate phosphatase but lack critical catalytic residues for phosphatase activity...
April 25, 2017: MBio
https://www.readbyqxmd.com/read/28438599/newly-identified-invertebrate-type-lysozyme-splys-i-in-mud-crab-scylla-paramamosain-exhibiting-muramidase-deficient-antimicrobial-activity
#6
Jian Zhou, Shu Zhao, Wen-Hong Fang, Jun-Fang Zhou, Jing-Xiao Zhang, Hongyu Ma, Jiang-Feng Lan, Xin-Cang Li
Lysozymes are widely distributed immune effectors exerting muramidase activity against the peptidoglycan of the bacterial cell wall to trigger cell lysis. However, some invertebrate-type (i-type) lysozymes deficient of muramidase activity still exhibit antimicrobial activity. To date, the mechanism underlying the antimicrobial effect of muramidase-deficient i-type lysozymes remains unclear. Accordingly, this study characterized a novel i-type lysozyme, Splys-i, in the mud crab Scylla paramamosain. Splys-i shared the highest identity with the Litopenaeus vannamei i-type lysozyme (Lvlys-i2, 54% identity) at the amino acid level...
April 21, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28435869/a-dynamic-hydrophobic-core-orchestrates-allostery-in-protein-kinases
#7
Jonggul Kim, Lalima G Ahuja, Fa-An Chao, Youlin Xia, Christopher L McClendon, Alexandr P Kornev, Susan S Taylor, Gianluigi Veglia
Eukaryotic protein kinases (EPKs) constitute a class of allosteric switches that mediate a myriad of signaling events. It has been postulated that EPKs' active and inactive states depend on the structural architecture of their hydrophobic cores, organized around two highly conserved spines: C-spine and R-spine. How the spines orchestrate the transition of the enzyme between catalytically uncommitted and committed states remains elusive. Using relaxation dispersion nuclear magnetic resonance spectroscopy, we found that the hydrophobic core of the catalytic subunit of protein kinase A, a prototypical and ubiquitous EPK, moves synchronously to poise the C subunit for catalysis in response to binding adenosine 5'-triphosphate...
April 2017: Science Advances
https://www.readbyqxmd.com/read/28434716/a-bioinformatics-analysis-of-3400-lytic-polysaccharide-oxidases-from-family-aa9
#8
Nicolas Lenfant, Matthieu Hainaut, Nicolas Terrapon, Elodie Drula, Vincent Lombard, Bernard Henrissat
Lytic polysaccharide monooxygenases of family AA9 catalyze the oxidative cleavage of glycosidic bonds in cellulose and related polysaccharides. The N-terminal half of AA9 LPMOs displays a huge sequence variability that is in contradiction with the substrate simplicity so far observed for these enzymes. To understand the cause of the high multigenicity that prevails in the family, we have performed a clustering analysis of the N-terminal region of 3400 sequences of family AA9 LPMOs, and have evaluated the coincidence of the clusters with distal visible features that may accompany functional differences...
April 13, 2017: Carbohydrate Research
https://www.readbyqxmd.com/read/28433636/malassezia-globosa-mgmdl2-lipase-crystal-structure-and-rational-modification-of-substrate-specificity
#9
Dongming Lan, Huan Xu, JinXin Xu, Grzegorz Dubin, Jinsong Liu, Yonghua Wang
Lipases play an important role in physiological metabolism and diseases, and also have multiple industrial applications. Rational modification of lipase specificity may increase the commercial utility of this group of enzymes, but is hindered by insufficient mechanistic understanding. Here, we report the 2.0 Å resolution crystal structure of a mono- and di-acylglycerols lipase from Malassezia globosa (MgMDL2). Interestingly, residues Phe278 and Glu282 were found to involve in substrate recognition because mutation on each residue led to convert MgMDL2 to a triacylglycerol (TAG) lipase...
April 19, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28432345/distant-phe345-mutation-compromises-the-stability-and-activity-of-mycobacterium-tuberculosis-isocitrate-lyase-by-modulating-its-structural-flexibility
#10
Harish Shukla, Rohit Shukla, Amit Sonkar, Tripti Pandey, Timir Tripathi
Isocitrate lyase (ICL), a potential anti-tubercular drug target, catalyzes the first step of the glyoxylate shunt. In the present investigation, we studied the conformational flexibility of MtbICL to better understand its stability and catalytic activity. Our biochemical results showed that a point mutation at Phe345, which is topologically distant (>10 Å) to the active site signature sequence ((189)KKCGH(193)), completely abolishes the activity of the enzyme. In depth computational analyses were carried out for understanding the structural alterations using molecular dynamics, time-dependent secondary structure and principal component analysis...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28430099/mutual-interaction-enables-the-mycobacterial-plasmid-pal5000-origin-binding-protein-repb-to-recruit-repa-the-plasmid-replicase-to-the-origin
#11
Soniya Chatterjee, Madhu Manti Patra, Sourabh Samaddar, Arnab Basu, Sujoy K Das Gupta
The Mycobacterium fortuitum plasmid, pAL5000, is the most-studied member of a family of plasmids that are found in Actinobacteria. Its replication is brought about by the combined action of two plasmid-encoded replication proteins, RepA and RepB. RepB has earlier been shown to be a sigma factor homologue that possesses origin-binding activity. The mechanism by which RepA functions, and its relationship with RepB, if any, has not been explored yet. In this study, we show that RepA shares a common catalytic domain, with proteins belonging to the primase-polymerase and DNA polymerase X families...
April 22, 2017: Microbiology
https://www.readbyqxmd.com/read/28428565/small-methyltransferase-rlmh-assembles-a-composite-active-site-to-methylate-a-ribosomal-pseudouridine
#12
Cha San Koh, Rohini Madireddy, Timothy J Beane, Phillip D Zamore, Andrei A Korostelev
Eubacterial ribosomal large-subunit methyltransferase H (RlmH) methylates 23S ribosomal RNA pseudouridine 1915 (Ψ1915), which lies near the ribosomal decoding center. The smallest member of the SPOUT superfamily of methyltransferases, RlmH lacks the RNA recognition domain found in larger methyltransferases. The catalytic mechanism of RlmH enzyme is unknown. Here, we describe the structures of RlmH bound to S-adenosyl-methionine (SAM) and the methyltransferase inhibitor sinefungin. Our structural and biochemical studies reveal catalytically essential residues in the dimer-mediated asymmetrical active site...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28426203/tyrosine-kinase-activation-and-conformational-flexibility-lessons-from-src-family-tyrosine-kinases
#13
Yilin Meng, Matthew P Pond, Benoît Roux
Protein kinases are enzymes that catalyze the covalent transfer of the γ-phosphate of an adenosine triphosphate (ATP) molecule onto a tyrosine, serine, threonine, or histidine residue in the substrate and thus send a chemical signal to networks of downstream proteins. They are important cellular signaling enzymes that regulate cell growth, proliferation, metabolism, differentiation, and migration. Unregulated protein kinase activity is often associated with a wide range of diseases, therefore making protein kinases major therapeutic targets...
April 20, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28426139/engineering-a-promiscuous-tautomerase-into-a-more-efficient-aldolase-for-self-condensations-of-linear-aliphatic-aldehydes
#14
Mehran Rahimi, Jan Ytzen van der Meer, Edzard Geertsema, Gerrit Jan Poelarends
4-Oxalocrotonate tautomerase (4-OT) from P. putida mt-2 takes part in a catabolic pathway for aromatic hydrocarbons, where it catalyzes the conversion of 2-hydroxyhexa-2,4-dienedioate into 2-oxohexa-3-enedioate. This tautomerase can also promiscuously catalyze carbon-carbon bond-forming reactions, including various types of aldol reactions, utilizing its N-terminal proline as a key catalytic residue. Here, we have used a systematic mutagenesis strategy to identify two 'hotspot' positions in 4-OT (Met-45 and Phe-50) at which single mutations give a marked improvement in aldolase activity for the self-condensation of propanal...
April 20, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28425861/role-of-cysteine-residues-in-regulation-of-peptidyl-prolyl-cis-trans-isomerase-activity-of-wheat-cyclophilin-tacypa-1
#15
Gundeep Kaur, Harpreet Singh, Kirandeep Kaur, Suchismita Roy, Ashwani Pareek, Prabhjeet Singh
Oxidative conditions result in inhibition of peptidyl-prolyl cis-trans isomerase (PPIase) activity of several cyclophilins. Thiol groups have been implicated in redox regulation of these proteins. In our previous study, we proposed that activity of wheat cyclophilin, TaCYPA-1, may be modulated through a novel dual mechanism of redox regulation. To further understand the regulation of PPIase activity of TaCYPA-1, we generated mutants of TaCYPA-1 by substituting cysteine residues at positions -40 and -122 with serine, and at -126 with proline...
April 17, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28425599/the-starch-binding-domain-family-cbm41-an-in-silico-analysis-of-evolutionary-relationships
#16
Štefan Janeček, Katarína Majzlová, Birte Svensson, E Ann MacGregor
Within the CAZy database, there are 81 carbohydrate-binding module (CBM) families. A CBM represents a non-catalytic domain in a modular arrangement of glycoside hydrolases (GHs). The present in silico study has been focused on starch-binding domains from the family CBM41 that are usually part of pullulanases from the α-amylase family GH13. Currently there are more than 1,600 sequences classified in the family CBM41, almost exclusively from Bacteria, and so a study was undertaken in an effort to divide the members into relevant groups (subfamilies) and also to contribute to the evolutionary picture of family CBM41...
April 20, 2017: Proteins
https://www.readbyqxmd.com/read/28425481/differences-in-salicylic-acid-glucose-conjugations-by-ugt74f1-and-ugt74f2-from-arabidopsis-thaliana
#17
Alayna M George Thompson, Cristina V Iancu, Kenneth E Neet, John V Dean, Jun-Yong Choe
Salicylic acid (SA) is a signaling molecule utilized by plants in response to various stresses. Through conjugation with small organic molecules such as glucose, an inactive form of SA is generated which can be transported into and stored in plant vacuoles. In the model organism Arabidopsis thaliana, SA glucose conjugates are formed by two homologous enzymes (UGT74F1 and UGT74F2) that transfer glucose from UDP-glucose to SA. Despite being 77% identical and with conserved active site residues, these enzymes catalyze the formation of different products: UGT74F1 forms salicylic acid glucoside (SAG), while UGT74F2 forms primarily salicylic acid glucose ester (SGE)...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28425134/record-broken-a-copper-peroxide-complex-with-enhanced-stability-and-faster-hydroxylation-catalysis
#18
Sonja Herres-Pawlis, Patricia Liebhäuser, Kristina Keisers, Alexander Hoffmann, Thomas Schnappinger, Isabella Sommer, Anne Thoma, Claudia Wilfer, Roland Schoch, Kai Stührenberg, Matthias Bauer, Maximilian Dürr, Ivana Ivanovic-Burmazovic
Tyrosinase model systems pinpoint pathways to translate nature´s synthetic abilities into useful synthetic catalysts. Mostly, they use N-donor ligands which mimic the histidine residues coordinating the two copper centres. Copper complexes with bis(pyrazolyl)methanes with pyridinyl or imidazolyl moieties are already reported as excellent tyrosinase models. Substitution of the pyridinyl donor results now in the new ligand HC(3 tBuPz)2(4 CO2MePy) which stabilises a room-temperature stable -2:2-peroxide dicopper(II) species upon oxygenation...
April 19, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28421433/modification-of-the-catalytic-subunit-of-plasma-fibrin-stabilizing-factor-under-induced-oxidation
#19
A D Vasilyeva, A V Bychkova, A E Bugrova, M I Indeykina, A P Chikunova, V B Leonova, E A Kostanova, M I Biryukova, M L Konstantinova, A S Kononikhin, E N Nikolaev, M A Rosenfeld
For the first time, by using mass-spectrometry method, the oxidation-mediated modification of the catalytic FXIII-A subunit of plasma fibrin-stabilizing factor, pFXIII, has been studied. The oxidative sites were identified to belong to all structural elements of the catalytic subunit: the β-sandwich (Tyr104, Tyr117, and Cys153), the catalytic core domain (Met160, Trp165, Met266, Cys328, Asp352, Pro387, Arg409, Cys410, Tyr442, Met475, Met476, Tyr482, and Met500), the β-barrel 1 (Met596), and the β-barrel 2 (Met647, Pro676, Trp692, Cys696, and Met710), which correspond to 3...
January 2017: Doklady. Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28421413/substrate-induced-conformational-changes-of-the-tyrocidine-synthetase-1-adenylation-domain-probed-by-intrinsic-trp-fluorescence
#20
Matilda Šprung, Barbara Soldo, Stjepan Orhanović, Viljemka Bučević-Popović
Nonribosomal peptide synthetases (NRPS) are multifunctional proteins that catalyze the synthesis of the peptide products with enormous biological potential. The process of biosynthesis starts with the adenylation (A) domain, which during the catalytic cycle undergoes extensive structural rearrangements. In this paper, we present the first study of the tyrocidine synthetase 1 A-domain (TycA-A) fluorescence properties. The TycA-A protein contains five potentially fluorescent Trp residues at positions 227, 301, 323, 376 and 406...
April 18, 2017: Protein Journal
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