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https://www.readbyqxmd.com/read/27932585/structural-and-functional-characterization-of-the-tyw3-taw3-class-of-sam-dependent-methyltransferases
#1
Mark A Currie, Greg Brown, Andrew Wong, Takayuki Ohira, Kei Sugiyama, Tsutomu Suzuki, Alexander F Yakunin, Zongchao Jia
S-adenosylmethionine (SAM)-dependent methyltransferases regulate a wide range of biological processes through the modification of proteins, nucleic acids, polysaccharides, as well as various metabolites. TYW3/Taw3 is a SAM-dependent methyltransferase responsible for the formation of a tRNA modification known as wybutosine and its derivatives that are required for accurate decoding in protein synthesis. Here, we report the crystal structure of Taw3, a homolog of TYW3 from Sulfolobus solfataricus, which revealed a novel α/β fold...
December 8, 2016: RNA
https://www.readbyqxmd.com/read/27928938/sequence-and-structure-based-analysis-of-proteins-involved-in-mirna-biogenesis
#2
Chhaya Sharma, Debasisa Mohanty
miRNA biogenesis is a multistage process for generation of a mature miRNA and involves several different proteins. In this work, we have carried out sequence as well as structure based analysis for crucial proteins involved in miRNA biogenesis, namely, Dicer, Drosha, Argonaute (Ago) and Exportin-5 to understand evolution of these proteins in animal kingdom and also to identify key sequence and structural features which are determinants of their function. Our analysis reveals that in animals the miRNA biogenesis pathway first originated in molluscs...
December 8, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27924260/molecular-mechanisms-of-substrate-specificities-of-uridinecytidine-kinase
#3
Wataru Tanaka, Mitsuo Shoji, Fumiaki Tomoike, Yuzuru Ujiie, Kyohei Hanaoka, Ryuhei Harada, Megumi Kayanuma, Katsumasa Kamiya, Toyokazu Ishida, Ryoji Masui, Seiki Kuramitsu, Yasuteru Shigeta
A uridine-cytidine kinase (UCK) catalyzes the phosphorylation of uridine (Urd) and cytidine (Cyd) and plays a significant role in the pyrimidine-nucleotide salvage pathway. Unlike ordinary ones, UCK from Thermus thermophilus HB8 (ttCK) loses catalytic activity on Urd due to lack of a substrate binding ability and possesses an unusual amino acid, i.e. tyrosine 93 (Tyr93) at the binding site, whereas histidine (His) is located in the other UCKs. Mutagenesis experiments revealed that a replacement of Tyr93 by His or glutamine (Gln) recovered catalytic activity on Urd...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27923179/structural-dynamics-of-casein-kinase-i-cki-from-malarial-parasite-plasmodium-falciparum-isolate-3d7-insights-from-theoretical-modelling-and-molecular-simulations
#4
Budheswar Dehury, Santosh Kumar Behera, Namita Mahapatra
The protein kinases (PKs), belonging to serine/threonine kinase (STKs), are important drug targets for a wide spectrum of diseases in human. Among protein kinases, the Casein Kinases (CKs) are vastly expanded in various organisms, where, the malarial parasite Plasmodium falciparum possesses a single member i.e., PfCKI, which can phosphorylate various proteins in parasite extracts in vitro condition. But, the structure-function relationship of PfCKI and dynamics of ATP binding is yet to be understood. Henceforth, an attempt was made to study the dynamics, stability, and ATP binding mechanisms of PfCKI through computational modelling, docking, molecular dynamics (MD) simulations, and MM/PBSA binding free energy estimation...
November 21, 2016: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/27923055/a-novel-rrm3-function-in-restricting-dna-replication-via-an-orc5-binding-domain-is-genetically-separable-from-rrm3-function-as-an-atpase-helicase-in-facilitating-fork-progression
#5
Salahuddin Syed, Claus Desler, Lene J Rasmussen, Kristina H Schmidt
In response to replication stress cells activate the intra-S checkpoint, induce DNA repair pathways, increase nucleotide levels, and inhibit origin firing. Here, we report that Rrm3 associates with a subset of replication origins and controls DNA synthesis during replication stress. The N-terminal domain required for control of DNA synthesis maps to residues 186-212 that are also critical for binding Orc5 of the origin recognition complex. Deletion of this domain is lethal to cells lacking the replication checkpoint mediator Mrc1 and leads to mutations upon exposure to the replication stressor hydroxyurea...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27922000/membrane-pyrophosphatases-from-thermotoga-maritima-and-vigna-radiata-suggest-a-conserved-coupling-mechanism
#6
Kun-Mou Li, Craig Wilkinson, Juho Kellosalo, Jia-Yin Tsai, Tommi Kajander, Lars J C Jeuken, Yuh-Ju Sun, Adrian Goldman
Membrane-bound pyrophosphatases (M-PPases), which couple proton/sodium ion transport to pyrophosphate synthesis/hydrolysis, are important in abiotic stress resistance and in the infectivity of protozoan parasites. Here, three M-PPase structures in different catalytic states show that closure of the substrate-binding pocket by helices 5-6 affects helix 13 in the dimer interface and causes helix 12 to move down. This springs a 'molecular mousetrap', repositioning a conserved aspartate and activating the nucleophilic water...
December 6, 2016: Nature Communications
https://www.readbyqxmd.com/read/27920203/a-highly-active-isoform-of-lentivirus-restriction-factor-samhd1-in-mouse
#7
Nicolin Bloch, Sabine Gläsker, Poojitha Sitaram, Henning Hofmann, Caitlin N Shepard, Megan L Schultz, Baek Kim, Nathaniel R Landau
The triphosphohydrolase SAMHD1 restricts HIV-1 replication in nondividing myeloid cells by depleting the dNTP pool, preventing reverse transcription. SAMHD1 is also reported to have ribonuclease activity that degrades the virus genomic RNA. Human SAMHD1 is regulated by phosphorylation of its carboxy-terminus at T592, which abrogates its antiviral function yet has only a small effect on its phosphohydrolase activity. In the mouse, SAMHD1 is expressed as two isoforms (ISF1 and ISF2) that differ at the carboxy-terminus due to alternative splicing of the last coding exon...
December 5, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27919681/mutational-analysis-of-kex2-recognition-sites-and-a-disulfide-bond-in-tannase-from-aspergillus-oryzae
#8
Takuya Koseki, Motohiro Otsuka, Toshiyuki Mizuno, Yoshihito Shiono
Aspergillus oryzae tannase (AoTanA), which contains two Kex2 recognition sites at positions Arg311 and Arg316, consists of two subunits that are generated by the cleavage of tannase gene product by the Kex2 protease. Based on the crystal structure of feruloyl esterase from Aspergillus oryzae (AoFaeB), which has been classified as a member of the fungal tannase family, the catalytic triad residues of AoTanA are predicted to be Ser195, Asp455, and His501, with the serine and histidine residues brought together by a disulfide bond of the neighboring cysteines, Cys194 and Cys502...
December 2, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27919027/phosphorylation-of-janus-kinase-1-jak1-by-amp-activated-protein-kinase-ampk-links-energy-sensing-to-anti-inflammatory-signaling
#9
Claire Rutherford, Claire Speirs, Jamie J L Williams, Marie-Ann Ewart, Sarah J Mancini, Simon A Hawley, Christian Delles, Benoit Viollet, Ana P Costa-Pereira, George S Baillie, Ian P Salt, Timothy M Palmer
Adenosine 5'-monophosphate-activated protein kinase (AMPK) is a pivotal regulator of metabolism at cellular and organismal levels. AMPK also suppresses inflammation. We found that pharmacological activation of AMPK rapidly inhibited the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway in various cells. In vitro kinase assays revealed that AMPK directly phosphorylated two residues (Ser(515) and Ser(518)) within the Src homology 2 domain of JAK1. Activation of AMPK enhanced the interaction between JAK1 and 14-3-3 proteins in cultured vascular endothelial cells and fibroblasts, an effect that required the presence of Ser(515) and Ser(518) and was abolished in cells lacking AMPK catalytic subunits...
November 8, 2016: Science Signaling
https://www.readbyqxmd.com/read/27919007/challenges-in-assignment-of-allosteric-effects-in-cytochrome-p450-catalyzed-substrate-oxidations-to-structural-dynamics-in-the-hemoprotein-architecture
#10
Peter Hlavica
Cytochrome P450s (CYP) represent a superfamily of b-type hemoproteins catalyzing NAD(P)H-dependent oxidative biotransformation of a vast array of natural and xenobiotic compounds. Many eu- and prokaryotic members of this class of monooxygenases display complex non-Michaelis-Menten saturation kinetics, suggestive of homo-/heterotropic cooperativity arising from substrate-/effector-induced allosteric interactions. Here, the paradigm of multiple-ligand occupancy of the catalytic pocket in combination with enzyme oligomerization provides the most favored explanations for the atypical kinetic patterns...
November 25, 2016: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/27918987/surfactant-assisted-selective-etching-strategy-for-generation-of-rattle-like-mesoporous-silica-nanoparticles
#11
Xingwen Liu, Zheng Jiao, Tingting Song, Minghong Wu, Haijiao Zhang
Nowadays, rattle-like or so-called yolk-shell nanostructures have set off a new wave of research in view of their prominent features including large surface area, tunable void and flexible functional core, etc. Herein, rattle-like mesoporous silica nanoparticles (RMSNs) with a pure silica core, a hollow cavity and a mesoporous shell have been successfully fabricated via a surfactant-assisted selective etching strategy. The synthetic approach involves the preparation of solid silica spheres with three-layer different structural silica containing the inner core of pure silica, middle layer of hybrid silica and outer shell of surfactant/SiO2 composite, followed by a hydrothermal treatment in hot water...
November 24, 2016: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/27918543/ficd-acts-bifunctionally-to-ampylate-and-de-ampylate-the-endoplasmic-reticulum-chaperone-bip
#12
Steffen Preissler, Claudia Rato, Luke A Perera, Vladimir Saudek, David Ron
Protein folding homeostasis in the endoplasmic reticulum (ER) is defended by an unfolded protein response that matches ER chaperone capacity to the burden of unfolded proteins. As levels of unfolded proteins decline, a metazoan-specific FIC-domain-containing ER-localized enzyme (FICD) rapidly inactivates the major ER chaperone BiP by AMPylating T518. Here we show that the single catalytic domain of FICD can also release the attached AMP, restoring functionality to BiP. Consistent with a role for endogenous FICD in de-AMPylating BiP, FICD(-/-) hamster cells are hypersensitive to introduction of a constitutively AMPylating, de-AMPylation-defective mutant FICD...
December 5, 2016: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/27917857/relocation-of-active-site-carboxylates-in-major-facilitator-superfamily-multidrug-transporter-lmrp-reveals-plasticity-in-proton-interactions
#13
Asha V Nair, Himansha Singh, Sagar Raturi, Arthur Neuberger, Zhen Tong, Ning Ding, Kelvin Agboh, Hendrik W van Veen
The expression of polyspecific membrane transporters is one important mechanism by which cells can obtain resistance to structurally different antibiotics and cytotoxic agents. These transporters reduce intracellular drug concentrations to subtoxic levels by mediating drug efflux across the cell envelope. The major facilitator superfamily multidrug transporter LmrP from Lactococcus lactis catalyses drug efflux in a membrane potential and chemical proton gradient-dependent fashion. To enable the interaction with protons and cationic substrates, LmrP contains catalytic carboxyl residues on the surface of a large interior chamber that is formed by transmembrane helices...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27915377/crystal-structure-and-characterization-of-esterase-est25-mutants-reveal-improved-enantioselectivity-toward-s-ketoprofen-ethyl-ester
#14
Jinyeong Kim, Seung-Hyeon Seok, Eunsoo Hong, Tae Hyeon Yoo, Min-Duk Seo, Yeonwoo Ryu
Esterases comprise a group of enzymes that catalyze the cleavage and synthesis of ester bonds. They are important in biotechnological applications owing to their enantioselectivity, regioselectivity, broad substrate specificity, and the fact that they do not require cofactors. In a previous study, we isolated the esterase Est25 from a metagenomic library. Est25 showed catalytic activity toward the (R,S)-ketoprofen ethyl ester but had low enantioselectivity toward the (S)-ketoprofen ethyl ester. Because (S)-ketoprofen has stronger anti-inflammatory effects and fewer side effects than (R)-ketoprofen, enantioselectivity of this esterase is important...
December 3, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27914332/amyloid-graphene-oxide-as-immobilization-platform-of-au-nanocatalysts-and-enzymes-for-improved-glucose-sensing-activity
#15
Xiaochen Wu, Mingjie Li, Zehui Li, Lili Lv, Yan Zhang, Chaoxu Li
Two-dimensional GO nanosheets and one-dimensional lysozyme nanofibrils were hybridized through electrostatic interaction to get a novel amyloid-GO composite, which promised a biocompatible immobilization platform for Au nanocatalysts as well as enzymes. The immobilization platform could load a large and tunable amount of Au NPs while maintaining their high catalytic activity. The immobilized catalysts showed high electrochemical behaviors, being ideal as glucose sensing systems. Furthermore, enzymes could also be immobilized on the residual bare surfaces of amyloid-GO, and served by a colorimetric method for a sensitive and selective analytical glucose-detecting platform...
November 16, 2016: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/27911800/an-%C3%AE-%C3%AE-hydrolase-fold-protein-in-the-biosynthesis-of-thiostrepton-exhibits-a-dual-activity-for-endopeptidyl-hydrolysis-and-epoxide-ring-opening-macrocyclization
#16
Qingfei Zheng, Shoufeng Wang, Panpan Duan, Rijing Liao, Dandan Chen, Wen Liu
Thiostrepton (TSR), an archetypal bimacrocyclic thiopeptide antibiotic that arises from complex posttranslational modifications of a genetically encoded precursor peptide, possesses a quinaldic acid (QA) moiety within the side-ring system of a thiopeptide-characteristic framework. Focusing on selective engineering of the QA moiety, i.e., by fluorination or methylation, we have recently designed and biosynthesized biologically more active TSR analogs. Using these analogs as chemical probes, we uncovered an unusual indirect mechanism of TSR-type thiopeptides, which are able to act against intracellular pathogens through host autophagy induction in addition to direct targeting of bacterial ribosome...
November 23, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911799/mechanism-of-the-intrinsic-arginine-finger-in-heterotrimeric-g-proteins
#17
Daniel Mann, Christian Teuber, Stefan A Tennigkeit, Grit Schröter, Klaus Gerwert, Carsten Kötting
Heterotrimeric G proteins are crucial molecular switches that maintain a large number of physiological processes in cells. The signal is encoded into surface alterations of the Gα subunit that carries GTP in its active state and GDP in its inactive state. The ability of the Gα subunit to hydrolyze GTP is essential for signal termination. Regulator of G protein signaling (RGS) proteins accelerates this process. A key player in this catalyzed reaction is an arginine residue, Arg178 in Gαi1, which is already an intrinsic part of the catalytic center in Gα in contrast to small GTPases, at which the corresponding GTPase-activating protein (GAP) provides the arginine "finger...
November 28, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27909822/generation-of-lycopene-overproducing-strains-of-the-fungus-mucor-circinelloides-reveals-important-aspects-of-lycopene-formation-and-accumulation
#18
Yingtong Zhang, Haiqin Chen, Eusebio Navarro, Sergio López-García, Yong Q Chen, Hao Zhang, Wei Chen, Victoriano Garre
OBJECTIVES: To generate lycopene-overproducing strains of the fungus Mucor circinelloides with interest for industrial production and to gain insight into the catalytic mechanism of lycopene cyclase and regulatory process during lycopene overaccumulation. RESULTS: Three lycopene-overproducing mutants were generated by classic mutagenesis techniques from a β-carotene-overproducing strain. They carried distinct mutations in the carRP gene encoding lycopene cyclase that produced loss of enzymatic activity to different extents...
December 1, 2016: Biotechnology Letters
https://www.readbyqxmd.com/read/27909311/insights-into-the-phosphoryl-transfer-mechanism-of-human-ubiquitous-mitochondrial-creatine-kinase
#19
Quanjie Li, Shuai Fan, Xiaoyu Li, Yuanyuan Jin, Weiqing He, Jinming Zhou, Shan Cen, ZhaoYong Yang
Human ubiquitous mitochondrial creatine kinase (uMtCK) is responsible for the regulation of cellular energy metabolism. To investigate the phosphoryl-transfer mechanism catalyzed by human uMtCK, in this work, molecular dynamic simulations of uMtCK∙ATP-Mg(2+)∙creatine complex and quantum mechanism calculations were performed to make clear the puzzle. The theoretical studies hereof revealed that human uMtCK utilizes a two-step dissociative mechanism, in which the E227 residue of uMtCK acts as the catalytic base to accept the creatine guanidinium proton...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27909055/molecular-identification-of-d-ribulokinase-in-budding-yeast-and-mammals
#20
Charandeep Singh, Enrico Glaab, Carole L Linster
Proteomes of even well characterized organisms still contain a high percentage of proteins with unknown or uncertain molecular and/or biological function. A significant fraction of those proteins are predicted to have catalytic properties. Here we aimed at identifying the function of the Saccharomyces cerevisiae Ydr109c protein and of its human homolog FGGY, both of which belong to the broadly conserved FGGY family of carbohydrate kinases. Functionally identified members of this family phosphorylate 3- to 7-carbon sugars or sugar derivatives, but the endogenous substrate of S...
December 1, 2016: Journal of Biological Chemistry
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