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https://www.readbyqxmd.com/read/29345925/catalytic-mechanism-of-the-ubiquitin-like-nedd8-transfer-in-ring-e3-e2-nedd8-target-complex-from-qm-mm-free-energy-simulations
#1
Yufei Yue, Yue Ma, Ping Qian, Hong Guo
Ubiquitin-like (UBL) protein modifications play a key role in regulating protein function. In contrast to the ubiquitin (UB) and small ubiquitin-like modifier (SUMO) which are ligated to a massive segment of proteome, the UBL NEDD8 is highly selective for modifying a lysine residue on closely related cullin proteins (CULs). In this study, the X-ray structure of a trapped E3-E2~NEDD8-target intermediate (RBX1-UBC1~NEDD8-CUL1-DCN1) is used to build computer models, and combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) and free energy (potential of mean force) simulations are performed to investigate the catalytic mechanism of the NEDD8 transfer from E2 to the lysine residue (K720) on the substrate in the complex...
January 18, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29344087/determination-of-the-native-features-of-the-exoglucanase-cel48s-from-clostridium-thermocellum
#2
Ya-Jun Liu, Shiyue Liu, Sheng Dong, Renmin Li, Yingang Feng, Qiu Cui
Background: Clostridium thermocellum is considered one of the most efficient natural cellulose degraders because of its cellulosomal system. As the major exoglucanase of cellulosome in C. thermocellum, Cel48S plays key roles and influences the activity and features of cellulosome to a great extent. Thus, it is of great importance to reveal the enzymatic features of Cel48S. However, Cel48S has not been well performed due to difficulties in purifying either recombinant or native Cel48S proteins...
2018: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29343822/the-micals-are-a-family-of-f-actin-dismantling-oxidoreductases-conserved-from-drosophila-to-humans
#3
Heng Wu, Hunkar Gizem Yesilyurt, Jimok Yoon, Jonathan R Terman
Cellular form and function - and thus normal development and physiology - are specified via proteins that control the organization and dynamic properties of the actin cytoskeleton. Using the Drosophila model, we have recently identified an unusual actin regulatory enzyme, Mical, which is directly activated by F-actin to selectively post-translationally oxidize and destabilize filaments - regulating numerous cellular behaviors. Mical proteins are also present in mammals, but their actin regulatory properties, including comparisons among different family members, remain poorly defined...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29343701/alanine-mutation-of-the-catalytic-sites-of-pantothenate-synthetase-causes-distinct-conformational-changes-in-the-atp-binding-region
#4
Bharati Pandey, Sonam Grover, Sukriti Goyal, Anchala Kumari, Aditi Singh, Salma Jamal, Jagdeep Kaur, Abhinav Grover
The enzyme Pantothenate synthetase (PS) represents a potential drug target in Mycobacterium tuberculosis. Its X-ray crystallographic structure has demonstrated the significance and importance of conserved active site residues including His44, His47, Asn69, Gln72, Lys160 and Gln164 in substrate binding and formation of pantoyl adenylate intermediate. In the current study, molecular mechanism of decreased affinity of the enzyme for ATP caused by alanine mutations was investigated using molecular dynamics (MD) simulations and free energy calculations...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29343611/structural-insights-into-the-catalytic-mechanism-of-cysteine-hydroxyl-lyase-from-the-hydrogen-sulfide-producing-oral-pathogen-fusobacterium-nucleatum
#5
Yuichiro Kezuka, Tetsuo Ishida, Yasuo Yoshida, Takamasa Nonaka
Hydrogen sulfide (H2S) plays important roles in the pathogenesis of periodontitis. Oral pathogens typically produce H2S from L-cysteine in addition to pyruvate and NH4+ However, fn1055 from Fusobacterium nucleatum subsp. nucleatum ATCC 25586 encodes a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the production of H2S and L-serine from L-cysteine and H2O, an unusual cysteine (hydroxyl) lyase reaction (β-replacement reaction). To reveal the reaction mechanism, the crystal structure of substrate-free Fn1055 was determined...
January 17, 2018: Biochemical Journal
https://www.readbyqxmd.com/read/29343584/human-herpesvirus-8-interferon-regulatory-factors-1-and-3-mediate-replication-and-latency-activities-via-interactions-with-usp7-deubiquitinase
#6
Qiwang Xiang, Hyunwoo Ju, Qian Li, Szu-Chieh Mei, Daming Chen, Young Bong Choi, John Nicholas
Human herpesvirus 8 (HHV-8) encodes four viral interferon regulatory factors (vIRFs 1-4) that likely function to suppress innate immune and cellular stress responses through inhibitory interactions with various cellular proteins involved in these activities. It is notable that vIRFs 1 and 4 have been reported to interact with the deubiquitinase USP7, substrates of which include p53 and p53-targeting and destabilizing ubiquitin E3 ligase MDM2. Structural studies of vIRF-1 and vIRF-4 USP7-binding sequences in association with USP7 have been reported; both involve interactions with N-terminal domain residues of USP7, via EGPS and ASTS motifs in vIRF-1 and vIRF-4, respectively, but vIRF-4 residues also contact the catalytic site...
January 17, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29342349/membrane-allostery-and-unique-hydrophobic-sites-promote-enzyme-substrate-specificity
#7
Varnavas D Mouchlis, Yuan Chen, J Andrew McCammon, Edward A Dennis
We demonstrate that lipidomics coupled with molecular dynamics reveals unique phospholipase A2 specificity toward membrane phospholipid substrates. We discovered unexpected head-group and acyl-chain specificity for three-major human phospholipases A2. These differences between each enzyme's specificity coupled with molecular dynamicsbased structural and binding studies revealed unique active site and interfacial surface binding moieties for each enzyme that explains the observed specificity at a hitherto inaccessible structural level...
January 17, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29341608/molecular-dynamics-pinpoint-the-global-fluorine-effect-in-balanoids-binding-to-pkc%C3%AE%C2%B5-and-pka
#8
Ari Hardianto, Fei Liu, Shoba Ranganathan
(-)-Balanol is an ATP mimic that inhibits protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA) with little selectivity. While PKA is known as a tumour promoter, PKC isozymes can be tumour promoters or suppressors. In particular, PKCε is frequently involved in tumorigenesis and a potential target for anticancer drugs. We recently reported that stereospecific fluorination of balanol yielded a balanoid with enhanced selectivity for PKCε over other PKC isozymes and PKA, although the global fluorine effect behind the selectivity enhancement is not fully understood...
January 17, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29341605/prediction-of-active-site-and-distal-residues-in-e-coli-dna-polymerase-iii-alpha-polymerase-activity
#9
Ramya Parasuram, Timothy A Coulther, Judith M Hollander, Elise Keston-Smith, Mary Jo Ondrechen, Penny J Beuning
The process of DNA replication is carried out with high efficiency and accuracy by DNA polymerases. The replicative polymerase in E. coli is DNA Pol III, which is a complex of 10 different subunits that coordinates simultaneous replication on the leading and lagging strands. The 1160-residue Pol III alpha subunit is responsible for the polymerase activity and copies DNA accurately, making one error per 105 nucleotide incorporations. The goal of this research is to determine the residues that contribute to the activity of the polymerase subunit...
January 17, 2018: Biochemistry
https://www.readbyqxmd.com/read/29341603/pokmt1-from-the-polyketomycin-biosynthetic-machinery-of-streptomyces-diastatochromogenes-t%C3%A3-6028-belongs-to-the-emerging-family-of-c-methyltransferases-that-act-on-coa-activated-aromatic-substrates
#10
Xun Guo, Ivana Crnovcic, Chin-Yuan Chang, Jun Luo, Jeremy R Lohman, Monica Papinski, Andreas Bechthold, Geoffrey P Horsman, Ben Shen
Recent biochemical characterizations of the MdpB2 CoA ligase and MdpB1 C-methyltransferase (C-MT) from the maduropeptin (MDP, 2) biosynthetic machinery revealed unusual pathway logic involving C-methylation occurring on a CoA-activated aromatic substrate. Here we confirmed this pathway logic for the biosynthesis of polyketomycin (POK, 3). Biochemical characterization unambiguously established that PokM3 and PokMT1 catalyze the sequential conversion of 6-methylsalicylic acid (6-MSA, 4) to form 3,6-dimethylsalicylyl-CoA (3,6-DMSA-CoA, 6), which serves as the direct precursor for the 3,6-dimethylsalicylic acid (3,6-DMSA) moiety in the biosynthesis of 3...
January 17, 2018: Biochemistry
https://www.readbyqxmd.com/read/29339556/evidence-of-a-sequestered-imine-intermediate-during-reduction-of-nitrile-to-amine-by-the-nitrile-reductase-quef-from-escherichia-coli
#11
Jihye Jung, Bernd Nidetzky
In the biosynthesis of the tRNA-inserted nucleoside queuosine, the nitrile reductase QueF catalyzes conversion of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1), a biologically unique four-electron reduction of a nitrile to an amine. The QueF mechanism involves a covalent thioimide adduct between the enzyme and preQ0 which undergoes reduction to preQ1 in two NADPH-dependent steps, presumably via an imine intermediate. Protecting a labile imine from interception by water is fundamental to QueF catalysis for proper enzyme function...
January 16, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29338603/emerging-roles-of-inositol-pyrophosphates-as-key-modulators-of-fungal-pathogenicity
#12
Hyun Ah Kang
Inositol pyrophosphates (PP-IPs) are energy-rich small molecules that are omnipresent in eukaryotic cells, from yeast to mammals, playing central roles in overall cellular homeostasis as a diverse and multifaceted class of intracellular messengers. Recent studies of the metabolic pathways and physiological roles of PP-IPs in the human pathogenic fungus Cryptococcus neoformans have revealed that the PP-IP5 (IP7) is a key metabolite essential for fungal metabolic adaptation to the host environment, immune recognition, and pathogenicity...
January 17, 2018: Virulence
https://www.readbyqxmd.com/read/29336543/histone-deacetylase-11-is-a-fatty-acid-deacylase
#13
Zsofia Kutil, Zora Novakova, Marat Meleshin, Jana Mikesova, Mike Schutkowski, Cyril Barinka
Histone deacetylase 11 (HDAC11) is a sole member of the class IV HDAC subfamily with negligible intrinsic deacetylation activity. Here we report in vitro profiling of HDAC11 deacylase activities, and our data unequivocally show that the enzyme efficiently removes acyl moieties spanning 8-18 carbons from the side chain nitrogen of the lysine residue of a peptidic substrate. Additionally, N-linked lipoic acid and biotin are removed by the enzyme, although with lower efficacy. Catalytic efficiencies toward dodecanoylated and myristoylated peptides were 77,700 M-1s-1 and 149,000 M-1s-1, respectively, making HDAC11 the most proficient fatty acid deacylase of the HDAC family...
January 16, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29336165/development-of-novel-delivery-system-for-nanoencapsulation-of-catalase-formulation-characterization-and-in-vivo-evaluation-using-oxidative-skin-injury-model
#14
Heidi Mohamed Abdel-Mageed, Afaf S Fahmy, Dalia S Shaker, Saleh A Mohamed
One of the main challenges for successful pharmaceutical application of Catalase (CAT) is maintaining its stability. Physical immobilization of CAT through nano-encapsulation was proposed to resolve this challenge. CAT encapsulating niosomes (e-CAT) were prepared using Brij® 30, 52, 76, 92, and 97 in the presence of cholesterol (Ch) by thin film hydration method. Niosomes were characterized for encapsulation efficiency % (EE), size, poly-dispersity index (PI), and morphology. Kinetic parameters, pH optimum, thermal stability, and reusability of CAT were determined...
January 16, 2018: Artificial Cells, Nanomedicine, and Biotechnology
https://www.readbyqxmd.com/read/29330648/cloning-expression-and-characterization-of-the-esterase-estut1-from-ureibacillus-thermosphaericus-which-belongs-to-a-new-lipase-family-xviii
#15
Yuliya V Samoylova, Ksenia N Sorokina, Margarita V Romanenko, Valentin N Parmon
A new esterase gene from thermophilic bacteria Ureibacillus thermosphaericus was cloned into the pET32b vector and expressed in Escherichia coli BL21(DE3). Alignment of the estUT1 amino acid sequence revealed the presence of a novel canonical pentapeptide (GVSLG) and 41-47% identity to the closest family of the bacterial lipases XIII. Thus the esterase estUT1 from U. thermosphaericus was assigned as a member of the novel family XVIII. It also showed a strong activity toward short-chain esters (C2-C8), with the highest activity for C2...
January 12, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29330521/rgs7-is-recurrently-mutated-in-melanoma-and-promotes-migration-and-invasion-of-human-cancer-cells
#16
Nouar Qutob, Ikuo Masuho, Michal Alon, Rafi Emmanuel, Isadora Cohen, Antonella Di Pizio, Jason Madore, Abdel Elkahloun, Tamar Ziv, Ronen Levy, Jared J Gartner, Victoria K Hill, Jimmy C Lin, Yael Hevroni, Polina Greenberg, Alexandra Brodezki, Steven A Rosenberg, Mickey Kosloff, Nicholas K Hayward, Arie Admon, Masha Y Niv, Richard A Scolyer, Kirill A Martemyanov, Yardena Samuels
Analysis of 501 melanoma exomes revealed RGS7, which encodes a GTPase-accelerating protein (GAP), to be a tumor-suppressor gene. RGS7 was mutated in 11% of melanomas and was found to harbor three recurrent mutations (p.R44C, p.E383K and p.R416Q). Structural modeling of the most common recurrent mutation of the three (p.R44C) predicted that it destabilizes the protein due to the loss of an H-bond and salt bridge network between the mutated position and the serine and aspartic acid residues at positions 58 as 61, respectively...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29329981/molecular-cloning-and-characterization-of-leucine-aminopeptidase-gene-from-taenia-pisiformis
#17
Shaohua Zhang, Xuepeng Cai, Xuenong Luo, Shuai Wang, Aijiang Guo, Junling Hou, Run Wu
Leucine aminopeptidase (LAP, EC: 3.4.11.1) is an important metalloexopeptidase that catalyze the hydrolysis of amino-terminal leucine residues from polypeptides and proteins. In this study, a full length of cDNA encoding leucine aminopeptidase of Taenia pisiformis (TpLAP) was cloned by rapid amplification of cDNA-ends using the polymerase chain reaction (RACE-PCR) method. The full-length cDNA of the TpLAP gene is 1823 bp and contains a 1569 bp ORF encoding 533 amino acids with a putative mass of 56.4 kDa...
January 9, 2018: Experimental Parasitology
https://www.readbyqxmd.com/read/29327308/methionine-in-proteins-it-s-not-just-for-protein-initiation-anymore
#18
Jung Mi Lim, Geumsoo Kim, Rodney L Levine
Methionine in proteins is often thought to be a generic hydrophobic residue, functionally replaceable with another hydrophobic residue such as valine or leucine. This is not the case, and the reason is that methionine contains sulfur that confers special properties on methionine. The sulfur can be oxidized, converting methionine to methionine sulfoxide, and ubiquitous methionine sulfoxide reductases can reduce the sulfoxide back to methionine. This redox cycle enables methionine residues to provide a catalytically efficient antioxidant defense by reacting with oxidizing species...
January 11, 2018: Neurochemical Research
https://www.readbyqxmd.com/read/29325872/structure-and-function-of-a-highly-active-bile-salt-hydrolase-bsh-from-enterococcus-faecalis-and-post-translational-processing-of-bsh-enzymes
#19
Deepak Chand, Priyabrata Panigrahi, Nishant Kumar Varshney, Sureshkumar Ramasamy, C G Suresh
Bile Salt Hydrolase (BSH), a member of Cholylglycine hydrolase family, catalyses the de-conjugation of bile acids and is evolutionarily related to penicillin V acylase (PVA) that hydrolyses a different substrate such as penicillin V. We report the three-dimensional structure of a BSH enzyme from the Gram-positive bacteria Enterococcus faecalis (EfBSH) which has manifold higher hydrolase activity compared to other known BSHs and displays unique allosteric catalytic property. The structural analysis revealed reduced secondary structure content compared to other known BSH structures, particularly devoid of an anti-parallel β-sheet in the assembly loop and part of a β-strand is converted to increase the length of a substrate binding loop 2...
January 8, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29321962/mutual-influence-of-secondary-and-key-drug-resistance-mutations-on-catalytic-properties-and-thermal-stability-of-tem-type-%C3%AE-lactamases
#20
Vitaly Grigorenko, Igor Uporov, Maya Rubtsova, Irina Andreeva, Dmitrii Shcherbinin, Alexander Veselovsky, Oksana Serova, Maria Ulyashova, Igor Ishtubaev, Alexey Egorov
Highly mutable β-lactamases are responsible for the ability of Gram-negative bacteria to resist β-lactam antibiotics. Using site-directed mutagenesis technique, we have produced in vitro a number of recombinant analogs of naturally occurring TEM-type β-lactamases, bearing the secondary substitution Q39K and key mutations related to the extended-spectrum (E104K, R164S) and inhibitor-resistant (M69V) β-lactamases. The mutation Q39K alone was found to be neutral and hardly affected the catalytic properties of β-lactamases...
January 2018: FEBS Open Bio
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