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FEBS Journal

Somasundaram Ramasamy, Mohammad Mahfuzul Haque, Mahinda Gangoda, Dennis J Stuehr
The NO synthases (NOS) catalyze a two-step oxidation of L-Arginine (Arg) to generate NO. In the first step, O2 activation involves one electron being provided to the heme by an enzyme-bound 6R-tetrahydro-L-biopterin cofactor (H4 B), which then forms a H4 B radical that must be reduced back to H4 B in order for NOS to continue catalysis. Although an NADPH-derived electron is used to reduce the H4 B radical, how this occurs is unknown. We hypothesized that the NOS flavoprotein domain might reduce the H4 B radical by utilizing the NOS heme porphyrin as a conduit to deliver the electron...
October 19, 2016: FEBS Journal
Buki Kwon, Palinda Ruvan Munashingha, Yong-Keol Shin, Chul-Hwan Lee, Bing Li, Yeon-Soo Seo
Highly conserved eukaryotic histones are polybasic proteins that package DNA into nucleosomes, a building block of chromatin, allowing extremely long DNA molecules to form compact and discrete chromosomes. The histone N-terminal tails that extend from the nucleosome core act as docking sites for many proteins through diverse posttranslational modifications, regulating various DNA transactions. In this report, we present evidence that the nucleosomes can positively regulate the enzymatic activity of Rad27 (yeast Fen1), a major processing enzyme important for Okazaki fragment in eukaryotes...
October 19, 2016: FEBS Journal
Ralph D Sanderson, Michael Elkin, Alan C Rapraeger, Neta Ilan, Israel Vlodavsky
Because of its impact on multiple biological pathways, heparanase has emerged as a major regulator of cancer, inflammation and other disease processes. Heparanase accomplishes this by degrading heparan sulfate which regulates the abundance and location of heparin-binding growth factors thereby influencing multiple signaling pathways that control gene expression, syndecan shedding and cell behavior. In addition, heparanase can act via non-enzymatic mechanisms that directly activate signaling at the cell surface...
October 18, 2016: FEBS Journal
Mariana Pavel, David C Rubinsztein
Autophagy (literally "self-eating") is an evolutionarily conserved degradation process where cytoplasmic components are engulfed by vesicles called autophagosomes, which are then delivered to lysosomes, where their contents are degraded. Under stress conditions, such as starvation or oxidative stress, autophagy is upregulated in order to degrade macromolecules and restore the nutrient balance. The source of membranes that participate in the initial formation of phagophores is still incompletely understood and many intracellular structures have been shown to act as lipid donors, including the endoplasmic reticulum, Golgi, nucleus, mitochondria and the plasma membrane...
October 18, 2016: FEBS Journal
Stefan Hofbauer, Georg Mlynek, Lisa Milazzo, Dominic Pühringer, Daniel Maresch, Irene Schaffner, Paul G Furtmüller, Giulietta Smulevich, Kristina Djinović-Carugo, Christian Obinger
Heme biosynthesis in Gram positive bacteria follows a recently described coproporphyrin-dependent pathway with HemQ catalyzing the decarboxylation of coproheme to heme b. Here we present the first crystal structure of a HemQ (homopentameric coproproheme-HemQ from Listeria monocytogenes) at 1.69 Å resolution and the conversion of coproheme to heme b followed by UV-vis and resonance Raman spectroscopy as well as mass spectrometry. The ferric 5-coordinated coproheme iron of HemQ is weakly bound by a neutral proximal histidine H174...
October 18, 2016: FEBS Journal
Leonardo Pellizza, Clara Smal, Raúl E Ithuralde, Adrián G Turjanski, Daniel O Cicero, Martin Aran
The TPM domain constitutes a family of recently characterized protein domains that are present in most living organisms. Although some progress has been made in understanding the cellular role of TPM-containing proteins, the relationship between structure and function it is not clear yet. We have recently solved the solution and crystal structure of one TPM domain (BA42) from the Antarctic bacterium Bizionia argentinensis. In this work we demonstrate that BA42 has phosphoric-monoester hydrolase activity. The activity of BA42 is strictly dependent on the binding of divalent metals and retains nearly 70% of the maximum at 4° C, a typical characteristic of cold adapted enzymes...
October 18, 2016: FEBS Journal
Geoffrey Masuyer, Gyles E Cozier, Glenna J Kramer, Brian O Bachmann, K Ravi Acharya
Several soil-derived actinobacteria produce secondary metabolites that are proven specific and potent inhibitors of the human angiotensin-I converting enzyme (ACE), a key target for the modulation of hypertension through its role in the renin-angiotensin-aldosterone system. K-26-DCP is a zinc dipeptidyl carboxypeptidase produced by Astrosporangium hypotensionis, and an ancestral homologue of ACE. Here we report the high resolution crystal structures of K-26-DCP and of its complex with the natural microbial tripeptide product K-26...
October 18, 2016: FEBS Journal
Prerna Sharma, Pallavi Kaila, Purnananda Guptasarma
Diverse unrelated enzymes that adopt the beta/alpha (or TIM) barrel topology display similar arrangements of beta/alpha units placed in a radial eight-fold symmetry around the barrel's axis. The TIM barrel was originally thought to be a single structural domain; however, it is now thought that TIM barrels arose from duplication and fusion of smaller half-barrels consisting of four beta/alpha units. We describe here the design, expression, and purification, as well as characterization of folding, activity and stability, of chimeras of two TIM barrel glycosyl hydrolases, made by fusing different half-barrel domains derived from an endoglucanase from Clostridium cellulolyticum, CelCCA, and a beta-glucosidase from Pyrococcus furiosus, CelB...
October 17, 2016: FEBS Journal
Naoaki Tsutsui, Tatsuya Sakamoto, Fumio Arisaka, Masaru Tanokura, Hiromichi Nagasawa, Koji Nagata
The crustacean hyperglycemic hormone (CHH) is one of the major hormones in crustaceans, and peptides belonging to the CHH superfamily have been found in diverse ecdysozoans. Although the basic function of CHH is to control energy metabolism, it also plays various roles in crustacean species, such as in molting and vitellogenesis. Here, we present the crystal structure of Pej-SGP-I-Gly, a partially active precursor of CHH from the kuruma prawn Marsupenaeus japonicus, which has an additional Gly residue in place of the C-terminal amide group of the mature Pej-SGP-I...
October 15, 2016: FEBS Journal
Cristiano S Mota, Ana Maria D Gonçalves, Daniele de Sanctis
DR2231 from Deinococcus radiodurans was previously functionally and structurally characterized as an all-α NTP pyrophosphohydrolase with specific dUTPase activity. dUTPases have a central role in the regulation of dUTP intracellular levels and dTTP nucleotide metabolism. DR2231 presents a conserved di-metal catalytic site, similar to the all-α dimeric dUTPases, but contrary to these enzymes, it is unable to process dUDP. In this article we present functional and structural evidence of single-point mutations that affect directly or indirectly the enzyme catalysis and provide a complete description of the all-α NTP pyrophosphohydrolase mechanism...
October 14, 2016: FEBS Journal
Stefania Brocca, Cristian Ferrari, Alberto Barbiroli, Alessandra Pesce, Marina Lotti, Marco Nardini
Life in cold environments requires an overall increase in the flexibility of macromolecular and supramolecular structures to allow biological processes to take place at low temperature. Conformational flexibility supports high catalytic rates of enzymes in the cold but in several cases is also a cause of instability. The three-dimensional structure of the psychrophilic acyl aminoacyl peptidase from Sporosarcina psychrophila (SpAAP) reported in this paper highlights adaptive molecular changes resulting in a fine-tuned trade-off between flexibility and stability...
October 14, 2016: FEBS Journal
Andrea von Zadow, Elisabeth Ignatz, Richard Pokorny, Lars-Oliver Essen, Gabriele Klug
Photolyases are efficient DNA repair enzymes that specifically repair either cyclobutane pyrimidine dimers (CPD) or (6-4) photoproducts in a light-dependent cleavage reaction. The closely related classical cryptochrome blue light photoreceptors do not repair DNA lesions, instead they are involved in regulatory processes. CryB of Rhodobacter sphaeroides was until now described as a cryptochrome that affects light-dependent and singlet oxygen-dependent gene expression and is unusual in terms of its cofactor composition...
October 14, 2016: FEBS Journal
Nicolás Herranz, Natàlia Dave, Alba Millanes-Romero, Laura Pascual, Lluis Morey, Víctor M Díaz, Víctor Lórenz-Fonfría, Ricardo Gutierrez-Gallego, Celia Jerónimo, Ane Iturbide, Luciano Di Croce, Antonio García de Herreros, Sandra Peiró
Methylation of histone H3 lysine 4 is linked to active transcription and can be removed by LSD1 or the JmjC domain-containing proteins by amino-oxidation or hydroxylation, respectively. Here we describe that its deamination can be catalyzed by lysyl oxidase-like 2 protein (LOXL2), presenting an unconventional chemical mechanism for H3K4 modification. Infrared spectroscopy and mass spectrometry analyses demonstrated that recombinant LOXL2 specifically deaminates trimethylated H3K4. Moreover, by regulating H3K4me3 deamination, LOXL2 activity is linked with the transcriptional control of the CDH1 gene...
October 13, 2016: FEBS Journal
Alexandre Duprey, William Nasser, Simon Léonard, Céline Brochier-Armanet, Sylvie Reverchon
After a gene duplication event, the resulting paralogous genes frequently acquire distinct expression profiles, roles and/or functions but the underlying mechanisms are poorly understood. While transcription start site (TSS) turnover, i.e. the repositioning of the TSS during evolution, is widespread in eukaryotes, it is less documented in Bacteria. Using pelD and pelE, two closely related paralogous genes encoding key virulence factors in Dickeya, a gamma proteobacterial genus of phytopathogens, we show that pelE has been selected as an initiator of bacterial aggression, while pelD acts at a later stage, thanks to modifications in the transcriptional regulation of these two genes...
October 11, 2016: FEBS Journal
Santhosh Kumar Sariki, Pushpendra Kumar Sahu, Upendarrao Golla, Vikash Singh, Gajendra Kumar Azad, Raghuvir S Tomar
Mutations in the Senataxin gene, SETX are known to cause the neurodegenerative disorders, ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis 4 (ALS4). However, the mechanism underlying disease pathogenesis is still unclear. The Senataxin N-terminal protein-interaction and C-terminal RNA/DNA helicase domains are conserved in the Saccharomyces cerevisiae homolog, Sen1p. Using genome-wide expression analysis, we first show alterations in key cellular pathways such as; redox, unfolded protein response and TOR in the yeastsen1ΔN mutant (N terminal truncation)...
October 8, 2016: FEBS Journal
(no author information available yet)
In this issue, we highlight work from J. Julian Blow and colleagues that shows how unreplicated DNA originating from double fork stalls are transmitted and resolved in daughter cells, a report by Yves Barral and colleagues on a potential role for diffusion barriers in ER compartmentalisation in C. elegans and a paper by Shan and colleagues reporting the first high-resolution crystal structure of M. tuberculosis trehalose-6-phosphate phosphatase.
October 5, 2016: FEBS Journal
Gautam Srivastava, Adi Moseri, Naama Kessler, Sabine R Akabayov, Boris Arshava, Fred Naider, Jacob Anglister
Weak protein-protein and protein-ligand interactions play important roles in biological recognition. In many cases, simplification of structural studies of large protein complexes is achieved by investigation of the interaction between the protein and a weakly binding segment of its protein ligand. Detection of pairwise interactions in such complexes is a major challenge for both X-ray crystallography and NMR. We demonstrate that transferrednuclear Overhauser effect, TRNOE, in combination with asymmetric deuteration of a protein and a peptide ligand can be used to detect intermolecular interactions in large protein complexes with molecular weights up to ~100 kDa...
October 4, 2016: FEBS Journal
So Young Lee, Yun Young Lee, Joong Sub Choi, Mee-Sup Yoon, Joong-Soo Han
Decidualization of human endometrial stromal cells (hESCs) is crucial for successful uterine implantation and maintaining pregnancy. We previously reported that phospholipase D1 (PLD1) is required for cAMP-induced decidualization of hESCs. However, the mechanism by which phosphatidic acid (PA), the product of PLD1 action, might regulate decidualization is not known. We confirmed that PA induced decidualization of hESCs by observing morphological changes and measuring increased levels of decidualization markers such as IGFBP1 and prolactin transcripts (P < 0...
October 3, 2016: FEBS Journal
David Pulido, Maria Flor Garcia-Mayoral, Mohammed Moussaoui, Diego Velázquez, Marc Torrent, Marta Bruix, Ester Boix
Acute infection by Gram-negative pathogens can induce an exacerbated immune response that leads to lethal septic shock syndrome. Bacterial lipopolysaccharide (LPS) is a major pathogen-associated molecular pattern (PAMP) molecule that can initiate massive and lethal immune system stimulation. Therefore, the development of new and effective LPS-neutralizing agents is a top priority. The eosinophil cationic protein (ECP) is an antimicrobial protein secreted in response to infection, with a remarkable affinity for LPS...
October 3, 2016: FEBS Journal
Xin-Yu Mei, Xia-Di He, Lei Huang, Da-Shi Qi, Ji Nie, Yang Li, Wen Si, Shi-Min Zhao
Hyperhomocysteinemia, which is characterised by elevated blood levels of the non-protein amino acid homocysteine (Hcy), is an independent risk factor for many diseases, including cardiovascular diseases, neurodegenerative diseases and birth defects. The incorporation of homocysteine into proteins, known as protein N-homocysteinylation, has been considered a major mechanism that contributes to hyperhomocysteinemia. However, the process of dehomocysteinylation, N-homocysteinylation substrates and regulatory enzyme(s), remain largely unknown...
October 1, 2016: FEBS Journal
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