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FAD binding protein

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https://www.readbyqxmd.com/read/28509930/elucidation-of-inhibitor-binding-pockets-of-d-amino-acid-oxidase-using-docking-simulation-and-n-sulfanylethylanilide-based-labeling-technology
#1
Taiki Kohiki, Yusuke Kato, Yusuke Nishikawa, Kazuko Yorita, Ikuko Sagawa, Masaya Denda, Tsubasa Inokuma, Akira Shigenaga, Kiyoshi Fukui, Akira Otaka
Because of the relevance of d-serine (d-Ser) to schizophrenia, inhibitors of d-amino acid oxidase (DAO), which catalyzes degradation of d-Ser in the presence of flavin adenine dinucleotide (FAD), are expected to be anti-schizophrenia therapeutics. In this study, binding pockets of DAO to its inhibitor 4-bromo-3-nitrobenzoic acid were searched by combining in silico docking simulation and labeling experiments employing an N-sulfanylethylanilide-based labeling technology that we have developed. The results clearly demonstrated that there are two binding pockets: one is shared with d-Ser and FAD, and the other is an unexpected cleft between the subunits of a DAO dimer...
May 16, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28429324/photomovement-in-euglena
#2
Donat-P Häder, Mineo Iseki
Motile microorganisms such as the green Euglena gracilis use a number of external stimuli to orient in their environment. They respond to light with photophobic responses, photokinesis and phototaxis, all of which can result in accumulations of the organisms in suitable habitats. The light responses operate synergistically with gravitaxis, aerotaxis and other responses. Originally the microscopically obvious stigma was thought to be the photoreceptor, but later the paraxonemal body (PAB, paraflagellar body) has been identified as the light responsive organelle, located in the trailing flagellum inside the reservoir...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28427558/a-computational-approach-to-identify-the-biophysical-and-structural-aspects-of-methylenetetrahydrofolate-reductase-mthfr-mutations-a222v-e429a-and-r594q-leading-to-schizophrenia
#3
Himani Tanwar, P Sneha, D Thirumal Kumar, R Siva, Charles Emmanuel Jebaraj Walter, C George Priya Doss
The association between depression and methylenetetrahydrofolate reductase (MTHFR) has been continually demonstrated in clinical studies, yet there are sparse resources available to build a relationship between the mutations associated with MTHFR and depression. The common mutations found to be associated with schizophrenia and MTHFR are A222V, E429A, and R594Q. Although abundant research on structural and functional effects caused by A222V mutation is available, very less amount of studies have been done on the other two mutants (E429A and R594Q)...
2017: Advances in Protein Chemistry and Structural Biology
https://www.readbyqxmd.com/read/28402850/fad-regulates-cryptochrome-protein-stability-and-circadian-clock-in-mice
#4
Arisa Hirano, Daniel Braas, Ying-Hui Fu, Louis J Ptáček
The circadian clock generates biological rhythms of metabolic and physiological processes, including the sleep-wake cycle. We previously identified a missense mutation in the flavin adenine dinucleotide (FAD) binding pocket of CRYPTOCHROME2 (CRY2), a clock protein that causes human advanced sleep phase. This prompted us to examine the role of FAD as a mediator of the clock and metabolism. FAD stabilized CRY proteins, leading to increased protein levels. In contrast, knockdown of Riboflavin kinase (Rfk), an FAD biosynthetic enzyme, enhanced CRY degradation...
April 11, 2017: Cell Reports
https://www.readbyqxmd.com/read/28393477/residues-at-a-single-site-differentiate-animal-cryptochromes-from-cyclobutane-pyrimidine-dimer-photolyases-by-affecting-the-proteins-preferences-for-reduced-fad
#5
Lei Xu, Bin Wen, Yuan Wang, Changqing Tian, Mingcai Wu, Guoping Zhu
Cryptochromes (CRYs) and photolyases belong to the cryptochrome/photolyase family (CPF). Reduced FAD is essential for photolyases to photorepair UV induced cyclobutane pyrimidine dimers (CPDs) or 6-4 photoproducts in DNA. In Drosophila CRY (dCRY, a type I animal CRY), FAD is converted to the anionic radical but not to the reduced state during illumination, which may induce a conformational change in the protein to relay the light signal downstream. To explore the foundation of these differences, multiple sequence alignment of 650 CPF protein sequences was performed...
April 10, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28373120/molecular-cloning-mrna-expression-and-nutritional-regulation-of-a-%C3%AE-6-fatty-acyl-desaturase-like-gene-of-mud-crab-scylla-paramamosain
#6
Zhideng Lin, Meilin Hao, Dashi Zhu, Shengkang Li, Xiaobo Wen
Fatty acyl desaturases (Fads) are critical enzymes in the pathways for the biosynthesis of the highly unsaturated fatty acids (HUFA). Here we report on the molecular cloning, tissue expression and nutritional regulation of a Δ6 fatty acyl desaturase-like (Δ6 Fad-like) gene from mud crab, Scylla paramamosain. The full-length cDNA was 1973bp, with a 201bp of 5'-UTR, a 443bp of 3'-UTR, and an ORF of 1329bp that encoded a protein of 442 amino acids. Bioinformatics analysis showed that the deduced peptide sequence possessed the typical features of the microsomal Fads, including N-terminal cytochrome b5 domain containing the heme-binding motif (H-P-G-G), three histidine-rich boxes and three membrane-spanning regions...
March 31, 2017: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/28295778/the-ricaft-ymca-ylbf-yaat-complex-carries-two-4fe-4s-2-clusters-and-may-respond-to-redox-changes
#7
Andrew W Tanner, Valerie J Carabetta, Ryan J Martinie, Ameya A Mashruwala, Jeffrey M Boyd, Carsten Krebs, David Dubnau
During times of environmental insult, Bacillus subtilis undergoes developmental changes leading to biofilm formation, sporulation and competence. Each of these states is regulated in part by the phosphorylated form of the master response regulator Spo0A (Spo0A∼P). The phosphorylation state of Spo0A is controlled by a multi-component phosphorelay. RicA, RicF and RicT (previously YmcA, YlbF and YaaT) have been shown to be important regulatory proteins for multiple developmental fates. These proteins directly interact and form a stable complex, which has been proposed to accelerate the phosphorelay...
June 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28291250/site-to-site-interdomain-communication-may-mediate-different-loss-of-function-mechanisms-in-a-cancer-associated-nqo1-polymorphism
#8
Encarnación Medina-Carmona, Jose L Neira, Eduardo Salido, Julian E Fuchs, Rogelio Palomino-Morales, David J Timson, Angel L Pey
Disease associated genetic variations often cause intracellular enzyme inactivation, dysregulation and instability. However, allosteric communication of mutational effects to distant functional sites leading to loss-of-function remains poorly understood. We characterize here interdomain site-to-site communication by which a common cancer-associated single nucleotide polymorphism (c.C609T/p.P187S) reduces the activity and stability in vivo of NAD(P)H:quinone oxidoreductase 1 (NQO1). NQO1 is a FAD-dependent, two-domain multifunctional stress protein acting as a Phase II enzyme, activating cancer pro-drugs and stabilizing p53 and p73α oncosuppressors...
March 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28270505/essential-role-of-the-flexible-linker-on-the-conformational-equilibrium-of-bacterial-peroxiredoxin-reductase-for-effective-regeneration-of-peroxiredoxin
#9
Neelagandan Kamariah, Birgit Eisenhaber, Frank Eisenhaber, Gerhard Grüber
Reactive oxygen species (ROS) can damage DNA, proteins, and lipids, so cells have antioxidant systems that regulate ROS. In many bacteria, a dedicated peroxiredoxin reductase, alkyl hydroperoxide reductase subunit F (AhpF), catalyzes the rapid reduction of the redox-active disulfide center of the antioxidant protein peroxiredoxin (AhpC) to detoxify ROS such as hydrogen peroxide, organic hydroperoxide, and peroxynitrite. AhpF is a flexible multidomain protein that enables a series of electron transfers among the redox centers by accepting reducing equivalents from NADH...
April 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28256579/proline-dehydrogenase-from-thermus-thermophilus-does-not-discriminate-between-fad-and-fmn-as-cofactor
#10
Mieke M E Huijbers, Marta Martínez-Júlvez, Adrie H Westphal, Estela Delgado-Arciniega, Milagros Medina, Willem J H van Berkel
Flavoenzymes are versatile biocatalysts containing either FAD or FMN as cofactor. FAD often binds to a Rossmann fold, while FMN prefers a TIM-barrel or flavodoxin-like fold. Proline dehydrogenase is denoted as an exception: it possesses a TIM barrel-like fold while binding FAD. Using a riboflavin auxotrophic Escherichia coli strain and maltose-binding protein as solubility tag, we produced the apoprotein of Thermus thermophilus ProDH (MBP-TtProDH). Remarkably, reconstitution with FAD or FMN revealed that MBP-TtProDH has no preference for either of the two prosthetic groups...
March 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28225078/distribution-of-valence-electrons-of-the-flavin-cofactor-in-nadh-cytochrome-b5-reductase
#11
Kiyofumi Takaba, Kazuki Takeda, Masayuki Kosugi, Taro Tamada, Kunio Miki
Flavin compounds such as flavin adenine dinucleotide (FAD), flavin mononucleotide and riboflavin make up the active centers in flavoproteins that facilitate various oxidoreductive processes. The fine structural features of the hydrogens and valence electrons of the flavin molecules in the protein environment are critical to the functions of the flavoproteins. However, information on these features cannot be obtained from conventional protein X-ray analyses at ordinary resolution. Here we report the charge density analysis of a flavoenzyme, NADH-cytochrome b5 reductase (b5R), at an ultra-high resolution of 0...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28091661/biochemical-characterization-of-the-selenoproteome-in-gallus-gallus-via-bioinformatics-analysis-structure-function-relationships-and-interactions-of-binding-molecules
#12
Shi-Yong Zhu, Xue-Nan Li, Xiao-Chen Sun, Jia Lin, Wei Li, Cong Zhang, Jin-Long Li
Knowledge about mammalian selenoproteins is increasing. However, the selenoproteome of birds remains considerably less understood, especially concerning its biochemical characterization, structure-function relationships and the interactions of binding molecules. In this work, the SECIS elements, subcellular localization, protein domains and interactions of binding molecules of the selenoproteome in Gallus gallus were analyzed using bioinformatics tools. We carried out comprehensive analyses of the structure-function relationships and interactions of the binding molecules of selenoproteins, to provide biochemical characterization of the selenoproteome in Gallus gallus...
January 16, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/27994211/proteome-changes-in-penicillium-expansum-grown-in-a-medium-derived-from-host-plant
#13
Xiaoshuang Xia, Huan Li, Fei Liu, Ye Zhang, Qi Zhang, Yun Wang, Peiwu Li
Penicillium expansum causes blue mold rot, a prevalent postharvest disease of pome fruit, and is also the main producer of the patulin. However, knowledge on the molecular mechanisms involved in this pathogen-host interaction remains largely unknown. In this work, a two-dimensional gel electrophoresis-based proteomic approach was applied to probe changes in P. expansum 3.3703 cultivated in apple juice medium, which was used to mimic the in planta condition. The results showed that the pH value and reducing sugar content in the apple juice medium decreased whereas the patulin content increased with the growing of P...
March 28, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27992645/crystal-structures-of-bacterial-6-4-photolyase-mutants-with-impaired-dna-repair-activity
#14
Fan Zhang, Hongju Ma, Kalinga Bowatte, Dennis Kwiatkowski, Esther Mittmann, Heba Qasem, Norbert Krauss, Xiaoli Zeng, Zhong Ren, Patrick Scheerer, Xiaojing Yang, Tilman Lamparter
PhrB from Agrobacterium fabrum is the first prokaryotic photolyase which repairs (6-4) UV DNA photoproducts. The protein harbors three cofactors: the enzymatically active FAD chromophore, a second chromophore, 6,7-dimethyl-8-ribityllumazine (DMRL) and a cubane-type Fe-S cluster. Tyr424 of PhrB is part of the DNA-binding site and could provide an electron link to the Fe-S cluster. The PhrBY424F mutant showed reduced binding of lesion DNA and loss of DNA repair. The mutant PhrBI51W is characterized by the loss of the DMRL chromophore, reduced photoreduction and reduced DNA repair capacity...
December 19, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27986991/recombinant-expression-and-characterization-of-a-l-amino-acid-oxidase-from-the-fungus-rhizoctonia-solani
#15
Katharina Hahn, Katrin Neumeister, Andreas Mix, Tilman Kottke, Harald Gröger, Gabriele Fischer von Mollard
L-Amino acid oxidases (L-AAOs) catalyze the oxidative deamination of L-amino acids to the corresponding α-keto acids, ammonia, and hydrogen peroxide. L-AAOs are homodimeric enzymes with FAD as a non-covalently bound cofactor. They are of potential interest for biotechnological applications. However, heterologous expression has not succeeded in producing large quantities of active recombinant L-AAOs with a broad substrate spectrum so far. Here, we report the heterologous expression of an active L-AAO from the fungus Rhizoctonia solani in Escherichia coli as a fusion protein with maltose-binding protein (MBP) as a solubility tag...
April 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27976856/unveiling-the-pathogenic-molecular-mechanisms-of-the-most-common-variant-p-k329e-in-medium-chain-acyl-coa-dehydrogenase-deficiency-by-in-vitro-and-in-silico-approaches
#16
Cátia A Bonito, Joana Nunes, João Leandro, Filipa Louro, Paula Leandro, Fátima V Ventura, Rita C Guedes
Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) is the most common genetic disorder affecting the mitochondrial fatty acid β-oxidation pathway. The mature and functional form of human MCAD (hMCAD) is a homotetramer assembled as a dimer of dimers (monomers A/B and C/D). Each monomer binds a FAD cofactor, necessary for the enzyme's activity. The most frequent mutation in MCADD results from the substitution of a lysine with a glutamate in position 304 of mature hMCAD (p.K329E in the precursor protein)...
December 27, 2016: Biochemistry
https://www.readbyqxmd.com/read/27935052/an-ethenoadenine-fad-analog-accelerates-uv-dimer-repair-by-dna-photolyase
#17
Madhavan Narayanan, Vijay R Singh, Goutham Kodali, Kimberly Jacoby, Katarina Moravcevic, Robert J Stanley
Reduced anionic flavin adenine dinucleotide (FADH-) is the critical cofactor in DNA photolyase (PL) for the repair of cyclobutane pyrimidine dimers (CPD) in UV-damaged DNA. The initial step involves photoinduced electron transfer from *FADH- to the CPD. The adenine (Ade) moiety is nearly stacked with the flavin ring, an unusual conformation compared to other FAD-dependent proteins. The role of this proximity has not been unequivocally elucidated. Some studies suggest that Ade is a radical intermediate, but others conclude that Ade modulates the electron transfer rate constant (kET) through superexchange...
December 9, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27923678/flavin-nucleotides-act-as-electron-shuttles-mediating-reduction-of-the-2fe-2s-clusters-in-mitochondrial-outer-membrane-protein-mitoneet
#18
Aaron P Landry, Yiming Wang, Zishuo Cheng, Robert B Crochet, Yong-Hwan Lee, Huangen Ding
MitoNEET, a primary target of type II diabetes drug pioglitazone, has an essential role in regulating energy metabolism, iron homeostasis, and production of reactive oxygen species in mitochondria. Structurally, mitoNEET is anchored to the mitochondrial outer membrane via its N-terminal transmembrane α-helix. The C-terminal cytosolic domain of mitoNEET hosts a redox active [2Fe-2S] cluster via three cysteine and one histidine residues. Here we report that the reduced flavin nucleotides can rapidly reduce the mitoNEET [2Fe-2S] clusters under anaerobic or aerobic conditions...
January 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/27901000/endoplasmic-reticulum-stress-induces-the-early-appearance-of-pro-apoptotic-and-anti-apoptotic-proteins-in-neurons-of-five-familial-alzheimer-s-disease-mice
#19
Hui Shen, Xiao-Dong Pan, Jing Zhang, Yu-Qi Zeng, Meng Zhou, Lu-Meng Yang, Bing Ye, Xiao-Man Dai, Yuan-Gui Zhu, Xiao-Chun Chen
BACKGROUND: Amyloid β (Aβ) deposits and the endoplasmic reticulum stress (ERS) are both well established in the development and progression of Alzheimer's disease (AD). However, the mechanism and role of Aβ-induced ERS in AD-associated pathological progression remain to be elucidated. METHODS: The five familial AD (5×FAD) mice and wild-type (WT) mice aged 2, 7, and 12 months were used in the present study. Morris water maze test was used to evaluate their cognitive performance...
December 5, 2016: Chinese Medical Journal
https://www.readbyqxmd.com/read/27864152/the-flavinyl-transferase-apbe-of-pseudomonas-stutzeri-matures-the-nosr-protein-required-for-nitrous-oxide-reduction
#20
Lin Zhang, Christian Trncik, Susana L A Andrade, Oliver Einsle
The copper-containing enzyme nitrous oxide reductase (N2OR) catalyzes the transformation of nitrous oxide (N2O) to dinitrogen (N2) in microbial denitrification. Several accessory factors are essential for assembling the two copper sites CuA and CuZ, and for maintaining the activity. In particular, the deletion of either the transmembrane iron-sulfur flavoprotein NosR or the periplasmic protein NosX, a member of the ApbE family, abolishes N2O respiration. Here we demonstrate through biochemical and structural studies that the ApbE protein from Pseudomonas stutzeri, where the nosX gene is absent, is a monomeric FAD-binding protein that can serve as the flavin donor for NosR maturation via covalent flavinylation of a threonine residue...
February 2017: Biochimica et Biophysica Acta
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