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Dehalogenase

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https://www.readbyqxmd.com/read/28696117/catalytic-cycle-of-haloalkane-dehalogenases-towards-unnatural-substrates-explored-by-computational-modeling
#1
Sérgio M Marques, Zuzana Dunajova, Zbynek Prokop, Radka Chaloupkova, Jan Brezovsky, Jiri Damborsky
The anthropogenic toxic compound 1,2,3-trichloropropane is poorly degradable by natural enzymes. We have previously constructed the haloalkane dehalogenase DhaA31 by focused directed evolution (Pavlova, M. et al., Nat. Chem. Biol. 2009, 5, 727-73), which is 32 times more active than the wild-type enzyme and is currently the most active variant known against that substrate. Recent evidence has shown that the structural basis responsible for the higher activity of DhaA31 was poorly understood. Here we have undertaken a comprehensive computational study of the main steps involved in the biocatalytic hydrolysis of 1,2,3-trichloropropane to decipher the structural basis for such enhancements...
July 11, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28690604/phenol-is-the-initial-product-formed-during-growth-and-degradation-of-bromobenzene-by-tropical-marine-yeast-yarrowia-lipolytica-ncim-3589-via-an-early-dehalogenation-step
#2
Aakanksha A Vatsal, Smita S Zinjarde, Ameeta RaviKumar
Bromobenzene (BrB), a hydrophobic, recalcitrant organic compound, is listed by the environmental protection agencies as an environmental and marine pollutant having hepatotoxic, mutagenic, teratogenic, and carcinogenic effects. The tropical marine yeast Yarrowia lipolytica 3589 was seen to grow aerobically on BrB and displayed a maximum growth rate (μmax) of 0.04 h(-1). Furthermore, we also observed an increase in cell size and sedimentation velocity for the cells grown on BrB as compared to the glucose grown cells...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28674849/metagenome-derived-haloalkane-dehalogenases-with-novel-catalytic-properties
#3
Michael Kotik, Pavel Vanacek, Antonin Kunka, Zbynek Prokop, Jiri Damborsky
Haloalkane dehalogenases (HLDs) are environmentally relevant enzymes cleaving a carbon-halogen bond in a wide range of halogenated pollutants. PCR with degenerate primers and genome-walking was used for the retrieval of four HLD-encoding genes from groundwater-derived environmental DNA. Using specific primers and the environmental DNA as a template, we succeeded in generating additional amplicons, resulting altogether in three clusters of sequences with each cluster comprising 8-13 closely related putative HLD-encoding genes...
July 3, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28671181/cobamide-mediated-enzymatic-reductive-dehalogenation-via-long-range-electron-transfer
#4
Cindy Kunze, Martin Bommer, Wilfred R Hagen, Marie Uksa, Holger Dobbek, Torsten Schubert, Gabriele Diekert
The capacity of metal-containing porphyrinoids to mediate reductive dehalogenation is implemented in cobamide-containing reductive dehalogenases (RDases), which serve as terminal reductases in organohalide-respiring microbes. RDases allow for the exploitation of halogenated compounds as electron acceptors. Their reaction mechanism is under debate. Here we report on substrate-enzyme interactions in a tetrachloroethene RDase (PceA) that also converts aryl halides. The shape of PceA's highly apolar active site directs binding of bromophenols at some distance from the cobalt and with the hydroxyl substituent towards the metal...
July 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/28666054/conversion-of-a-dehalogenase-to-a-nitroreductase-by-swapping-its-flavin-cofactor-with-a-5-deazaflavin-analog
#5
Qi Su, Petrina A Boucher, Steve Rokita
Natural and engineered nitroreductases have rarely supported full reduction of nitroaromatics to their amine products and more typically transformations are limited to formation of the hydroxylamine intermediates. Efficient use of these enzymes also requires a regenerating system for NAD(P)H to avoid the costs associated with this natural reductant. Iodotyrosine deiodinase is a member of the same structural superfamily of many nitroreductases but does not directly consume reducing equivalents from NAD(P)H nor demonstrates a nitroreductase activity...
June 30, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28654328/biochemistry-of-catabolic-reductive-dehalogenation
#6
REVIEW
Maeva Fincker, Alfred M Spormann
A wide range of phylogenetically diverse microorganisms couple the reductive dehalogenation of organohalides to energy conservation. Key enzymes of such anaerobic catabolic pathways are corrinoid and Fe-S cluster-containing, membrane-associated reductive dehalogenases. These enzymes catalyze the reductive elimination of a halide and constitute the terminal reductases of a short electron transfer chain. Enzymatic and physiological studies revealed the existence of quinone-dependent and quinone-independent reductive dehalogenases that are distinguishable at the amino acid sequence level, implying different modes of energy conservation in the respective microorganisms...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28648508/iodide-handling-disorders-nis-tpo-tg-iyd
#7
REVIEW
Héctor M Targovnik, Cintia E Citterio, Carina M Rivolta
Iodide Handling Disorders lead to defects of the biosynthesis of thyroid hormones (thyroid dyshormonogenesis, TD) and thereafter congenital hypothyroidism (CH), the most common endocrine disease characterized by low levels of circulating thyroid hormones. The prevalence of CH is 1 in 2000-3000 live births. Prevention of CH is based on prenatal diagnosis, carrier identification, and genetic counseling. In neonates a complete diagnosis of TD should include clinical examination, biochemical thyroid tests, thyroid ultrasound, radioiodine or technetium scintigraphy and perchlorate discharge test (PDT)...
March 2017: Best Practice & Research. Clinical Endocrinology & Metabolism
https://www.readbyqxmd.com/read/28648395/the-complete-genome-of-the-tetrachloroethene-respiring-epsilonproteobacterium-sulfurospirillum-halorespirans
#8
Tobias Goris, Benjamin Schenz, Johannes Zimmermann, Mikael Lemos, Jörg Hackermüller, Torsten Schubert, Gabriele Diekert
Sulfurospirillum halorespirans is a bacterium that couples the reductive dehalogenation of chlorinated ethenes to growth. This process is called organohalide respiration (OHR), which can be of importance for bioremediation. Here, we report the complete genome of S. halorespirans, the second one of an organohalide-respiring Epsilonproteobacterium after that of Sulfurospirillum multivorans. With both genomes at hand, we were able to ascertain that the genomic region encoding OHR proteins in Epsilonproteobacteria differs from that found in organohalide-respiring bacteria (OHRB) affiliated to other phyla and that the production of a unique cobamide, norpseudo-B12, might not be limited to the model organism S...
June 22, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28641560/functional-and-catalytic-characterization-of-the-detoxifying-enzyme-haloalkane-dehalogenase-from-rhizobium-leguminosarum
#9
Nikolaos Georgakis, Evangelia Chronopoulou, Maria Anna Gad, Dimitrios Skliros, Rodica Efrose, Emmanouil Flemetakis, Nikolaos E Labrou
Haloalkanes are acutely toxic to animals and humans and their toxic effects are mainly observed in the liver, kidneys and central nervous system. In the present work, the haloalkane dehalogenase from Rhizobium leguminosarum bv. trifolii (DrlA) was characterized. Reverse transcription polymerase chain reaction analysis and enzyme activity assays revealed that the DrlA gene expression in R. leguminosarum bv. trifolii is induced by 1,2-dibromoethane (1,2-DBE) during the early exponential phase. The gene of the enzyme was isolated, cloned and expressed in E...
June 20, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28637831/oshad1-a-haloacid-dehalogenase-like-apase-enhances-phosphate-accumulation
#10
Bipin Kumar Pandey, Poonam Mehra, Lokesh Verma, Jyoti Bhadouria, Jitender Giri
Phosphorus (P) deficiency limits plant growth and crop yield. Since, plants can absorb only inorganic form of P (Pi), a large portion of soil P (organic and inorganic P complexes) remains largely unused. Here, we identified and characterized a PHR2 regulated; novel low Pi responsive haloacid dehalogenase (HAD)-like hydrolase, OsHAD1. While, OsHAD1 is a functional HAD protein having both acid phosphatase and phytase activity; it showed little homology with other known low Pi responsive HAD superfamily members...
June 21, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28631300/a-bacterial-chloroform-reductive-dehalogenase-purification-and-biochemical-characterization
#11
Bat-Erdene Jugder, Susanne Bohl, Helene Lebhar, Robert D Healey, Mike Manefield, Christopher P Marquis, Matthew Lee
We report herein the purification of a chloroform (CF)-reducing enzyme, TmrA, from the membrane fraction of a strict anaerobe Dehalobacter sp. strain UNSWDHB to apparent homogeneity with an approximate 23-fold increase in relative purity compared to crude lysate. The membrane fraction obtained by ultracentrifugation was solubilized in Triton X-100 in the presence of glycerol, followed by purification by anion exchange chromatography. The molecular mass of the purified TmrA was determined to be 44.5 kDa by SDS-PAGE and MALDI-TOF/TOF...
June 20, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28631290/a-h2-oxidizing-1-2-3-trichlorobenzene-reducing-multienzyme-complex-isolated-from-the-obligately-organohalide-respiring-bacterium-dehalococcoides-mccartyi-strain-cbdb1
#12
Stefanie Hartwig, Nadya Dragomirova, Anja Kublik, Dominique Türkowsky, Martin von Bergen, Ute Lechner, Lorenz Adrian, R Gary Sawers
Dehalococcoides mccartyi is a small, slow-growing bacterium of the phylum Chloroflexi that conserves energy using aliphatic and aromatic organohalides as electron acceptors, and hydrogen as sole electron donor. A recent study identified a protein complex in the membrane of strain CBDB1 comprising a Hup hydrogenase, a complex iron-sulphur molybdoprotein and a reductive dehalogenase (RdhA) that catalyses reduction of 1,2,3,4-tetrachlorobenzene. Using a combination of size-exclusion chromatography, in-gel hydrogenase activity-staining, immunological analysis and mass spectrometry, we identified here a large molecular mass protein complex solubilized from the cytoplasmic membrane of D...
June 19, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28618195/novel-reductive-dehalogenases-from-the-marine-sponge-associated-bacterium-desulfoluna-spongiiphila
#13
Jie Liu, Nora Lopez, Young-Beom Ahn, Tatyana Goldberg, Yana Bromberg, Lee J Kerkhof, Max M Häggblom
Desulfoluna spongiiphila strain AA1 is an organohalide respiring bacterium, isolated from the marine sponge Aplysina aerophoba, that can use brominated and iodinated phenols, in addition to sulfate and thiosulfate as terminal electron acceptors. The genome of Desulfoluna spongiiphila strain AA1 is approximately 6.5 Mb. Three putative reductive dehalogenase (rdhA) genes involved in respiratory metabolism of organohalides were identified within the sequence. Conserved motifs found in respiratory reductive dehalogenases (a twin arginine translocation signal sequence and two iron-sulfur clusters) were present in all three putative AA1 rdhA genes...
June 15, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28618081/loss-of-the-ssra-genome-island-led-to-partial-debromination-in-the-pbde-respiring-dehalococcoides-mccartyi-strain-gy50
#14
Chang Ding, Matthew J Rogers, Kun-Lin Yang, Jianzhong He
Polybrominated diphenyl ethers (PBDEs), chemicals commonly used as flame-retardants in consumer products, are emerging persistent organic pollutants that are ubiquitous in the environment. In this study, we report a PBDE-respiring isolate - Dehalococcoides mccartyi strain GY50, which debrominates the most toxic tetra- and penta-BDE congeners (∼1.4 µM) to diphenyl ether within 12 days with hydrogen as the electron donor. The complete genome sequence revealed 26 reductive dehalogenase homologous genes (rdhAs), among which three genes (pbrA1, pbrA2 and pbrA3) were highly expressed during PBDE debromination...
June 15, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28593475/functional-metagenomics-of-oil-impacted-mangrove-sediments-reveals-high-abundance-of-hydrolases-of-biotechnological-interest
#15
Júlia Ronzella Ottoni, Lucélia Cabral, Sanderson Tarciso Pereira de Sousa, Gileno Vieira Lacerda Júnior, Daniela Ferreira Domingos, Fábio Lino Soares Junior, Mylenne Calciolari Pinheiro da Silva, Joelma Marcon, Armando Cavalcante Franco Dias, Itamar Soares de Melo, Anete Pereira de Souza, Fernando Dini Andreote, Valéria Maia de Oliveira
Mangroves are located in coastal wetlands and are susceptible to the consequences of oil spills, what may threaten the diversity of microorganisms responsible for the nutrient cycling and the consequent ecosystem functioning. Previous reports show that high concentration of oil favors the incidence of epoxide hydrolases and haloalkane dehalogenases in mangroves. This finding has guided the goals of this study in an attempt to broaden the analysis to other hydrolases and thereby verify whether oil contamination interferes with the prevalence of particular hydrolases and their assigned microorganisms...
July 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28587829/pegylation-with-the-thiosuccinimido-butylamine-linker-significantly-increases-the-stability-of-haloalkane-dehalogenase-dhaa
#16
Yuan-Zhong Zhao, Wei-Li Yu, He Zheng, Xuan Guo, Nan Guo, Tao Hu, Jin-Yi Zhong
Haloalkane dehalogenase (HLD) can catalyze the hydrolytic dehalogenation of halogenated compounds. However, HLD suffers from the poor stability to resist the environmental stress. PEGylation is an effective approach to enhance the stability of enzymes. The linker is an important stabilization factor of PEGylation. Thus, the linkers of the PEGylated HLD were optimized to improve the stability of HLD in the present study. The PEGylated haloalkane dehalogenase DhaAs with methylamine (Ml), carbamate (Cm) and thiosuccinimido butylamine (Tb) linkers were prepared, respectively...
June 3, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28533514/isolation-and-genomic-characterization-of-a-dehalococcoides-strain-suggests-genomic-rearrangement-during-culture
#17
Masafumi Yohda, Kentaro Ikegami, Yuto Aita, Mizuki Kitajima, Ayane Takechi, Megumi Iwamoto, Tomomi Fukuda, Noriyoshi Tamura, Junji Shibasaki, Seiji Koike, Daisuke Komatsu, Sakari Miyagi, Minoru Nishimura, Yoshihito Uchino, Akino Shiroma, Makiko Shimoji, Hinako Tamotsu, Noriko Ashimine, Misuzu Shinzato, Shun Ohki, Kazuma Nakano, Kuniko Teruya, Kazuhito Satou, Takashi Hirano, Osami Yagi
We have developed and characterized a bacterial consortium that reductively dechlorinates trichloroethene to ethene. Quantitative PCR analysis for the 16S rRNA and reductive dehalogenase genes showed that the consortium is highly enriched with Dehalococcoides spp. that have two vinyl chloride reductive dehalogenase genes, bvcA and vcrA, and a trichloroethene reductive dehalogenase gene, tceA. The metagenome analysis of the consortium by the next generation sequencer SOLiD 3 Plus suggests that a Dehalococcoides sp...
May 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28527381/enantioselectivity-of-haloalkane-dehalogenase-linb-on-the-degradation-of-1-2-dichloropropane-a-qm-mm-study
#18
Xiaowen Tang, Ruiming Zhang, Yanwei Li, Qingzhu Zhang, Wenxing Wang
The hydrolysis dechlorination mechanism of a chiral organochlorinepollutant, 1,2-dichloropropane (DCP), catalyzed by haloalkane dehalogenase LinB has been investigated by using a combined quantum mechanics/molecular mechanics method. LinB was confirmed to be enantioselective towards the catabolism of the racemic mixture. Based on the SN2 nucleophilic substitution mechanism, the dechlorination process was identified as the rate-determining step in LinB-catalyzed degradation of 1,2-dichloropropane, the Boltzmann-weighted average potential barrier of which is 18...
May 12, 2017: Bioorganic Chemistry
https://www.readbyqxmd.com/read/28499743/resolution-of-the-uncertainty-in-the-kinetic-mechanism-for-the-trans-3-chloroacrylic-acid-dehalogenase-catalyzed-reaction
#19
Jamison P Huddleston, Susan C Wang, Kenneth A Johnson, Christian P Whitman
trans- and cis-3-Chloroacrylic acid dehalogenase (CaaD and cis-CaaD, respectively) catalyze the hydrolytic dehalogenation of their respective isomers and represent key steps in the bacterial conversion of 1,3-dichloropropene to acetaldehyde. In prior work, a kinetic mechanism for the CaaD-catalyzed reaction could not be unequivocally determined because (1) the order of product release could not be determined and (2) the fluorescence factor for the enzyme species, E*PQ (where P = bromide and Q = malonate semialdehyde, the two products of the reaction) could not be assigned...
June 1, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28424844/microbial-reductive-dehalogenation-of-trihalomethanes-by-a-dehalobacter-containing-co-culture
#20
Siyan Zhao, Matthew J Rogers, Jianzhong He
Trihalomethanes such as chloroform and bromoform, although well-known as a prominent class of disinfection by-products, are ubiquitously distributed in the environment due to widespread industrial usage in the past decades. Chloroform and bromoform are particularly concerning, of high concentrations detected and with long half-lives up to several hundred days in soils and groundwater. In this study, we report a Dehalobacter- and Desulfovibrio-containing co-culture that exhibits dehalogenation of chloroform (~0...
July 2017: Applied Microbiology and Biotechnology
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