Genomes and Genes
Summary: Non-heme iron-containing enzymes that incorporate two atoms of OXYGEN into the substrate. They are important in biosynthesis of FLAVONOIDS; GIBBERELLINS; and HYOSCYAMINE; and for degradation of AROMATIC HYDROCARBONS.
- Cliffe L, Hirsch G, Wang J, Ekanayake D, Bullard W, Hu M, et al. JBP1 and JBP2 proteins are Fe2+/2-oxoglutarate-dependent dioxygenases regulating hydroxylation of thymidine residues in trypanosome DNA. J Biol Chem. 2012;287:19886-95 pubmed publisher..530 nm attributed to metal chelation of 2-OG bound to JBP, a spectroscopic signature of Fe(2+)/2-OG-dependent dioxygenases. The N-terminal thymidine hydroxylase domain of JBP1 is sufficient for full activity and mutation of residues ..
- Whitteck J, Malova P, Peck S, Cicchillo R, Hammerschmidt F, van der Donk W. On the stereochemistry of 2-hydroxyethylphosphonate dioxygenase. J Am Chem Soc. 2011;133:4236-9 pubmed publisher..As a result, the mechanisms previously proposed for HEPD must be re-evaluated. ..
- Brandi F, Bar E, Mourgues F, Horváth G, Turcsi E, Giuliano G, et al. Study of 'Redhaven' peach and its white-fleshed mutant suggests a key role of CCD4 carotenoid dioxygenase in carotenoid and norisoprenoid volatile metabolism. BMC Plant Biol. 2011;11:24 pubmed publisher..Batsch.), and the role of carotenoid dioxygenases in determining differences in flesh color phenotype and volatile composition, the expression patterns of ..
- Sun L, Zhang M, Ren J, Qi J, Zhang G, Leng P. Reciprocity between abscisic acid and ethylene at the onset of berry ripening and after harvest. BMC Plant Biol. 2010;10:257 pubmed publisher..While after harvest, abiotic stresses principally (such as dehydration, harvest shock) could induce the transcription of VvNCED1 and the accumulation of ABA, thus starting the process of fruit senescence. ..
- Ogawa J, Kodera T, Smirnov S, Hibi M, Samsonova N, Koyama R, et al. A novel L-isoleucine metabolism in Bacillus thuringiensis generating (2S,3R,4S)-4-hydroxyisoleucine, a potential insulinotropic and anti-obesity amino acid. Appl Microbiol Biotechnol. 2011;89:1929-38 pubmed publisher..These novel findings pave a new way for the commercial production of HIL and also for AMKP. ..
- Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, et al. Duplex interrogation by a direct DNA repair protein in search of base damage. Nat Struct Mol Biol. 2012;19:671-6 pubmed publisher..Overall, the combination of duplex interrogation and oxidation chemistry allows ALKBH2 to detect and process diverse lesions efficiently and correctly. ..
- Chen H, Hwang S, Chen S, Shii C, Cheng W. ABA-mediated heterophylly is regulated by differential expression of 9-cis-epoxycarotenoid dioxygenase 3 in lilies. Plant Cell Physiol. 2011;52:1806-21 pubmed publisher..Collectively, our results demonstrate that NCED3 plays a key role in ABA-mediated heterophylly in lilies. ..
- Shah D, Conrad J, Heinz B, Brownlee J, Moran G. Evidence for the mechanism of hydroxylation by 4-hydroxyphenylpyruvate dioxygenase and hydroxymandelate synthase from intermediate partitioning in active site variants. Biochemistry. 2011;50:7694-704 pubmed publisher..The relatively small magnitude of this value argues best for a hydrogen atom abstraction/rebound mechanism. These data are the first definitive evidence for the nature of the hydroxylation reactions of HPPD and HMS. ..
- Seshagiri S, Stawiski E, Durinck S, Modrusan Z, Storm E, Conboy C, et al. Recurrent R-spondin fusions in colon cancer. Nature. 2012;488:660-4 pubmed publisher..The R-spondin gene fusions and several other gene mutations identified in this study provide new potential opportunities for therapeutic intervention in colon cancer. ..
- Sun L, Yuan B, Zhang M, Wang L, Cui M, Wang Q, et al. Fruit-specific RNAi-mediated suppression of SlNCED1 increases both lycopene and ?-carotene contents in tomato fruit. J Exp Bot. 2012;63:3097-108 pubmed publisher..In conclusion, ABA potentially regulated the degree of pigmentation and carotenoid composition during ripening and could control, at least in part, ethylene production and action in climacteric tomato fruit. ..
- Nordstrand L, Svärd J, Larsen E, Nilsen A, Ougland R, Furu K, et al. Mice lacking Alkbh1 display sex-ratio distortion and unilateral eye defects. PLoS ONE. 2010;5:e13827 pubmed publisher..Mouse AlkB homolog 1 (Alkbh1) is one of eight members of the newly discovered family of mammalian dioxygenases. In the present study we show non-Mendelian inheritance of the Alkbh1 targeted allele in mice...
- Di Giuro C, Buongiorno D, Leitner E, Straganz G. Exploring the catalytic potential of the 3-His mononuclear nonheme Fe(II) center: discovery and characterization of an unprecedented maltol cleavage activity. J Inorg Biochem. 2011;105:1204-11 pubmed publisher..3mM(-1)s(-1) and a strict coupling of O(2) reduction and substrate oxidation. Furthermore, the catalytic potential of the 3-His metal center for O(2) dependent catechol ring-cleavage and phenylpyruvate oxidation (PP) is demonstrated. ..
- Zheng G, Dahl J, Niu Y, Fedorcsak P, Huang C, Li C, et al. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol Cell. 2013;49:18-29 pubmed publisher..The discovery of this RNA demethylase strongly suggests that the reversible m(6)A modification has fundamental and broad functions in mammalian cells. ..
- Leihne V, Kirpekar F, Vågbø C, van den Born E, Krokan H, Grini P, et al. Roles of Trm9- and ALKBH8-like proteins in the formation of modified wobble uridines in Arabidopsis tRNA. Nucleic Acids Res. 2011;39:7688-701 pubmed publisher..The present study reveals a role in for several hitherto uncharacterized Arabidopsis proteins in the formation of modified wobble uridines. ..
- Shen L, Zhang Y. 5-Hydroxymethylcytosine: generation, fate, and genomic distribution. Curr Opin Cell Biol. 2013;25:289-96 pubmed publisher..converted to 5-hydroxymethylcytosine (5hmC) in mammalian cells by the ten-eleven translocation (Tet) family of dioxygenases. While 5mC has been extensively studied, we have just started to understand the distribution and function of ..
- Lashbrooke J, Young P, Dockrall S, Vasanth K, Vivier M. Functional characterisation of three members of the Vitis vinifera L. carotenoid cleavage dioxygenase gene family. BMC Plant Biol. 2013;13:156 pubmed publisher..The identification and functional characterisation of VvCCD4a and VvCCD4b suggest that these enzymes are primarily responsible for catalysing the cleavage of plastidial carotenoids...
- Hirao H, Morokuma K. Ferric superoxide and ferric hydroxide are used in the catalytic mechanism of hydroxyethylphosphonate dioxygenase: a density functional theory investigation. J Am Chem Soc. 2010;132:17901-9 pubmed publisher..The overall reaction pathway does not require the use of a high-valent ferryl intermediate but does require ferric superoxide and ferric hydroxide intermediates. ..
- Amengual J, Lobo G, Golczak M, Li H, Klimova T, Hoppel C, et al. A mitochondrial enzyme degrades carotenoids and protects against oxidative stress. FASEB J. 2011;25:948-59 pubmed publisher..Mammalian cells thus express a mitochondrial carotenoid-oxygenase that degrades carotenoids to protect these vital organelles. ..
- Hibi M, Kawashima T, Kodera T, Smirnov S, Sokolov P, Sugiyama M, et al. Characterization of Bacillus thuringiensis L-isoleucine dioxygenase for production of useful amino acids. Appl Environ Microbiol. 2011;77:6926-30 pubmed publisher..Consequently, the effective production of various modified amino acids would be possible using IDO as the biocatalyst. ..
- Lobo G, Isken A, Hoff S, Babino D, von Lintig J. BCDO2 acts as a carotenoid scavenger and gatekeeper for the mitochondrial apoptotic pathway. Development. 2012;139:2966-77 pubmed publisher..Thus, our study identifying BCDO2 as a crucial protective component against oxidative stress establishes this enzyme as mitochondrial carotenoid scavenger and a gatekeeper of the intrinsic apoptotic pathway. ..
- Bjørnstad L, Zoppellaro G, Tomter A, Falnes P, Andersson K. Spectroscopic and magnetic studies of wild-type and mutant forms of the Fe(II)- and 2-oxoglutarate-dependent decarboxylase ALKBH4. Biochem J. 2011;434:391-8 pubmed publisher..The present results demonstrate that ALKBH4 represents an active Fe(II)/2OG-dependent decarboxylase and suggest that the cysteine cluster is involved in processes other than Fe co-ordination. ..
- Ono Y, Minami A, Noike M, Higuchi Y, Toyomasu T, Sassa T, et al. Dioxygenases, key enzymes to determine the aglycon structures of fusicoccin and brassicicene, diterpene compounds produced by fungi. J Am Chem Soc. 2011;133:2548-55 pubmed publisher..to yield an aldehyde (8?-hydroxyfusicocca-1,10(14)-dien-16-al), although both dioxygenases had 51% amino acid sequence identity...
- Zhao H, Chen T. Tet family of 5-methylcytosine dioxygenases in mammalian development. J Hum Genet. 2013;58:421-7 pubmed publisher..in 2009, when the ten-eleven translocation (Tet) family of proteins was discovered as 5-methylcytosine (5mC) dioxygenases that convert 5mC to 5-hydroxymethylcytosine (5hmC)...
- Xu Y, Xu C, Kato A, Tempel W, Abreu J, Bian C, et al. Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development. Cell. 2012;151:1200-13 pubmed publisherTen-Eleven Translocation (Tet) family of dioxygenases dynamically regulates DNA methylation and has been implicated in cell lineage differentiation and oncogenesis...
- Iyer L, Zhang D, Burroughs A, Aravind L. Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA. Nucleic Acids Res. 2013;41:7635-55 pubmed publisherDiscovery of the TET/JBP family of dioxygenases that modify bases in DNA has sparked considerable interest in novel DNA base modifications and their biological roles...
- von Lintig J. Provitamin A metabolism and functions in mammalian biology. Am J Clin Nutr. 2012;96:1234S-44S pubmed publisher..Here, the advanced knowledge of ?-carotene metabolism is reviewed, which provides a molecular framework for understanding the role of this important micronutrient in health and disease. ..
- Lando D, Balmer J, Laue E, Kouzarides T. The S. pombe histone H2A dioxygenase Ofd2 regulates gene expression during hypoxia. PLoS ONE. 2012;7:e29765 pubmed publisher..Together, these data uncover a novel histone H2A modifying activity involved in the regulation of gene expression during hypoxia. ..
- Gan H, Shahir S, Yahya A. Cloning and functional analysis of the genes coding for 4-aminobenzenesulfonate 3,4-dioxygenase from Hydrogenophaga sp. PBC. Microbiology. 2012;158:1933-41 pubmed publisher..This is the first discovery, to our knowledge, of the functional genetic components for 4-ABS aromatic ring hydroxylation in the bacterial domain. ..
- Smirnov S, Sokolov P, Kodera T, Sugiyama M, Hibi M, Shimizu S, et al. A novel family of bacterial dioxygenases that catalyse the hydroxylation of free L-amino acids. FEMS Microbiol Lett. 2012;331:97-104 pubmed publisher..An investigation of enzyme kinetics suggested the existence of a novel subfamily of bacterial dioxygenases within the PF10014 family for which free L-amino acids could be accepted as in vivo substrates...
- Borel P. Genetic variations involved in interindividual variability in carotenoid status. Mol Nutr Food Res. 2012;56:228-40 pubmed publisher..g. copy number variants and epigenetic modifications, can modulate carotenoid status. One potential application of such research could be personalized dietary guidelines for carotenoids according to individual genetic characteristics...
- Bittner M, Kraus D, Lindeman S, Popescu C, Fiedler A. Synthetic, spectroscopic, and DFT studies of iron complexes with iminobenzo(semi)quinone ligands: implications for o-aminophenol dioxygenases. Chemistry. 2013;19:9686-98 pubmed publisherThe oxidative C-C bond cleavage of o-aminophenols by nonheme Fe dioxygenases is a critical step in both human metabolism (the kynurenine pathway) and the microbial degradation of nitroaromatic pollutants...
- Amengual J, Gouranton E, van Helden Y, Hessel S, Ribot J, Kramer E, et al. Beta-carotene reduces body adiposity of mice via BCMO1. PLoS ONE. 2011;6:e20644 pubmed publisher..Our study evidences an important role of BC for the control of body adiposity in mice and identifies Bcmo1 as critical molecular player for the regulation of PPAR? activity in adipocytes. ..
- Tittabutr P, Cho I, Li Q. Phn and Nag-like dioxygenases metabolize polycyclic aromatic hydrocarbons in Burkholderia sp. C3. Biodegradation. 2011;22:1119-33 pubmed publisher..PAHs), a class of ubiquitous pollutants, through multiple pathways, indicating existence of multiple dioxygenases (Seo et al., in Biodegradation 18:123-131, 2006a)...
- Ferraroni M, Matera I, Steimer L, Burger S, Scozzafava A, Stolz A, et al. Crystal structures of salicylate 1,2-dioxygenase-substrates adducts: A step towards the comprehension of the structural basis for substrate selection in class III ring cleaving dioxygenases. J Struct Biol. 2012;177:431-8 pubmed publisher..SDO is markedly different from the known gentisate 1,2-dioxygenases or 1-hydroxy-2-naphthoate dioxygenases, belonging to the same class, because of its unique ability to ..
- Korvald H, M lstad Moe A, Cederkvist F, Thiede B, Laerdahl J, Bj r s M, et al. Schizosaccharomyces pombe Ofd2 is a nuclear 2-oxoglutarate and iron dependent dioxygenase interacting with histones. PLoS ONE. 2011;6:e25188 pubmed publisher2-Oxoglutarate (2OG) dependent dioxygenases are ubiquitous iron containing enzymes that couple substrate oxidation to the conversion of 2OG to succinate and carbon dioxide...
- Peurala E, Koivunen P, Bloigu R, Haapasaari K, Jukkola Vuorinen A. Expressions of individual PHDs associate with good prognostic factors and increased proliferation in breast cancer patients. Breast Cancer Res Treat. 2012;133:179-88 pubmed publisher..PHD3 may be an important regulator of apoptosis and it is mainly found in tumors with good prognosis. PHD2 expression is likely to be involved in increased survival. ..
- Reuter K, Pittelkow M, Bursy J, Heine A, Craan T, Bremer E. Synthesis of 5-hydroxyectoine from ectoine: crystal structure of the non-heme iron(II) and 2-oxoglutarate-dependent dioxygenase EctD. PLoS ONE. 2010;5:e10647 pubmed publisher..for ectoine hydroxylation (EctD) is a member of the non-heme iron(II)-containing and 2-oxoglutarate-dependent dioxygenases (EC 1.14.11)...
- Nojiri H. Structural and molecular genetic analyses of the bacterial carbazole degradation system. Biosci Biotechnol Biochem. 2012;76:1-18 pubmed
- Ratcliffe P. Oxygen sensing and hypoxia signalling pathways in animals: the implications of physiology for cancer. J Physiol. 2013;591:2027-42 pubmed publisher..The oxygen-sensitive signal is generated by a series of non-haem Fe(II)- and 2-oxoglutarate-dependent dioxygenases that catalyse the post-translational hydroxylation of specific residues in the transcription factor hypoxia-..
- Su Y, Loos M, Giese N, Hines O, Diebold I, Gorlach A, et al. PHD3 regulates differentiation, tumour growth and angiogenesis in pancreatic cancer. Br J Cancer. 2010;103:1571-9 pubmed publisher..In vivo, PHD3 inhibited tumour growth by abrogation of tumour angiogenesis. Our results indicate essential functions of PHD3 in tumour growth, apoptosis and angiogenesis and through HIF-1-dependent and HIF-1-independent pathways. ..
- Bredebach M, Matern U, Martens S. Three 2-oxoglutarate-dependent dioxygenase activities of Equisetum arvense L. forming flavone and flavonol from (2S)-naringenin. Phytochemistry. 2011;72:557-63 pubmed publisher..The latter three activities were characterized as soluble, 2-oxoglutarate-dependent dioxygenases by their typical cofactor requirements and peculiar inhibition...
- Wu S, Xu W, Liu S, Chen B, Wang X, Wang Y, et al. Down-regulation of ALKBH2 increases cisplatin sensitivity in H1299 lung cancer cells. Acta Pharmacol Sin. 2011;32:393-8 pubmed publisher..Combined treatment modalities of ALKBH2 knockdown and cDDP chemotherapy have the potential to improve the efficacy in the treatment of NSCLC. ..
- Deplus R, Delatte B, Schwinn M, Defrance M, MÃ©ndez J, Murphy N, et al. TET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS. EMBO J. 2013;32:645-55 pubmed publisher..Together, our results unveil a step-wise model, involving TET-OGT interactions, promotion of GlcNAcylation, and influence on H3K4me3 via SET1/COMPASS, highlighting a novel means by which TETs may induce transcriptional activation. ..
- Ju K, Parales R. Application of nitroarene dioxygenases in the design of novel strains that degrade chloronitrobenzenes. Microb Biotechnol. 2009;2:241-52 pubmed publisher..These first-generation engineered strains demonstrate the utility of nitroarene dioxygenases in expanding the metabolic capabilities of bacteria and provide new options for improved biotreatment of ..
- Kiss J, Kirchberg J, Schneider M. Molecular oxygen sensing: implications for visceral surgery. Langenbecks Arch Surg. 2012;397:603-10 pubmed publisher..Here, we outline specific functions of PHD enzymes in surgically relevant pathological conditions, and discuss how these functions might be exploited in order to support the treatment of surgically relevant diseases. ..
- Yang H, Liu Y, Bai F, Zhang J, Ma S, Liu J, et al. Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation. Oncogene. 2013;32:663-9 pubmed publisherThe TET (ten-eleven translocation) family of ?-ketoglutarate (?-KG)-dependent dioxygenases catalyzes the sequential oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine and 5-carboxylcytosine, leading to ..
- Xu W, Yang H, Liu Y, Yang Y, Wang P, Kim S, et al. Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of ?-ketoglutarate-dependent dioxygenases. Cancer Cell. 2011;19:17-30 pubmed publisher..Here we demonstrate that 2-HG is a competitive inhibitor of multiple ?-KG-dependent dioxygenases, including histone demethylases and the TET family of 5-methlycytosine (5mC) hydroxylases...
- Nieminuszczy J, Grzesiuk E. Bacterial DNA repair genes and their eukaryotic homologues: 3. AlkB dioxygenase and Ada methyltransferase in the direct repair of alkylated DNA. Acta Biochim Pol. 2007;54:459-68 pubmed..1meA and 3meC are corrected by AlkB DNA dioxygenase. The mechanisms of action of E. coli AlkB dioxygenase and its human homologs ABH2 and ABH3 are described in more details. ..
- Martens S, Preuss A, Matern U. Multifunctional flavonoid dioxygenases: flavonol and anthocyanin biosynthesis in Arabidopsis thaliana L. Phytochemistry. 2010;71:1040-9 pubmed publisher..In vitro experiments suggested that the dioxygenases involved in their biosynthesis, flavonol synthase and anthocyanidin synthase, are "multifunctional" ..
- Brownlee J, He P, Moran G, Harrison D. Two roads diverged: the structure of hydroxymandelate synthase from Amycolatopsis orientalis in complex with 4-hydroxymandelate. Biochemistry. 2008;47:2002-13 pubmed publisher..It is suggested that this difference in the ring orientation of the substrate and the corresponding intermediates influences the site of hydroxylation. ..