We are analyzing https://link.springer.com/article/10.1186/gb-2001-2-3-research0007.

Title:
The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases | Genome Biology
Description:
Background Protein fold recognition using sequence profile searches frequently allows prediction of the structure and biochemical mechanisms of proteins with an important biological function but unknown biochemical activity. Here we describe such predictions resulting from an analysis of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenases, a class of enzymes that are widespread in eukaryotes and bacteria and catalyze a variety of reactions typically involving the oxidation of an organic substrate using a dioxygen molecule. Results We employ sequence profile analysis to show that the DNA repair protein AlkB, the extracellular matrix protein leprecan, the disease-resistance-related protein EGL-9 and several uncharacterized proteins define novel families of enzymes of the 2OG-Fe(II) oxygenase superfamily. The identification of AlkB as a member of the 2OG-Fe(II) oxygenase superfamily suggests that this protein catalyzes oxidative detoxification of alkylated bases. More distant homologs of AlkB were detected in eukaryotes and in plant RNA viruses, leading to the hypothesis that these proteins might be involved in RNA demethylation. The EGL-9 protein from Caenorhabditis elegans is necessary for normal muscle function and its inactivation results in resistance against paralysis induced by the Pseudomonas aeruginosa toxin. EGL-9 and leprecan are predicted to be novel protein hydroxylases that might be involved in the generation of substrates for protein glycosylation. Conclusions Here, using sequence profile searches, we show that several previously undetected protein families contain 2OG-Fe(II) oxygenase fold. This allows us to predict the catalytic activity for a wide range of biologically important, but biochemically uncharacterized proteins from eukaryotes and bacteria.
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Keywords {🔍}

proteins, protein, pubmed, cas, alkb, article, google, scholar, sequence, ogfeii, family, superfamily, conserved, egl, enzymes, families, structure, synthase, dioxygenase, secondary, eukaryotes, dna, figure, bacteria, dioxygenases, searches, predicted, hydroxylases, acid, database, alignment, leprecan, members, residues, plant, involved, aeruginosa, structures, dsbh, domain, biol, homologs, multiple, core, histidine, structural, virus, individual, central, function,

Topics {✒️}

article number research0007 amino-terminal segment rich disease-resistance-related protein egl-9 normal muscle function l-cysteinyl-d-valine patchy phyletic distribution growth factor-responsive gene carboxy-terminal globular part dna-repair protein alkb small-molecule hydroxylases early conserved amino-terminal extensions conserved carboxy-terminal histidine position-specific gap penalties position-specific scoring matrices dna-repair proteins typified double-stranded β-helix amino-terminal α helix methylated single-stranded dna modified active-site configuration superfamilyby sequence-based methods alkane omega-hydroxylase typified amino-acid hydroxylases show full size image predicted amino-acid hydroxylases protein lysyl/prolyl hydroxylases secondary metabolite biosynthesis phyletic distribution normal egg laying privacy choices/manage cookies swiss-pdb-viewer program [33] carboxy-terminal histidine related subjects dioxygen molecule dioxygen molecule [1 escherichia coli related ipns/ethylene-forming enzyme amino-terminal alkb ligand-binding properties detectable sequence similarity 2-oxoglutarate-binding sites human cdna encoding arabinose-binding domain epigenetic biomarkers related sequence profile searches specific extensions typical drastic sequence divergence amino acid residues database searches initiated iterative database searches article aravind

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         headline:The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases
         description:Protein fold recognition using sequence profile searches frequently allows prediction of the structure and biochemical mechanisms of proteins with an important biological function but unknown biochemical activity. Here we describe such predictions resulting from an analysis of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenases, a class of enzymes that are widespread in eukaryotes and bacteria and catalyze a variety of reactions typically involving the oxidation of an organic substrate using a dioxygen molecule. We employ sequence profile analysis to show that the DNA repair protein AlkB, the extracellular matrix protein leprecan, the disease-resistance-related protein EGL-9 and several uncharacterized proteins define novel families of enzymes of the 2OG-Fe(II) oxygenase superfamily. The identification of AlkB as a member of the 2OG-Fe(II) oxygenase superfamily suggests that this protein catalyzes oxidative detoxification of alkylated bases. More distant homologs of AlkB were detected in eukaryotes and in plant RNA viruses, leading to the hypothesis that these proteins might be involved in RNA demethylation. The EGL-9 protein from Caenorhabditis elegans is necessary for normal muscle function and its inactivation results in resistance against paralysis induced by the Pseudomonas aeruginosa toxin. EGL-9 and leprecan are predicted to be novel protein hydroxylases that might be involved in the generation of substrates for protein glycosylation. Here, using sequence profile searches, we show that several previously undetected protein families contain 2OG-Fe(II) oxygenase fold. This allows us to predict the catalytic activity for a wide range of biologically important, but biochemically uncharacterized proteins from eukaryotes and bacteria.
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            Phyletic Distribution
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            Microbial Genetics and Genomics
            Bioinformatics
            Evolutionary Biology
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      headline:The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases
      description:Protein fold recognition using sequence profile searches frequently allows prediction of the structure and biochemical mechanisms of proteins with an important biological function but unknown biochemical activity. Here we describe such predictions resulting from an analysis of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenases, a class of enzymes that are widespread in eukaryotes and bacteria and catalyze a variety of reactions typically involving the oxidation of an organic substrate using a dioxygen molecule. We employ sequence profile analysis to show that the DNA repair protein AlkB, the extracellular matrix protein leprecan, the disease-resistance-related protein EGL-9 and several uncharacterized proteins define novel families of enzymes of the 2OG-Fe(II) oxygenase superfamily. The identification of AlkB as a member of the 2OG-Fe(II) oxygenase superfamily suggests that this protein catalyzes oxidative detoxification of alkylated bases. More distant homologs of AlkB were detected in eukaryotes and in plant RNA viruses, leading to the hypothesis that these proteins might be involved in RNA demethylation. The EGL-9 protein from Caenorhabditis elegans is necessary for normal muscle function and its inactivation results in resistance against paralysis induced by the Pseudomonas aeruginosa toxin. EGL-9 and leprecan are predicted to be novel protein hydroxylases that might be involved in the generation of substrates for protein glycosylation. Here, using sequence profile searches, we show that several previously undetected protein families contain 2OG-Fe(II) oxygenase fold. This allows us to predict the catalytic activity for a wide range of biologically important, but biochemically uncharacterized proteins from eukaryotes and bacteria.
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         Dioxygen Molecule
         Phyletic Distribution
         Normal Muscle Function
         AlkB Homolog
         Oxygenase Superfamily
         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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