We are analyzing https://link.springer.com/article/10.1186/1471-2164-4-48.

Title:
Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB | BMC Genomics
Description:
Background Combination of biochemical and bioinformatic analyses led to the discovery of oxidative demethylation – a novel DNA repair mechanism catalyzed by the Escherichia coli AlkB protein and its two human homologs, hABH2 and hABH3. This discovery was based on the prediction made by Aravind and Koonin that AlkB is a member of the 2OG-Fe2+ oxygenase superfamily. Results In this article, we report identification and sequence analysis of five human members of the (2OG-Fe2+) oxygenase superfamily designated here as hABH4 through hABH8. These experimentally uncharacterized and poorly annotated genes were not associated with the AlkB family in any database, but are predicted here to be phylogenetically and functionally related to the AlkB family (and specifically to the lineage that groups together hABH2 and hABH3) rather than to any other oxygenase family. Our analysis reveals the history of ABH gene duplications in the evolution of vertebrate genomes. Conclusions We hypothesize that hABH 4–8 could either be back-up enzymes for hABH1-3 or may code for novel DNA or RNA repair activities. For example, enzymes that can dealkylate N3-methylpurines or N7-methylpurines in DNA have not been described. Our analysis will guide experimental confirmation of these novel human putative DNA repair enzymes.
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Keywords {🔍}

article, alkb, habh, pubmed, google, scholar, cas, human, analysis, dna, protein, members, oxygenase, ogfe, superfamily, abhs, repair, database, tree, phylogenetic, family, genome, homologs, sequence, enzymes, proteins, nucleic, nature, gene, acids, central, coli, oxygenases, orthologs, res, demethylation, abh, genomes, found, bioinformatics, data, information, prediction, predicted, ensembl, genomics, identification, access, analyses, oxidative,

Topics {✒️}

double-stranded β-helix fold x-ray crystallographic studies embo/hhmi young investigator dna-repair protein alkb c-terminal β-strand similar physico-chemical character open access license article download pdf dna/rna modification genuine β-helix oxygenases individual genes/contigs/transcripts 2og-fe2+ oxygenase superfamily protein fold-recognition method wayne state university dna alkylation damage protein fold-recognition analysis 2og-fe2+ oxygenase family double-stranded dna nucleic acid repair full size image rna-binding domain suggests human-mouse chromosome synteny privacy choices/manage cookies genome-wide search trewick sc protein fold-recognition authors’ original file large-scale searches rna repair activities iron-dependent dioxygenases bona fide members catalyze oxidative demethylation full access maximum likelihood method article kurowski protein structure analyses bacterial alkb carries oxygenase superfamily designated secondary structure prediction eukaryotic protein families oxidative ring expansion lysine side chains 2og-fe2+ oxygenases [2] 2og-fe2+ oxygenases bmc genomics 4 full size table coli alkb mutant epigenetic biomarkers related related subjects c-terminal residues

Schema {🗺️}

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         headline:Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB
         description:Combination of biochemical and bioinformatic analyses led to the discovery of oxidative demethylation – a novel DNA repair mechanism catalyzed by the Escherichia coli AlkB protein and its two human homologs, hABH2 and hABH3. This discovery was based on the prediction made by Aravind and Koonin that AlkB is a member of the 2OG-Fe2+ oxygenase superfamily. In this article, we report identification and sequence analysis of five human members of the (2OG-Fe2+) oxygenase superfamily designated here as hABH4 through hABH8. These experimentally uncharacterized and poorly annotated genes were not associated with the AlkB family in any database, but are predicted here to be phylogenetically and functionally related to the AlkB family (and specifically to the lineage that groups together hABH2 and hABH3) rather than to any other oxygenase family. Our analysis reveals the history of ABH gene duplications in the evolution of vertebrate genomes. We hypothesize that hABH 4–8 could either be back-up enzymes for hABH1-3 or may code for novel DNA or RNA repair activities. For example, enzymes that can dealkylate N3-methylpurines or N7-methylpurines in DNA have not been described. Our analysis will guide experimental confirmation of these novel human putative DNA repair enzymes.
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            dealkylation
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            Animal Genetics and Genomics
            Microbial Genetics and Genomics
            Plant Genetics and Genomics
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      headline:Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB
      description:Combination of biochemical and bioinformatic analyses led to the discovery of oxidative demethylation – a novel DNA repair mechanism catalyzed by the Escherichia coli AlkB protein and its two human homologs, hABH2 and hABH3. This discovery was based on the prediction made by Aravind and Koonin that AlkB is a member of the 2OG-Fe2+ oxygenase superfamily. In this article, we report identification and sequence analysis of five human members of the (2OG-Fe2+) oxygenase superfamily designated here as hABH4 through hABH8. These experimentally uncharacterized and poorly annotated genes were not associated with the AlkB family in any database, but are predicted here to be phylogenetically and functionally related to the AlkB family (and specifically to the lineage that groups together hABH2 and hABH3) rather than to any other oxygenase family. Our analysis reveals the history of ABH gene duplications in the evolution of vertebrate genomes. We hypothesize that hABH 4–8 could either be back-up enzymes for hABH1-3 or may code for novel DNA or RNA repair activities. For example, enzymes that can dealkylate N3-methylpurines or N7-methylpurines in DNA have not been described. Our analysis will guide experimental confirmation of these novel human putative DNA repair enzymes.
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         phylogenomics
         bioinformatics
         dealkylation
         demethylation
         dioxygenases
         Life Sciences
         general
         Microarrays
         Proteomics
         Animal Genetics and Genomics
         Microbial Genetics and Genomics
         Plant Genetics and Genomics
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