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    alkB DNA oxidative demethylase [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 946708, updated on 3-Dec-2024

    Summary

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    Official Symbol
    alkB
    Official Full Name
    DNA oxidative demethylase
    Primary source
    ECOCYC:EG10037
    Locus tag
    b2212
    See related
    ASAP:ABE-0007308
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Escherichia coli str. K-12 substr. MG1655 (strain: K-12, substrain: MG1655)
    Lineage
    Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia
    Also known as
    aidD; ECK2204
    Summary
    AlkB mutants are extremely sensitive to MMS. [More information is available at EcoGene: EG10037]. AlkB is a Fe(II)-containing, 2-oxoglutarate-dependent dioxygenase involved in the adaptive DNA-repair response of Escherichia coli to alkylating agents. [More information is available at EcoCyc: EG10037].
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    Genomic context

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    Sequence:
    NC_000913.3 (2308691..2309341, complement)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene malate:quinone oxidoreductase Neighboring gene ABC transporter family protein/microcin J25 efflux protein Neighboring gene DNA-binding transcriptional dual regulator/DNA repair protein Ada Neighboring gene FAD:protein FMN transferase

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_000913.3

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Demethylation of 3-methylthymine in DNA by bacterial and human DNA dioxygenases. Koivisto P, et al. J Biol Chem, 2004 Sep 24. PMID 15269201
    2. Molecular biology: A fix for RNA. Begley TJ, et al. Nature, 2003 Feb 20. PMID 12594492
    3. Probing the structure and function of the Escherichia coli DNA alkylation repair AlkB protein through chemical cross-linking. Mishina Y, et al. J Am Chem Soc, 2003 Jul 23. PMID 12862460
    4. Minimal methylated substrate and extended substrate range of Escherichia coli AlkB protein, a 1-methyladenine-DNA dioxygenase. Koivisto P, et al. J Biol Chem, 2003 Nov 7. PMID 12944387
    5. DNA repair by bacterial AlkB proteins. Falnes PØ, et al. Res Microbiol, 2003 Oct. PMID 14527653

    See all (90) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Insights into the Direct Oxidative Repair of Etheno Lesions: MD and QM/MM Study on the Substrate Scope of ALKBH2 and AlkB.
      Title: Insights into the Direct Oxidative Repair of Etheno Lesions: MD and QM/MM Study on the Substrate Scope of ALKBH2 and AlkB.
    2. Transient kinetic analysis of oxidative dealkylation by the direct reversal DNA repair enzyme AlkB.
      Title: Transient kinetic analysis of oxidative dealkylation by the direct reversal DNA repair enzyme AlkB.
    3. SSB-AlkB interaction promotes faster repair of the methyl DNA adducts.
      Title: Escherichia coli single-stranded DNA binding protein SSB promotes AlkB-mediated DNA dealkylation repair.
    4. AlkB has a wide variety of substrates, including monoalkyl and exocyclic bridged adducts. (Review)
      Title: The AlkB Family of Fe(II)/α-Ketoglutarate-dependent Dioxygenases: Repairing Nucleic Acid Alkylation Damage and Beyond.
    5. AlkB dioxygenase preferentially repairs protonated substrates: specificity against exocyclic adducts and molecular mechanism of action
      Title: AlkB dioxygenase preferentially repairs protonated substrates: specificity against exocyclic adducts and molecular mechanism of action.
    6. The AlkB dioxygenase plays a major role in decreasing the level of AT-->TA mutations, thus in the repair of Etheno-DNA adducts in E.coli cells.
      Title: The role of AlkB protein in repair of 1,N⁶-ethenoadenine in Escherichia coli cells.
    7. Cocrystal structures provide insight into the structural basis of this "k(cat)/K(m) compensation," which makes a significant contribution to promiscuous substrate recognition by AlkB.
      Title: Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB.
    8. N-terminus verified by Edman degradation on complete protein
      Title: Structure and expression of the alkB gene of Escherichia coli related to the repair of alkylated DNA.
    9. work provides direct evidence that AlkB suppresses both genotoxicity and mutagenesis by physiologically realistic low doses of 1-alkylpurine and 3-alkylpyrimidine DNA damage in vivo
      Title: Mutagenesis, genotoxicity, and repair of 1-methyladenine, 3-alkylcytosines, 1-methylguanine, and 3-methylthymine in alkB Escherichia coli.
    10. AlkB dioxygenase, PolV (UmuD'C), and AlkA have roles in preventing MMS-induced mutagenesis in Escherichia coli
      Title: AlkB dioxygenase in preventing MMS-induced mutagenesis in Escherichia coli: effect of Pol V and AlkA proteins.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by EcoCyc

    Function Evidence Code Pubs
    enables broad specificity oxidative DNA demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables broad specificity oxidative DNA demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables broad specificity oxidative DNA demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables dioxygenase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ferrous iron binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ferrous iron binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidative RNA demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables oxidative RNA demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA alkylation repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA repair IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in RNA repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in oxidative RNA demethylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within oxidative demethylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to methyl methanesulfonate IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytosol IC
    Inferred by Curator
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    DNA oxidative demethylase
    NP_416716.1

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_000913.3 Reference assembly

      Range
      2308691..2309341 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_416716.1 DNA oxidative demethylase [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_416716.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A5C9AA01
      Conserved Domains (1) summary
      PRK15401
      Location:1 → 212
      PRK15401; DNA oxidative demethylase AlkB
    Nucleotide Protein
    Heading Accession and Version

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