U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 946708, updated on 26-Mar-2025

Summary

Go to the top of the page Help
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].
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help
Genomic Sequence:
NC_000913.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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 oxidoreductase activity IEA
Inferred from Electronic Annotation
more info
  
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 damage response IEA
Inferred from Electronic Annotation
more info
  
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

Go to the top of the page Help
Preferred Names
DNA oxidative demethylase
NP_416716.1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.