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Showing Protein Alpha-ketoglutarate-dependent dioxygenase AlkB (HMDBP12305)

IdentificationBiological propertiesGene propertiesProtein propertiesExternal linksReferencesXMLShow 1 metabolite
Identification
HMDB Protein ID HMDBP12305
Secondary Accession Numbers None
Name Alpha-ketoglutarate-dependent dioxygenase AlkB
Synonyms
  1. Alkylated DNA repair protein AlkB
  2. DNA oxidative demethylase AlkB
Gene Name ALKB
Protein Type Unknown
Biological Properties
General Function Not Available
Specific Function Dioxygenase that repairs alkylated DNA and RNA containing 3-methylcytosine or 1-methyladenine by oxidative demethylation. Has highest activity towards 3-methylcytosine. Has lower activity towards alkylated DNA containing ethenoadenine, and no detectable activity towards 1-methylguanine or 3-methylthymine. Accepts double-stranded and single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron. Provides extensive resistance to alkylating agents such as MMS and DMS (SN2 agents), but not to MMNG and MNU (SN1 agents).
Pathways Not Available
Reactions Not Available
GO Classification
Biological Process
DNA repair
oxidative single-stranded DNA demethylation
oxidative single-stranded RNA demethylation
DNA dealkylation involved in DNA repair
oxidative RNA demethylation
oxidative demethylation
RNA repair
DNA demethylation
Cellular Component
cytoplasm
Molecular Function
ferrous iron binding
oxidative DNA demethylase activity
oxidative RNA demethylase activity
1-ethyladenine demethylase activity
DNA-N1-methyladenine dioxygenase activity
dioxygenase activity
Cellular Location Not Available
Gene Properties
Chromosome Location Not Available
Locus Not Available
SNPs Not Available
Gene Sequence Not Available
Protein Properties
Number of Residues 216
Molecular Weight 24075.315
Theoretical pI 7.869
Pfam Domain Function
Signals Not Available
Transmembrane Regions Not Available
Protein Sequence Not Available
GenBank ID Protein Not Available
UniProtKB/Swiss-Prot ID P05050
UniProtKB/Swiss-Prot Entry Name ALKB_ECOLI
PDB IDs
GenBank Gene ID Not Available
GeneCard ID Not Available
GenAtlas ID Not Available
HGNC ID Not Available
References
General References
  1. Aas PA, Otterlei M, Falnes PO, Vagbo CB, Skorpen F, Akbari M, Sundheim O, Bjoras M, Slupphaug G, Seeberg E, Krokan HE: Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA. Nature. 2003 Feb 20;421(6925):859-63. [PubMed:12594517 ]
  2. Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C: Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Nature. 2008 Apr 24;452(7190):961-5. doi: 10.1038/nature06889. [PubMed:18432238 ]
  3. Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y: The complete genome sequence of Escherichia coli K-12. Science. 1997 Sep 5;277(5331):1453-62. [PubMed:9278503 ]
  4. Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H, Horiuchi T: Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol. 2006;2:2006.0007. Epub 2006 Feb 21. [PubMed:16738553 ]
  5. Itoh T, Aiba H, Baba T, Hayashi K, Inada T, Isono K, Kasai H, Kimura S, Kitakawa M, Kitagawa M, Makino K, Miki T, Mizobuchi K, Mori H, Mori T, Motomura K, Nakade S, Nakamura Y, Nashimoto H, Nishio Y, Oshima T, Saito N, Sampei G, Seki Y, Horiuchi T, et al.: A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map. DNA Res. 1996 Dec 31;3(6):379-92. [PubMed:9097040 ]
  6. Kondo H, Nakabeppu Y, Kataoka H, Kuhara S, Kawabata S, Sekiguchi M: Structure and expression of the alkB gene of Escherichia coli related to the repair of alkylated DNA. J Biol Chem. 1986 Nov 25;261(33):15772-7. [PubMed:3536913 ]
  7. Demple B, Sedgwick B, Robins P, Totty N, Waterfield MD, Lindahl T: Active site and complete sequence of the suicidal methyltransferase that counters alkylation mutagenesis. Proc Natl Acad Sci U S A. 1985 May;82(9):2688-92. doi: 10.1073/pnas.82.9.2688. [PubMed:3887409 ]
  8. Chen BJ, Carroll P, Samson L: The Escherichia coli AlkB protein protects human cells against alkylation-induced toxicity. J Bacteriol. 1994 Oct;176(20):6255-61. doi: 10.1128/jb.176.20.6255-6261.1994. [PubMed:7928996 ]
  9. Falnes PO, Johansen RF, Seeberg E: AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli. Nature. 2002 Sep 12;419(6903):178-82. doi: 10.1038/nature01048. [PubMed:12226668 ]
  10. Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF: Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB. Nature. 2006 Feb 16;439(7078):879-84. doi: 10.1038/nature04561. [PubMed:16482161 ]
  11. Yu B, Hunt JF: Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB. Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14315-20. doi: 10.1073/pnas.0812938106. Epub 2009 Aug 11. [PubMed:19706517 ]
  12. Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X, Yang CG, Cui Q, He C: Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase. Nature. 2010 Nov 11;468(7321):330-3. doi: 10.1038/nature09497. [PubMed:21068844 ]
  13. Holland PJ, Hollis T: Structural and mutational analysis of Escherichia coli AlkB provides insight into substrate specificity and DNA damage searching. PLoS One. 2010 Jan 13;5(1):e8680. doi: 10.1371/journal.pone.0008680. [PubMed:20084272 ]