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Protein

Alpha-ketoglutarate-dependent dioxygenase AlkB

Gene

alkB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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).6 Publications

Catalytic activityi

DNA-base-CH3 + 2-oxoglutarate + O2 = DNA-base + formaldehyde + succinate + CO2.3 Publications

Cofactori

Fe2+PROSITE-ProRule annotation4 PublicationsNote: Binds 1 Fe2+ ion per subunit.PROSITE-ProRule annotation4 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei69 – 691Substrate2 Publications
Metal bindingi131 – 1311Iron; catalyticPROSITE-ProRule annotation1 Publication
Metal bindingi133 – 1331Iron; catalyticPROSITE-ProRule annotation1 Publication
Binding sitei135 – 1351Substrate2 Publications
Binding sitei161 – 1611Substrate2 Publications
Metal bindingi187 – 1871Iron; catalyticPROSITE-ProRule annotation1 Publication

GO - Molecular functioni

  • cytosine C-5 DNA demethylase activity Source: UniProtKB
  • dioxygenase activity Source: EcoCyc
  • DNA-N1-methyladenine dioxygenase activity Source: UniProtKB
  • ferrous iron binding Source: UniProtKB
  • oxidative RNA demethylase activity Source: UniProtKB

GO - Biological processi

  • DNA dealkylation involved in DNA repair Source: UniProtKB
  • DNA demethylation Source: UniProtKB
  • DNA repair Source: EcoCyc
  • oxidative demethylation Source: UniProtKB
  • oxidative single-stranded DNA demethylation Source: UniProtKB
  • oxidative single-stranded RNA demethylation Source: UniProtKB
  • RNA repair Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Dioxygenase, Oxidoreductase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10037-MONOMER.
ECOL316407:JW2200-MONOMER.
MetaCyc:EG10037-MONOMER.
BRENDAi1.14.11.33. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Alpha-ketoglutarate-dependent dioxygenase AlkB (EC:1.14.11.33)
Alternative name(s):
Alkylated DNA repair protein AlkB
DNA oxidative demethylase AlkB
Gene namesi
Name:alkB
Synonyms:aidD
Ordered Locus Names:b2212, JW2200
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10037. alkB.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi51 – 511T → A: Slighly reduced activity towards single-stranded DNA containing 1-methyladenine. Reduces affinity for undamaged DNA. 1 Publication
Mutagenesisi69 – 691W → A: Abolishes activity towards single-stranded DNA containing 1-methyladenine. 1 Publication
Mutagenesisi76 – 761Y → A: Reduces affinity for damaged DNA and activity towards single-stranded DNA containing 1-methyladenine. 1 Publication
Mutagenesisi135 – 1351D → A: Abolishes activity towards single-stranded DNA containing 1-methyladenine. Alters substrate specificity, so that the enzyme gains activity towards single-stranded DNA containing 1-methylguanine. 1 Publication
Mutagenesisi161 – 1611R → A: No effect on enzyme activity. Decreases affinity for damaged DNA. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 216216Alpha-ketoglutarate-dependent dioxygenase AlkBPRO_0000066665Add
BLAST

Proteomic databases

PaxDbiP05050.

Interactioni

Protein-protein interaction databases

BioGridi4261918. 29 interactions.
DIPiDIP-9085N.
IntActiP05050. 12 interactions.
MINTiMINT-1258339.
STRINGi511145.b2212.

Structurei

Secondary structure

1
216
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi13 – 164Combined sources
Beta strandi19 – 224Combined sources
Turni23 – 297Combined sources
Helixi30 – 4314Combined sources
Beta strandi58 – 7215Combined sources
Beta strandi75 – 817Combined sources
Turni83 – 853Combined sources
Beta strandi86 – 883Combined sources
Helixi94 – 10613Combined sources
Beta strandi115 – 1228Combined sources
Beta strandi128 – 1314Combined sources
Beta strandi143 – 1508Combined sources
Beta strandi152 – 1565Combined sources
Beta strandi158 – 1636Combined sources
Beta strandi166 – 1705Combined sources
Beta strandi175 – 1784Combined sources
Helixi180 – 1845Combined sources
Beta strandi187 – 1893Combined sources
Turni198 – 2003Combined sources
Beta strandi204 – 2096Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2FD8X-ray2.30A12-216[»]
2FDFX-ray2.10A12-216[»]
2FDGX-ray2.20A12-216[»]
2FDHX-ray2.10A12-216[»]
2FDIX-ray1.80A12-216[»]
2FDJX-ray2.10A12-216[»]
2FDKX-ray2.30A12-216[»]
3BI3X-ray1.90A13-213[»]
3BIEX-ray1.68A13-214[»]
3BKZX-ray1.65A14-214[»]
3I2OX-ray1.70A12-216[»]
3I3MX-ray1.50A12-216[»]
3I3QX-ray1.40A/B12-216[»]
3I49X-ray1.60A12-216[»]
3KHBX-ray2.90A/B1-216[»]
3KHCX-ray2.20A/B1-216[»]
3O1MX-ray1.75A12-216[»]
3O1OX-ray1.92A12-216[»]
3O1PX-ray1.51A12-216[»]
3O1RX-ray1.77A12-216[»]
3O1SX-ray1.58A12-216[»]
3O1TX-ray1.48A12-216[»]
3O1UX-ray1.54A12-216[»]
3O1VX-ray1.90A12-216[»]
3T3YX-ray2.00A12-216[»]
3T4HX-ray1.65B12-216[»]
3T4VX-ray1.73A12-216[»]
4JHTX-ray1.18A12-216[»]
4NIDX-ray1.58A12-216[»]
4NIGX-ray1.52A12-216[»]
4NIHX-ray1.37A12-216[»]
4NIIX-ray1.62A12-216[»]
4RFRX-ray1.50B14-216[»]
4ZHNX-ray1.33A12-216[»]
ProteinModelPortaliP05050.
SMRiP05050. Positions 14-214.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP05050.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini113 – 213101Fe2OG dioxygenasePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni76 – 783Substrate binding
Regioni120 – 1223Alpha-ketoglutarate binding
Regioni204 – 2107Alpha-ketoglutarate binding

Sequence similaritiesi

Belongs to the alkB family.Curated
Contains 1 Fe2OG dioxygenase domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4105CF1. Bacteria.
COG3145. LUCA.
HOGENOMiHOG000122276.
InParanoidiP05050.
KOiK03919.
OMAiFEMSVAL.
OrthoDBiEOG62G5PV.
PhylomeDBiP05050.

Family and domain databases

Gene3Di2.60.120.590. 1 hit.
InterProiIPR004574. Alkb.
IPR027450. AlkB-like.
IPR005123. Oxoglu/Fe-dep_dioxygenase.
[Graphical view]
PANTHERiPTHR16557. PTHR16557. 2 hits.
PfamiPF13532. 2OG-FeII_Oxy_2. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00568. alkb. 1 hit.
PROSITEiPS51471. FE2OG_OXY. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P05050-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLDLFADAEP WQEPLAAGAV ILRRFAFNAA EQLIRDINDV ASQSPFRQMV
60 70 80 90 100
TPGGYTMSVA MTNCGHLGWT THRQGYLYSP IDPQTNKPWP AMPQSFHNLC
110 120 130 140 150
QRAATAAGYP DFQPDACLIN RYAPGAKLSL HQDKDEPDLR APIVSVSLGL
160 170 180 190 200
PAIFQFGGLK RNDPLKRLLL EHGDVVVWGG ESRLFYHGIQ PLKAGFHPLT
210
IDCRYNLTFR QAGKKE
Length:216
Mass (Da):24,076
Last modified:August 13, 1987 - v1
Checksum:i494FE1E70EABD278
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02607 Genomic DNA. Translation: AAA23416.1.
U00008 Genomic DNA. Translation: AAA16409.1.
U00096 Genomic DNA. Translation: AAC75272.1.
AP009048 Genomic DNA. Translation: BAA15995.1.
M10315 Genomic DNA. Translation: AAA23414.1.
PIRiA24605. BVECKB.
RefSeqiNP_416716.1. NC_000913.3.
WP_000884971.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75272; AAC75272; b2212.
BAA15995; BAA15995; BAA15995.
GeneIDi946708.
KEGGiecj:JW2200.
eco:b2212.
PATRICi32119783. VBIEscCol129921_2301.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02607 Genomic DNA. Translation: AAA23416.1.
U00008 Genomic DNA. Translation: AAA16409.1.
U00096 Genomic DNA. Translation: AAC75272.1.
AP009048 Genomic DNA. Translation: BAA15995.1.
M10315 Genomic DNA. Translation: AAA23414.1.
PIRiA24605. BVECKB.
RefSeqiNP_416716.1. NC_000913.3.
WP_000884971.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2FD8X-ray2.30A12-216[»]
2FDFX-ray2.10A12-216[»]
2FDGX-ray2.20A12-216[»]
2FDHX-ray2.10A12-216[»]
2FDIX-ray1.80A12-216[»]
2FDJX-ray2.10A12-216[»]
2FDKX-ray2.30A12-216[»]
3BI3X-ray1.90A13-213[»]
3BIEX-ray1.68A13-214[»]
3BKZX-ray1.65A14-214[»]
3I2OX-ray1.70A12-216[»]
3I3MX-ray1.50A12-216[»]
3I3QX-ray1.40A/B12-216[»]
3I49X-ray1.60A12-216[»]
3KHBX-ray2.90A/B1-216[»]
3KHCX-ray2.20A/B1-216[»]
3O1MX-ray1.75A12-216[»]
3O1OX-ray1.92A12-216[»]
3O1PX-ray1.51A12-216[»]
3O1RX-ray1.77A12-216[»]
3O1SX-ray1.58A12-216[»]
3O1TX-ray1.48A12-216[»]
3O1UX-ray1.54A12-216[»]
3O1VX-ray1.90A12-216[»]
3T3YX-ray2.00A12-216[»]
3T4HX-ray1.65B12-216[»]
3T4VX-ray1.73A12-216[»]
4JHTX-ray1.18A12-216[»]
4NIDX-ray1.58A12-216[»]
4NIGX-ray1.52A12-216[»]
4NIHX-ray1.37A12-216[»]
4NIIX-ray1.62A12-216[»]
4RFRX-ray1.50B14-216[»]
4ZHNX-ray1.33A12-216[»]
ProteinModelPortaliP05050.
SMRiP05050. Positions 14-214.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261918. 29 interactions.
DIPiDIP-9085N.
IntActiP05050. 12 interactions.
MINTiMINT-1258339.
STRINGi511145.b2212.

Proteomic databases

PaxDbiP05050.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75272; AAC75272; b2212.
BAA15995; BAA15995; BAA15995.
GeneIDi946708.
KEGGiecj:JW2200.
eco:b2212.
PATRICi32119783. VBIEscCol129921_2301.

Organism-specific databases

EchoBASEiEB0036.
EcoGeneiEG10037. alkB.

Phylogenomic databases

eggNOGiENOG4105CF1. Bacteria.
COG3145. LUCA.
HOGENOMiHOG000122276.
InParanoidiP05050.
KOiK03919.
OMAiFEMSVAL.
OrthoDBiEOG62G5PV.
PhylomeDBiP05050.

Enzyme and pathway databases

BioCyciEcoCyc:EG10037-MONOMER.
ECOL316407:JW2200-MONOMER.
MetaCyc:EG10037-MONOMER.
BRENDAi1.14.11.33. 2026.

Miscellaneous databases

EvolutionaryTraceiP05050.
PROiP05050.

Family and domain databases

Gene3Di2.60.120.590. 1 hit.
InterProiIPR004574. Alkb.
IPR027450. AlkB-like.
IPR005123. Oxoglu/Fe-dep_dioxygenase.
[Graphical view]
PANTHERiPTHR16557. PTHR16557. 2 hits.
PfamiPF13532. 2OG-FeII_Oxy_2. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00568. alkb. 1 hit.
PROSITEiPS51471. FE2OG_OXY. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Structure and expression of the alkB gene of Escherichia coli related to the repair of alkylated DNA."
    Kondo H., Nakabeppu Y., Kataoka H., Kuhara S., Kawabata S., Sekiguchi M.
    J. Biol. Chem. 261:15772-15777(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-30.
  2. "Automated multiplex sequencing of the E.coli genome."
    Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K., Church G.M.
    Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / BHB2600.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "Active site and complete sequence of the suicidal methyltransferase that counters alkylation mutagenesis."
    Demple B., Sedgwick B., Robins P., Totty N., Waterfield M.D., Lindahl T.
    Proc. Natl. Acad. Sci. U.S.A. 82:2688-2692(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-53.
    Strain: B.
  7. "The Escherichia coli AlkB protein protects human cells against alkylation-induced toxicity."
    Chen B.J., Carroll P., Samson L.
    J. Bacteriol. 176:6255-6261(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  8. "AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli."
    Falnes P.O., Johansen R.F., Seeberg E.
    Nature 419:178-182(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: CATALYTIC ACTIVITY, FUNCTION.
  9. "Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA."
    Aas P.A., Otterlei M., Falnes P.O., Vaagboe C.B., Skorpen F., Akbari M., Sundheim O., Bjoeraas M., Slupphaug G., Seeberg E., Krokan H.E.
    Nature 421:859-863(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  10. "Crystal structures of catalytic complexes of the oxidative DNA/RNA repair enzyme AlkB."
    Yu B., Edstrom W.C., Benach J., Hamuro Y., Weber P.C., Gibney B.R., Hunt J.F.
    Nature 439:879-884(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 12-216 IN COMPLEX WITH SUBSTRATE; ALPHA-KETOGLUTARATE AND IRON, FUNCTION, COFACTOR.
  11. "Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA."
    Yang C.G., Yi C., Duguid E.M., Sullivan C.T., Jian X., Rice P.A., He C.
    Nature 452:961-965(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF 14-214 IN COMPLEX WITH DS-DNA; ALPHA-KETOGLUTARATE AND METAL IONS.
  12. "Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB."
    Yu B., Hunt J.F.
    Proc. Natl. Acad. Sci. U.S.A. 106:14315-14320(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) OF 12-216 IN COMPLEXES WITH TRINUCLEOTIDE SUBSTRATES; ALPHA-KETOGLUTARATE AND METAL IONS, COFACTOR, FUNCTION.
  13. "Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase."
    Yi C., Jia G., Hou G., Dai Q., Zhang W., Zheng G., Jian X., Yang C.G., Cui Q., He C.
    Nature 468:330-333(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.92 ANGSTROMS) OF 12-216 IN COMPLEXES WITH REACTION INTERMEDIATES; 2-OXOGLUTARIC ACID AND IRON, CATALYTIC ACTIVITY, FUNCTION, COFACTOR.
  14. "Structural and mutational analysis of Escherichia coli AlkB provides insight into substrate specificity and DNA damage searching."
    Holland P.J., Hollis T.
    PLoS ONE 5:E8680-E8680(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF MUTANT ALA-135 IN COMPLEX WITH 2-OXOGLUTARIC ACID AND SUBSTRATE, CATALYTIC ACTIVITY, FUNCTION, COFACTOR, MUTAGENESIS OF THR-51; TRP-69; TYR-76; ASP-135 AND ARG-161.

Entry informationi

Entry nameiALKB_ECOLI
AccessioniPrimary (citable) accession number: P05050
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: August 13, 1987
Last modified: June 8, 2016
This is version 136 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.