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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)DescriptionActionsGraphical viewLength
Binding sitei69Substrate2 Publications1
Metal bindingi131Iron; catalyticPROSITE-ProRule annotation1 Publication1
Metal bindingi133Iron; catalyticPROSITE-ProRule annotation1 Publication1
Binding sitei135Substrate2 Publications1
Binding sitei161Substrate2 Publications1
Metal bindingi187Iron; catalyticPROSITE-ProRule annotation1 Publication1

GO - Molecular functioni

  • 1-ethyladenine demethylase activity Source: UniProtKB-EC
  • 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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10037. alkB.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi51T → A: Slighly reduced activity towards single-stranded DNA containing 1-methyladenine. Reduces affinity for undamaged DNA. 1 Publication1
Mutagenesisi69W → A: Abolishes activity towards single-stranded DNA containing 1-methyladenine. 1 Publication1
Mutagenesisi76Y → A: Reduces affinity for damaged DNA and activity towards single-stranded DNA containing 1-methyladenine. 1 Publication1
Mutagenesisi135D → 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 Publication1
Mutagenesisi161R → A: No effect on enzyme activity. Decreases affinity for damaged DNA. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000666651 – 216Alpha-ketoglutarate-dependent dioxygenase AlkBAdd BLAST216

Proteomic databases

PaxDbiP05050.
PRIDEiP05050.

Interactioni

Protein-protein interaction databases

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

Structurei

Secondary structure

1216
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi13 – 16Combined sources4
Beta strandi19 – 22Combined sources4
Turni23 – 29Combined sources7
Helixi30 – 43Combined sources14
Beta strandi58 – 72Combined sources15
Beta strandi75 – 81Combined sources7
Turni83 – 85Combined sources3
Beta strandi86 – 88Combined sources3
Helixi94 – 106Combined sources13
Beta strandi115 – 122Combined sources8
Beta strandi128 – 131Combined sources4
Beta strandi143 – 150Combined sources8
Beta strandi152 – 156Combined sources5
Beta strandi158 – 163Combined sources6
Beta strandi166 – 170Combined sources5
Beta strandi175 – 178Combined sources4
Helixi180 – 184Combined sources5
Beta strandi187 – 189Combined sources3
Turni198 – 200Combined sources3
Beta strandi204 – 209Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP05050.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini113 – 213Fe2OG dioxygenasePROSITE-ProRule annotationAdd BLAST101

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni76 – 78Substrate binding3
Regioni120 – 122Alpha-ketoglutarate binding3
Regioni204 – 210Alpha-ketoglutarate binding7

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.
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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Proteomic databases

PaxDbiP05050.
PRIDEiP05050.

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.
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...

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: November 30, 2016
This is version 140 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.