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Protein

Alpha-ketoglutarate-dependent dioxygenase AlkB

Gene

alkB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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
  • dioxygenase activity Source: EcoCyc
  • DNA-N1-methyladenine dioxygenase activity Source: UniProtKB
  • ferrous iron binding Source: UniProtKB
  • methylcytosine dioxygenase activity Source: GO_Central
  • 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

Keywordsi

Molecular functionDioxygenase, Oxidoreductase
Biological processDNA damage, DNA repair
LigandIron, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10037-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

Subcellular locationi

GO - Cellular componenti

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
STRINGi316385.ECDH10B_2369

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

Phylogenomic databases

eggNOGiENOG4105CF1 Bacteria
COG3145 LUCA
HOGENOMiHOG000122276
InParanoidiP05050
KOiK03919
OMAiNCGPLGW
PhylomeDBiP05050

Family and domain databases

Gene3Di2.60.120.590, 1 hit
InterProiView protein in InterPro
IPR004574 Alkb
IPR027450 AlkB-like
IPR037151 AlkB-like_sf
IPR005123 Oxoglu/Fe-dep_dioxygenase
PANTHERiPTHR16557 PTHR16557, 1 hit
PfamiView protein in Pfam
PF13532 2OG-FeII_Oxy_2, 1 hit
TIGRFAMsiTIGR00568 alkb, 1 hit
PROSITEiView protein in PROSITE
PS51471 FE2OG_OXY, 1 hit

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
PATRICifig|1411691.4.peg.23

Similar proteinsi

Entry informationi

Entry nameiALKB_ECOLI
AccessioniPrimary (citable) accession number: P05050
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: August 13, 1987
Last modified: March 28, 2018
This is version 147 of the entry and version 1 of the sequence. See 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
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Main funding by: National Institutes of Health