Reviewed, UniProtKB/Swiss-Prot P05050 (ALKB_ECOLI)

Names and origin

Protein names

Recommended name:
    Alpha-ketoglutarate-dependent dioxygenase alkB
    EC=1.14.11.-
Alternative name(s):
    Alkylated DNA repair protein alkB

Gene names

Name:	alkB
Synonyms:	aidD
Ordered Locus Names:	b2212, JW2200

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	216 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Dioxygenase that repairs alkylated DNA and RNA containing 1-methyladenine and 3-methylcytosine by oxidative demethylation. 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). Ref.8
Cofactor	Binds 1 Fe2+ ion per subunit.
Sequence similarities	Belongs to the alkB family.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Ligand	Iron Metal-binding
Molecular function	Dioxygenase Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 216

216

Alpha-ketoglutarate-dependent dioxygenase alkB

PRO_0000066665

Regions

Region

76 – 78

3

Substrate binding

Region

204 – 210

7

Alpha-ketoglutarate binding

Sites

Metal binding

131

1

Iron; catalytic

Metal binding

133

1

Iron; catalytic

Metal binding

187

1

Iron; catalytic

Binding site

69

1

Substrate

Binding site

120

1

Alpha-ketoglutarate

Binding site

122

1

Alpha-ketoglutarate

Binding site

135

1

Substrate

Secondary structure

1

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216

Helix Strand Turn

Details...

Beta strand

17 – 22

6

Turn

23 – 29

7

Helix

30 – 41

12

Beta strand

58 – 71

14

Beta strand

76 – 81

6

Turn

83 – 85

3

Beta strand

86 – 88

3

Helix

94 – 107

14

Beta strand

116 – 122

7

Beta strand

128 – 131

4

Beta strand

143 – 150

8

Beta strand

152 – 156

5

Beta strand

166 – 170

5

Beta strand

175 – 178

4

Helix

180 – 184

5

Beta strand

187 – 189

3

Turn

198 – 200

3

Beta strand

204 – 209

6

Sequences

	Sequence		Length	Mass (Da)
	P05050-1 [UniParc]. Last modified August 13, 1987. Version 1. Checksum: 494FE1E70EABD278	FASTA	216	24,076
	10 20 30 40 50 60 MLDLFADAEP WQEPLAAGAV ILRRFAFNAA EQLIRDINDV ASQSPFRQMV TPGGYTMSVA 70 80 90 100 110 120 MTNCGHLGWT THRQGYLYSP IDPQTNKPWP AMPQSFHNLC QRAATAAGYP DFQPDACLIN 130 140 150 160 170 180 RYAPGAKLSL HQDKDEPDLR APIVSVSLGL PAIFQFGGLK RNDPLKRLLL EHGDVVVWGG 190 200 210 ESRLFYHGIQ PLKAGFHPLT IDCRYNLTFR QAGKKE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 3536913] [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]	"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." Itoh T., Aiba H., Baba T., Fujita K., 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., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y., Horiuchi T. DNA Res. 3:379-392(1996) [PubMed: 9097040] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] 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: 16738553] [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: 3887409] [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: 7928996] [Abstract] Cited for: CHARACTERIZATION.
[8]	"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: 12594517] [Abstract] Cited for: FUNCTION.
[9]	"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: 16482161] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 12-216 IN COMPLEX WITH SUBSTRATE; ALPHA-KETOGLUTARATE AND IRON.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

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.

PIR

BVECKB. A24605.

RefSeq

AP_002808.1.
NP_416716.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2FD8	X-ray	2.30	A	12-216	[»]
2FDF	X-ray	2.10	A	12-216	[»]
2FDG	X-ray	2.20	A	12-216	[»]
2FDH	X-ray	2.10	A	12-216	[»]
2FDI	X-ray	1.80	A	12-216	[»]
2FDJ	X-ray	2.10	A	12-216	[»]
2FDK	X-ray	2.30	A	12-216	[»]
3BI3	X-ray	1.90	A	13-213	[»]
3BIE	X-ray	1.68	A	13-214	[»]
3BKZ	X-ray	1.65	A	14-214	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:9085N.

Genome annotation databases

GeneID

946708.

GenomeReviews

Gene locus JW2200 in contig AP009048_GR.
Gene locus b2212 in contig U00096_GR.

KEGG

ecj:JW2200.
eco:b2212.

Organism-specific databases

EchoBASE

EB0036.

EcoGene

EG10037. alkB.

CMR

Search...

Phylogenomic databases

HOGENOM

P05050.

OMA

P05050. MVTPGGF.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10037-MON.
MetaCyc:EG10037-MON.

Family and domain databases

InterPro

IPR004574. Alkb.
IPR005123. Oxoglutarate/Fe-dep_Oase.
[Graphical view]

Pfam

PF03171. 2OG-FeII_Oxy. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00568. alkb. 1 hit.

ProtoNet

Search...

Entry information

Entry name

ALKB_ECOLI

Accession

Primary (citable) accession number: P05050

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 13, 1987
Last sequence update:	August 13, 1987
Last modified:	June 16, 2009
This is version 78 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)