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Standard Name	alkB
Gene Synonym(s)	ECK2204, b2212, JW2200, aidD^[1], aidD
Product Desc.	AlkB repair system for alkylated DNA and RNA^[2]^[3] Alkylated DNA repair enzyme; alpha-ketoglutarate- and Fe(II)-dependent dioxygenase^[4]; releases replication blocks by oxidative demethylation of 1-methyladenine and 3-methylcytosine residues in ssDNA and dsDNA^[5]
Product Synonyms(s)	oxidative demethylase of N1-methyladenine or N3-methylcytosine DNA lesions^[1], B2212^[2]^[1], AidD^[2]^[1], AlkB^[2]^[1] , aidD, ECK2204, JW2200, b2212
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ada-alkB^[2], OP00100, alkB^[2]
Regulation/Activity
Quick Links
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Notes

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AlkB mutants are extremely sensitive to MMS. Also repairs alkylated mRNA and tRNA in vivo and in vitro, the first example of direct RNA repair. Repairs epsilonA and epsilonC. Ada regulon.^[6]

Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	alkB
Mnemonic	Alkylation
Synonyms	ECK2204, b2212, JW2200, aidD^[1], aidD
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	49.72 minutes, 49.72 minutes	MG1655: 2307363..2306713 <gbrowseImage> name=NC_000913:2306713..2307363 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2259445..2258795 <gbrowseImage> name=NC_012967:2258795..2259445 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2192518..2193168 <gbrowseImage> name=NC_012759:2192518..2193168 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2312675..2312025 <gbrowseImage> name=NC_007779:2312025..2312675 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2398351..2397701 <gbrowseImage> name=NC_010473:2397701..2398351 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
Coding Start (SO:0000323)	MG1655	2306713	Edman degradation	PMID:3536913
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Reference	Availability	Comments
ΔalkB (Keio:JW2200)	deletion	deletion	PMID:16738554	Shigen CGSC9779^[7]
alkB::Tn5KAN-2 (FB20706)	Insertion at nt 334 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20706	contains pKD46
alkB::Tn5KAN-2 (FB20707)	Insertion at nt 334 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20707	does not contain pKD46
ΔalkB765::kan			PMID:16738554	CGSC:99968
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW2200	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTTGGATCTGTTTGCCGATGC Primer 2:CCTTCTTTTTTACCTGCCTGACG
19D1	Kohara Phage	Genobase	PMID:3038334
22A6	Kohara Phage	Genobase	PMID:3038334
napA722::Tn10	Linked marker	CAG12098 = CGSC7400^[7]	est. P1 cotransduction: 83% ^[8] Synonyms:zeg-722, zei-722::Tn10
atoS298::Tn10	Linked marker	CAG12177 gyrA+ = CGSC7525^[7]	est. P1 cotransduction: 63% ^[8] Synonyms:zeh-298::Tn10, zej-298::Tn10 nnnThe original CAG12177 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10037	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10037	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000034	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946708	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0036	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007308	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	AlkB
Synonyms	oxidative demethylase of N1-methyladenine or N3-methylcytosine DNA lesions^[1], B2212^[2]^[1], AidD^[2]^[1], AlkB^[2]^[1] , aidD, ECK2204, JW2200, b2212
Product description	AlkB repair system for alkylated DNA and RNA^[2]^[3] Alkylated DNA repair enzyme; alpha-ketoglutarate- and Fe(II)-dependent dioxygenase^[4]; releases replication blocks by oxidative demethylation of 1-methyladenine and 3-methylcytosine residues in ssDNA and dsDNA^[5]
EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0223	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	P	Seeded from EcoCyc (v14.0)	complete
	GO:0051213	dioxygenase activity	PMID:12226667	IDA: Inferred from Direct Assay		F		complete
	GO:0070989	oxidative demethylation	PMID:12226668	IDA: Inferred from Direct Assay		P		complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	References	Evidence
Protein	dusB	PMID:16606699	Experiment(s):EBI-1142184
Protein	rpsI	PMID:16606699	Experiment(s):EBI-1142184
Protein	groL	PMID:16606699	Experiment(s):EBI-1142184
Protein	rplQ	PMID:16606699	Experiment(s):EBI-1142184
Protein	ydfK	PMID:16606699	Experiment(s):EBI-1142184
Protein	sufC	PMID:16606699	Experiment(s):EBI-1142184
Protein	ycgE	PMID:16606699	Experiment(s):EBI-1142184
Protein	rplB	PMID:16606699	Experiment(s):EBI-1142184
Protein	ynaE	PMID:16606699	Experiment(s):EBI-1142184
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MLDLFADAEP WQEPLAAGAV ILRRFAFNAA EQLIRDINDV ASQSPFRQMV TPGGYTMSVA MTNCGHLGWT THRQGYLYSP IDPQTNKPWP AMPQSFHNLC QRAATAAGYP DFQPDACLIN RYAPGAKLSL HQDKDEPDLR APIVSVSLGL PAIFQFGGLK RNDPLKRLLL EHGDVVVWGG ESRLFYHGIQ PLKAGFHPLT IDCRYNLTFR QAGKKE
Length	216
Mol. Wt	24.075 kDa
pI	8.0 (calculated)
Extinction coefficient	32,430 - 32,930 (calc based on 7 Y, 4 W, and 4 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	Notes	References
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=alkB taxon=562,83333 </beststructure>

Models

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16130149	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946708	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007308	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P05050	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10037	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10037	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946708	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000034	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0036	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	E. coli K-12 MG1655	22	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	17	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	2^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
ada-alkB
alkB
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:2307343..2307383 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b2212 (EcoliWiki Page)	NCBI GEO profiles for alkB
microarray	GenExpDB:b2212 (EcoliWiki Page)	Summary of data for alkB from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to alkB Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10037	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0036	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2212
EcoGene	EcoGene:EG10037	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000034	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007308	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000019384 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT3G14160 (score: 1.000; bootstrap: 53%) AT5G01780 (score: 1.000; bootstrap: 54%) AT3G14140 (score: 0.680)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000010693 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00036645 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-050522-196 (score: 1.000; bootstrap: 100%) ZDB-CDNA-050522-196 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0186580 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0065035 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000017055 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000006492 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC13G14c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00005439001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	ALKB	From SHIGELLACYC
E. coli O157	ALKB	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Superfamily (EcoliWiki Page)	SUPERFAMILY:51197
Panther (EcoliWiki Page)	PTHR16557:SF0
EcoCyc	EcoCyc:EG10037	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10037	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000034	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0036	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007308	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 ^1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 ^2.9 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 Falnes, PØ et al. (2002) AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli. Nature 419 178-82 PubMed
↑ ^5.0 ^5.1 Trewick, SC et al. (2002) Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage. Nature 419 174-8 PubMed
↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^7.0 ^7.1 ^7.2 CGSC: The Coli Genetics Stock Center
↑ ^8.0 ^8.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

alkB:On One Page

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to alkB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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