RegulonDB RegulonDB 10.9: Gene Form
   

alkB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yojI ada ftp alkB Ada Ada Lrp Lrp Lrp Lrp Lrp Lrp terminator adap adap alkBp alkBp yojIp yojIp

Gene      
Name: alkB    Texpresso search in the literature
Synonym(s): ECK2204, EG10037, aidD, b2212
Genome position(nucleotides): 2308691 <-- 2309341 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.69
External database links:  
ASAP:
ABE-0007308
CGSC:
18544
ECHOBASE:
EB0036
ECOLIHUB:
alkB
OU-MICROARRAY:
b2212
STRING:
511145.b2212
COLOMBOS: alkB


Product      
Name: DNA oxidative demethylase
Synonym(s): alpha;-ketoglutarate-dependent dioxygenase, AidD, AlkB, alkyladenine-DNA dioxygenase
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 24.076
Isoelectric point: 7.995
Motif(s):
 
Type Positions Sequence
69 -> 69 W
161 -> 161 R
76 -> 76 Y
120 -> 122 NRY
21 -> 210 ILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAKLSLHQDKDEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFR

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.4 - DNA repair
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0035516 - oxidative DNA demethylase activity
GO:0005515 - protein binding
GO:0046872 - metal ion binding
GO:0016491 - oxidoreductase activity
GO:0008198 - ferrous iron binding
GO:0051213 - dioxygenase activity
GO:0035515 - oxidative RNA demethylase activity
GO:0043734 - DNA-N1-methyladenine dioxygenase activity
GO:0103053 - 1-ethyladenine demethylase activity
biological_process GO:0072702 - response to methyl methanesulfonate
GO:0006281 - DNA repair
GO:0006974 - cellular response to DNA damage stimulus
GO:0042245 - RNA repair
GO:0055114 - oxidation-reduction process
GO:0006307 - DNA dealkylation involved in DNA repair
GO:0070989 - oxidative demethylation
GO:0035552 - oxidative single-stranded DNA demethylation
GO:0035553 - oxidative single-stranded RNA demethylation
GO:0080111 - DNA demethylation
Note(s): Note(s): ...[more].
Reference(s): [1] Aravind L., et al., 2001
[2] Bian K., et al., 2019
[3] Bleijlevens B., et al., 2012
[4] Chang SC., et al., 2015
[5] Chen BJ., et al., 1994
[6] Chen F., et al., 2017
[7] Cozen AE., et al., 2015
[8] Dai Q., et al., 2017
[9] Dylewska M., et al., 2017
[10] Ergel B., et al., 2014
[11] Henshaw TF., et al., 2004
[12] Hrabeta-Robinson E., et al., 2017
[13] Kanazhevskaya LY., et al., 2019
[14] Kondo H., et al., 1986
[15] Li D., et al., 2010
[16] Li D., et al., 2013
[17] Li Q., et al., 2016
[18] Li X., et al., 2016
[19] Liu H., et al., 2009
[20] Mielecki D., et al., 2016
[21] Mishina Y., et al., 2003
[22] Mishina Y., et al., 2004
[23] Mohan M., et al., 2018
[24] Nieminuszczy J., et al., 2006
[25] Nigam R., et al., 2018
[26] Nigam R., et al., 2018
[27] Quesne MG., et al., 2014
[28] Rebeck GW., et al., 1988
[29] Sedgwick B., et al., 2006
[30] Shivarattan T., et al., 2005
[31] Shrivastav N., et al., 2014
[32] Sikora A., et al., 2015
[33] Sikora A., et al., 2010
[34] Sundheim O., et al., 2008
[35] Wang G., et al., 1995
[36] Watanabe K., et al., 1990
[37] Welford RW., et al., 2005
[38] Wrzesinski M., et al., 2010
[39] van den Born E., et al., 2009
External database links:  
DIP:
DIP-9085N
ECOCYC:
EG10037-MONOMER
ECOLIWIKI:
b2212
INTERPRO:
IPR037151
INTERPRO:
IPR027450
INTERPRO:
IPR004574
INTERPRO:
IPR005123
PANTHER:
PTHR16557
PDB:
3I3Q
PDB:
4ZHN
PDB:
4RFR
PDB:
4NII
PDB:
4NIH
PDB:
4NIG
PDB:
4NID
PDB:
4JHT
PDB:
2FD8
PDB:
2FDF
PDB:
2FDG
PDB:
2FDH
PDB:
2FDI
PDB:
2FDJ
PDB:
2FDK
PDB:
3BI3
PDB:
3BIE
PDB:
3BKZ
PDB:
3I2O
PDB:
3I3M
PDB:
3I49
PDB:
3KHB
PDB:
3KHC
PDB:
3O1M
PDB:
3O1O
PDB:
3O1P
PDB:
3O1R
PDB:
3O1S
PDB:
3O1T
PDB:
3O1U
PDB:
3O1V
PDB:
3T3Y
PDB:
3T4H
PDB:
3T4V
PFAM:
PF13532
PRIDE:
P05050
PRODB:
PRO_000022078
PROSITE:
PS51471
REFSEQ:
NP_416716
SMR:
P05050
SWISSMODEL:
P05050
UNIPROT:
P05050


Operon      
Name: ada-alkB         
Operon arrangement:
Transcription unit        Promoter
alkB
ada-alkB
ada-alkB


Transcriptional Regulation      
Display Regulation             
Activated by: Ada
Repressed by: Ada


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References


Reference(s)    

 [1] Aravind L., Koonin EV., 2001, The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases., Genome Biol 2(3):RESEARCH0007

 [2] Bian K., Lenz SAP., Tang Q., Chen F., Qi R., Jost M., Drennan CL., Essigmann JM., Wetmore SD., Li D., 2019, DNA repair enzymes ALKBH2, ALKBH3, and AlkB oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in vitro., Nucleic Acids Res 47(11):5522-5529

 [3] Bleijlevens B., Shivarattan T., van den Boom KS., de Haan A., van der Zwan G., Simpson PJ., Matthews SJ., 2012, Changes in protein dynamics of the DNA repair dioxygenase AlkB upon binding of Fe(2+) and 2-oxoglutarate., Biochemistry 51(16):3334-41

 [4] Chang SC., Fedeles BI., Wu J., Delaney JC., Li D., Zhao L., Christov PP., Yau E., Singh V., Jost M., Drennan CL., Marnett LJ., Rizzo CJ., Levine SS., Guengerich FP., Essigmann JM., 2015, Next-generation sequencing reveals the biological significance of the N(2),3-ethenoguanine lesion in vivo., Nucleic Acids Res 43(11):5489-500

 [5] Chen BJ., Carroll P., Samson L., 1994, The Escherichia coli AlkB protein protects human cells against alkylation-induced toxicity., J Bacteriol 176(20):6255-61

 [6] Chen F., Bian K., Tang Q., Fedeles BI., Singh V., Humulock ZT., Essigmann JM., Li D., 2017, Oncometabolites d- and l-2-Hydroxyglutarate Inhibit the AlkB Family DNA Repair Enzymes under Physiological Conditions., Chem Res Toxicol 30(4):1102-1110

 [7] Cozen AE., Quartley E., Holmes AD., Hrabeta-Robinson E., Phizicky EM., Lowe TM., 2015, ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments., Nat Methods 12(9):879-84

 [8] Dai Q., Zheng G., Schwartz MH., Clark WC., Pan T., 2017, Selective Enzymatic Demethylation of N(2) ,N(2) -Dimethylguanosine in RNA and Its Application in High-Throughput tRNA Sequencing., Angew Chem Int Ed Engl 56(18):5017-5020

 [9] Dylewska M., Kusmierek JT., Pilzys T., Poznanski J., Maciejewska AM., 2017, 1,N(6)-α-hydroxypropanoadenine, the acrolein adduct to adenine, is a substrate for AlkB dioxygenase., Biochem J 474(11):1837-1852

 [10] Ergel B., Gill ML., Brown L., Yu B., Palmer AG., Hunt JF., 2014, Protein dynamics control the progression and efficiency of the catalytic reaction cycle of the Escherichia coli DNA-repair enzyme AlkB., J Biol Chem 289(43):29584-601

 [11] Henshaw TF., Feig M., Hausinger RP., 2004, Aberrant activity of the DNA repair enzyme AlkB., J Inorg Biochem 98(5):856-61

 [12] Hrabeta-Robinson E., Marcus E., Cozen AE., Phizicky EM., Lowe TM., 2017, High-Throughput Small RNA Sequencing Enhanced by AlkB-Facilitated RNA de-Methylation (ARM-Seq)., Methods Mol Biol 1562:231-243

 [13] Kanazhevskaya LY., Alekseeva IV., Fedorova OS., 2019, A Single-Turnover Kinetic Study of DNA Demethylation Catalyzed by Fe(II)/α-Ketoglutarate-Dependent Dioxygenase AlkB., Molecules 24(24)

 [14] Kondo H., Nakabeppu Y., Kataoka H., Kuhara S., Kawabata S., Sekiguchi M., 1986, Structure and expression of the alkB gene of Escherichia coli related to the repair of alkylated DNA., J Biol Chem 261(33):15772-7

 [15] Li D., Delaney JC., Page CM., Chen AS., Wong C., Drennan CL., Essigmann JM., 2010, Repair of DNA Alkylation Damage by the Escherichia coli Adaptive Response Protein AlkB as Studied by ESI-TOF Mass Spectrometry., J Nucleic Acids 369434

 [16] Li D., Fedeles BI., Shrivastav N., Delaney JC., Yang X., Wong C., Drennan CL., Essigmann JM., 2013, Removal of N-alkyl modifications from N(2)-alkylguanine and N(4)-alkylcytosine in DNA by the adaptive response protein AlkB., Chem Res Toxicol 26(8):1182-7

 [17] Li Q., Huang Y., Liu X., Gan J., Chen H., Yang CG., 2016, Rhein Inhibits AlkB Repair Enzymes and Sensitizes Cells to Methylated DNA Damage., J Biol Chem 291(21):11083-93

 [18] Li X., Xiong X., Wang K., Wang L., Shu X., Ma S., Yi C., 2016, Transcriptome-wide mapping reveals reversible and dynamic N(1)-methyladenosine methylome., Nat Chem Biol 12(5):311-6

 [19] Liu H., Llano J., Gauld JW., 2009, A DFT study of nucleobase dealkylation by the DNA repair enzyme AlkB., J Phys Chem B 113(14):4887-98

 [20] Mielecki D., Sikora A., Wrzesinski M., Nieminuszczy J., Detman A., Zuchniewicz K., Gromadka R., Grzesiuk E., 2016, Evaluation of the Escherichia coli HK82 and BS87 strains as tools for AlkB studies., DNA Repair (Amst) 39:34-40

 [21] Mishina Y., He C., 2003, Probing the structure and function of the Escherichia coli DNA alkylation repair AlkB protein through chemical cross-linking., J Am Chem Soc 125(29):8730-1

 [22] Mishina Y., Lee CH., He C., 2004, Interaction of human and bacterial AlkB proteins with DNA as probed through chemical cross-linking studies., Nucleic Acids Res 32(4):1548-54

 [23] Mohan M., Pandya V., Anindya R., 2018, Escherichia coli AlkB and single-stranded DNA binding protein SSB interaction explored by Molecular Dynamics Simulation., J Mol Graph Model 84:29-35

 [24] Nieminuszczy J., Sikora A., Wrzesinski M., Janion C., Grzesiuk E., 2006, AlkB dioxygenase in preventing MMS-induced mutagenesis in Escherichia coli: effect of Pol V and AlkA proteins., DNA Repair (Amst) 5(2):181-8

 [25] Nigam R., Anindya R., 2018, Escherichia coli single-stranded DNA binding protein SSB promotes AlkB-mediated DNA dealkylation repair., Biochem Biophys Res Commun 496(2):274-279

 [26] Nigam R., Mohan M., Shivange G., Dewangan PK., Anindya R., 2018, Escherichia coli AlkB interacts with single-stranded DNA binding protein SSB by an intrinsically disordered region of SSB., Mol Biol Rep 45(5):865-870

 [27] Quesne MG., Latifi R., Gonzalez-Ovalle LE., Kumar D., de Visser SP., 2014, Quantum mechanics/molecular mechanics study on the oxygen binding and substrate hydroxylation step in AlkB repair enzymes., Chemistry 20(2):435-46

 [28] Rebeck GW., Coons S., Carroll P., Samson L., 1988, A second DNA methyltransferase repair enzyme in Escherichia coli., Proc Natl Acad Sci U S A 85(9):3039-43

 [29] Sedgwick B., Robins P., Lindahl T., 2006, Direct removal of alkylation damage from DNA by AlkB and related DNA dioxygenases., Methods Enzymol 408:108-20

 [30] Shivarattan T., Chen HA., Simpson P., Sedgwick B., Matthews S., 2005, Resonance assignments of Escherichia coli AlkB: a key 2-oxoglutarate and Fe(II) dependent dioxygenase of the adaptive DNA-repair response., J Biomol NMR 33(2):138

 [31] Shrivastav N., Fedeles BI., Li D., Delaney JC., Frick LE., Foti JJ., Walker GC., Essigmann JM., 2014, A chemical genetics analysis of the roles of bypass polymerase DinB and DNA repair protein AlkB in processing N2-alkylguanine lesions in vivo., PLoS One 9(4):e94716

 [32] Sikora A., Maciejewska AM., Poznanski J., Pilzys T., Marcinkowski M., Dylewska M., Piwowarski J., Jakubczak W., Pawlak K., Grzesiuk E., 2015, Effects of changes in intracellular iron pool on AlkB-dependent and AlkB-independent mechanisms protecting E.coli cells against mutagenic action of alkylating agent., Mutat Res 778:52-60

 [33] Sikora A., Mielecki D., Chojnacka A., Nieminuszczy J., Wrzesinski M., Grzesiuk E., 2010, Lethal and mutagenic properties of MMS-generated DNA lesions in Escherichia coli cells deficient in BER and AlkB-directed DNA repair., Mutagenesis 25(2):139-47

 [34] Sundheim O., Talstad VA., Vagbo CB., Slupphaug G., Krokan HE., 2008, AlkB demethylases flip out in different ways., DNA Repair (Amst) 7(11):1916-23

 [35] Wang G., Palejwala VA., Dunman PM., Aviv DH., Murphy HS., Rahman MS., Humayun MZ., 1995, Alkylating agents induce UVM, a recA-independent inducible mutagenic phenomenon in Escherichia coli., Genetics 141(3):813-23

 [36] Watanabe K., Ohta T., Watanabe M., Kato T., Shirasu Y., 1990, Inhibition of induction of adaptive response by o-vanillin in Escherichia coli B., Mutat Res 243(4):273-80

 [37] Welford RW., Kirkpatrick JM., McNeill LA., Puri M., Oldham NJ., Schofield CJ., 2005, Incorporation of oxygen into the succinate co-product of iron(II) and 2-oxoglutarate dependent oxygenases from bacteria, plants and humans., FEBS Lett 579(23):5170-4

 [38] Wrzesinski M., Nieminuszczy J., Sikora A., Mielecki D., Chojnacka A., Kozlowski M., Krwawicz J., Grzesiuk E., 2010, Contribution of transcription-coupled DNA repair to MMS-induced mutagenesis in E. coli strains deficient in functional AlkB protein., Mutat Res 688(1-2):19-27

 [39] van den Born E., Bekkelund A., Moen MN., Omelchenko MV., Klungland A., Falnes PO., 2009, Bioinformatics and functional analysis define four distinct groups of AlkB DNA-dioxygenases in bacteria., Nucleic Acids Res 37(21):7124-36


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