RegulonDB RegulonDB 10.9: Gene Form
   

ada 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: ada    Texpresso search in the literature
Synonym(s): ECK2205, EG10029, b2213
Genome position(nucleotides): 2309341 <-- 2310405 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
56.9
External database links:  
ASAP:
ABE-0007311
CGSC:
1043
ECHOBASE:
EB0028
ECOLIHUB:
ada
OU-MICROARRAY:
b2213
STRING:
511145.b2213
COLOMBOS: ada


Shine dalgarno      
Sequence: ccttaaccagGGAGCTgatTAT


Product      
Name: DNA-binding transcriptional dual regulator / DNA repair protein Ada
Synonym(s): Ada
Sequence: Get amino acid sequence Fasta Format
Regulator Family: AraC/XylS
Cellular location: cytosol
Molecular weight: 39.324
Isoelectric point: 8.799
Motif(s):
 
Type Positions Sequence
75 -> 75 E
102 -> 121 LEALADQVAMSPFHLHRLFK
189 -> 266 VRYALADCELGRCLVAESERGICAILLGDDDATLISELQQMFPAADNAPADLMFQQHVREVIASLNQRDTPLTLPLDI
330 -> 330 T
79 -> 80 AQ

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.1 - DNA related --> 2.1.4 - DNA repair
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003824 - catalytic activity
GO:0005515 - protein binding
GO:0008168 - methyltransferase activity
GO:0016740 - transferase activity
GO:0046872 - metal ion binding
GO:0003700 - DNA-binding transcription factor activity
GO:0008270 - zinc ion binding
GO:0003908 - methylated-DNA-[protein]-cysteine S-methyltransferase activity
GO:0043565 - sequence-specific DNA binding
biological_process GO:0008152 - metabolic process
GO:0006281 - DNA repair
GO:0006355 - regulation of transcription, DNA-templated
GO:0006974 - cellular response to DNA damage stimulus
GO:0045892 - negative regulation of transcription, DNA-templated
GO:0045893 - positive regulation of transcription, DNA-templated
GO:0032259 - methylation
GO:0006307 - DNA dealkylation involved in DNA repair
GO:0080111 - DNA demethylation
GO:0018125 - peptidyl-cysteine methylation
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
[APPHINH] Assay of protein purified to homogeneity from its native host
[IDA] Inferred from direct assay
[IMP] Inferred from mutant phenotype
Reference(s): [1] Demple B. 1986
[2] Habazettl J., et al., 1996
[3] Karran P., et al., 1979
[4] Landini P., et al., 1998
[5] Lemotte PK., et al., 1985
[6] Lin Y., et al., 2001
[7] Mackay WJ., et al., 1994
[8] Margison GP., et al., 1985
[9] Myers LC., et al., 1994
[10] Myers LC., et al., 1995
[11] Nakabeppu Y., et al., 1985
[12] Nakabeppu Y., et al., 1986
[13] Rebeck GW., et al., 1991
[14] Robins P., et al., 1979
[15] Saget BM., et al., 1994
[16] Sakashita H., et al., 1995
[17] Schendel PF., et al., 1978
[18] Shevell DE., et al., 1988
[19] Takano K., et al., 1988
[20] Taketomi A., et al., 1996
[21] Takinowaki H., et al., 2006
[22] Taverna P., et al., 1996
[23] Teo I., et al., 1986
[24] Uphoff S. 2018
[25] Vaughan P., et al., 1991
[26] Vericat JA., et al., 1988
[27] Volkert MR. 1989
External database links:  
DIP:
DIP-9055N
ECOCYC:
PD00230
ECOLIWIKI:
b2213
INTERPRO:
IPR036217
INTERPRO:
IPR036631
INTERPRO:
IPR036388
INTERPRO:
IPR035451
INTERPRO:
IPR018062
INTERPRO:
IPR018060
INTERPRO:
IPR016221
INTERPRO:
IPR014048
INTERPRO:
IPR009057
INTERPRO:
IPR008332
INTERPRO:
IPR004026
INTERPRO:
IPR001497
MODBASE:
P06134
PDB:
1SFE
PDB:
1EYF
PDB:
1U8B
PDB:
1WPK
PDB:
1ZGW
PDB:
1ADN
PFAM:
PF01035
PFAM:
PF02805
PFAM:
PF02870
PFAM:
PF12833
PRIDE:
P06134
PRODB:
PRO_000022054
PROSITE:
PS00041
PROSITE:
PS00374
PROSITE:
PS01124
REFSEQ:
NP_416717
SMART:
SM00342
SMR:
P06134
UNIPROT:
P06134


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] Demple B., 1986, Mutant Escherichia coli Ada proteins simultaneously defective in the repair of O6-methylguanine and in gene activation., Nucleic Acids Res 14(14):5575-89

 [2] Habazettl J., Myers LC., Yuan F., Verdine GL., Wagner G., 1996, Backbone dynamics, amide hydrogen exchange, and resonance assignments of the DNA methylphosphotriester repair domain of Escherichia coli Ada using NMR., Biochemistry 35(29):9335-48

 [3] Karran P., Lindahl T., Griffin B., 1979, Adaptive response to alkylating agents involves alteration in situ of O6-methylguanine residues in DNA., Nature 280(5717):76-7

 [4] Landini P., Bown JA., Volkert MR., Busby SJ., 1998, Ada protein-RNA polymerase sigma subunit interaction and alpha subunit-promoter DNA interaction are necessary at different steps in transcription initiation at the Escherichia coli Ada and aidB promoters., J Biol Chem 273(21):13307-12

 [5] Lemotte PK., Walker GC., 1985, Induction and autoregulation of ada, a positively acting element regulating the response of Escherichia coli K-12 to methylating agents., J Bacteriol 161(3):888-95

 [6] Lin Y., Dotsch V., Wintner T., Peariso K., Myers LC., Penner-Hahn JE., Verdine GL., Wagner G., 2001, Structural basis for the functional switch of the E. coli Ada protein., Biochemistry 40(14):4261-71

 [7] Mackay WJ., Han S., Samson LD., 1994, DNA alkylation repair limits spontaneous base substitution mutations in Escherichia coli., J Bacteriol 176(11):3224-30

 [8] Margison GP., Cooper DP., Brennand J., 1985, Cloning of the E. coli O6-methylguanine and methylphosphotriester methyltransferase gene using a functional DNA repair assay., Nucleic Acids Res 13(6):1939-52

 [9] Myers LC., Cushing TD., Wagner G., Verdine GL., 1994, Metal-coordination sphere in the methylated Ada protein-DNA co-complex., Chem Biol 1(2):91-7

 [10] Myers LC., Jackow F., Verdine GL., 1995, Metal dependence of transcriptional switching in Escherichia coli Ada., J Biol Chem 270(12):6664-70

 [11] Nakabeppu Y., Kondo H., Kawabata S., Iwanaga S., Sekiguchi M., 1985, Purification and structure of the intact Ada regulatory protein of Escherichia coli K12, O6-methylguanine-DNA methyltransferase., J Biol Chem 260(12):7281-8

 [12] Nakabeppu Y., Sekiguchi M., 1986, Regulatory mechanisms for induction of synthesis of repair enzymes in response to alkylating agents: ada protein acts as a transcriptional regulator., Proc Natl Acad Sci U S A 83(17):6297-301

 [13] Rebeck GW., Samson L., 1991, Increased spontaneous mutation and alkylation sensitivity of Escherichia coli strains lacking the ogt O6-methylguanine DNA repair methyltransferase., J Bacteriol 173(6):2068-76

 [14] Robins P., Cairns J., 1979, Quantitation of the adaptive response to alkylating agents., Nature 280(5717):74-6

 [15] Saget BM., Walker GC., 1994, The Ada protein acts as both a positive and a negative modulator of Escherichia coli's response to methylating agents., Proc Natl Acad Sci U S A 91(21):9730-4

 [16] Sakashita H., Sakuma T., Akitomo Y., Ohkubo T., Kainosho M., Sekiguchi M., Morikawa K., 1995, Sequence-specific DNA recognition of the Escherichia coli Ada protein associated with the methylation-dependent functional switch for transcriptional regulation., J Biochem 118(6):1184-91

 [17] Schendel PF., Robins PE., 1978, Repair of O6-methylguanine in adapted Escherichia coli., Proc Natl Acad Sci U S A 75(12):6017-20

 [18] Shevell DE., LeMotte PK., Walker GC., 1988, Alteration of the carboxyl-terminal domain of Ada protein influences its inducibility, specificity, and strength as a transcriptional activator., J Bacteriol 170(11):5263-71

 [19] Takano K., Nakabeppu Y., Sekiguchi M., 1988, Functional sites of the Ada regulatory protein of Escherichia coli. Analysis by amino acid substitutions., J Mol Biol 201(2):261-71

 [20] Taketomi A., Nakabeppu Y., Ihara K., Hart DJ., Furuichi M., Sekiguchi M., 1996, Requirement for two conserved cysteine residues in the Ada protein of Escherichia coli for transactivation of the ada promoter., Mol Gen Genet 250(5):523-32

 [21] Takinowaki H., Matsuda Y., Yoshida T., Kobayashi Y., Ohkubo T., 2006, The solution structure of the methylated form of the N-terminal 16-kDa domain of Escherichia coli Ada protein., Protein Sci 15(3):487-97

 [22] Taverna P., Sedgwick B., 1996, Generation of an endogenous DNA-methylating agent by nitrosation in Escherichia coli., J Bacteriol 178(17):5105-11

 [23] Teo I., Sedgwick B., Kilpatrick MW., McCarthy TV., Lindahl T., 1986, The intracellular signal for induction of resistance to alkylating agents in E. coli., Cell 45(2):315-24

 [24] Uphoff S., 2018, Real-time dynamics of mutagenesis reveal the chronology of DNA repair and damage tolerance responses in single cells., Proc Natl Acad Sci U S A 115(28):E6516-E6525

 [25] Vaughan P., Sedgwick B., Hall J., Gannon J., Lindahl T., 1991, Environmental mutagens that induce the adaptive response to alkylating agents in Escherichia coli., Carcinogenesis 12(2):263-8

 [26] Vericat JA., Guerrero R., Barbe J., 1988, Inhibition of the SOS response of Escherichia coli by the Ada protein., J Bacteriol 170(3):1354-9

 [27] Volkert MR., 1989, Altered induction of the adaptive response to alkylation damage in Escherichia coli recF mutants., J Bacteriol 171(1):99-103


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