RegulonDB

Gene
Name:	ada
Synonym(s):	ECK2205, EG10029, b2213
Genome position(nucleotides):	2309341 <-- 2310405
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

Gene

Name:

ada

Synonym(s):

ECK2205, EG10029, b2213

Genome position(nucleotides):

2309341 <-- 2310405

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

56.9

External database links:

ASAP:

CGSC:

ECHOBASE:

ECOLIHUB:

OU-MICROARRAY:

STRING:

COLOMBOS:

Shine dalgarno
Sequence:	ccttaaccagGGAGCTgatTAT

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	Comment
	1 -> 171	MKKATCLTDDQRWQSVLARDPNADGEFVFAVRTTGIFCRPSCRARHALRENVSFYANASEALAAGFRPCKRCQPEKANAQQHRLDKITHACRLLEQETPVTLEALADQVAMSPFHLHRLFKATTGMTPKAWQQAWRARRLRESLAKGESVTTSILNAGFPDSSSYYRKADE	UniProt: Methylphosphotriester-DNA--protein-cysteine methyltransferase; Sequence Annotation Type: region of interest.
	11 -> 75	QRWQSVLARDPNADGEFVFAVRTTGIFCRPSCRARHALRENVSFYANASEALAAGFRPCKRCQPE
	69 -> 69	C	alternate sequence C → A: protein is unable to accept a methyl group from methylphosphotriesters but retains ability to transactivate ada promoter
	75 -> 75	E	UniProt: In strain: B..
	79 -> 80	AQ	UniProt: In strain: B..

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:

[EXP-IDA] Inferred from direct assay
[EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
[EXP-IMP] Inferred from mutant phenotype
[IDA-PURIFIED-PROTEIN-NH] Assay of protein purified to homogeneity from its native host

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:

ALPHAFOLD:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

INTERPRO:

MODBASE:

PDB:

PDB:

PDB:

PDB:

PDB:

PDB:

PFAM:

PFAM:

PFAM:

PFAM:

PRIDE:

PRODB:

PROSITE:

PROSITE:

PROSITE:

REFSEQ:

SMART:

SMR:

UNIPROT:

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

Transcriptional Regulation

Display Regulation

Activated by:

Ada

Repressed by:

Ada

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

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