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P06134 (ADA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 156. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Bifunctional transcriptional activator/DNA repair enzyme Ada
Alternative name(s):
Regulatory protein of adaptive response

Including the following 2 domains:

  1. Methylphosphotriester-DNA--protein-cysteine S-methyltransferase
    EC=2.1.1.n11
    Alternative name(s):
    Methylphosphotriester-DNA methyltransferase
  2. Methylated-DNA--protein-cysteine methyltransferase
    EC=2.1.1.63
    Alternative name(s):
    O6-methylguanine-DNA alkyltransferase
Gene names
Name:ada
Ordered Locus Names:b2213, JW2201
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length354 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Is involved in the adaptive response to alkylation damage in DNA caused by alkylating agents. Repairs O6-methylguanine and 04-methylthymine residues in alkylated DNA by a direct and irreversible transfer of the methyl group from the base to one of its own cysteine residues (Cys-321). Also specifically repairs the Sp diastereomer of DNA methylphosphotriester lesions by the same mechanism, although the methyl transfer occurs onto a different cysteine residue (Cys-38). Can not demethylate the other diastereomer, Rp-methylphosphotriester. Ref.11

The methylation of Ada by methylphosphotriesters in DNA leads to its activation as a transcriptional regulator that activates the transcription of its own gene, ada, and other alkylation resistance genes, alkA, alkB and aidB. Ref.11

Catalytic activity

DNA (containing Sp-methylphosphotriester) + protein L-cysteine = DNA (without Sp-methylphosphotriester) + protein S-methyl-L-cysteine. Ref.11

DNA (containing 6-O-methylguanine) + protein L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L-cysteine. Ref.11

Cofactor

Binds 1 zinc ion per subunit.

Induction

Up-regulated by methylated Ada itself in response to the exposure to alkylating agents.

Domain

Consists of two domains. The 20 kDa N-terminal domain repairs the Sp diastereomer of methylphosphotriesters and, in its methylated form, binds DNA in a sequence-specific manner. The 19 kDa C-terminal domain repairs the mutagenic lesions O6-methylguanine. Each domain retains its activity when separated form the other. Ref.12

Miscellaneous

This enzyme catalyzes only one turnover and therefore is not strictly catalytic. According to one definition, an enzyme is a biocatalyst that acts repeatedly and over many reaction cycles.

Sequence similarities

In the C-terminal section; belongs to the MGMT family.

Contains 1 HTH araC/xylS-type DNA-binding domain.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

hdaP699313EBI-1119501,EBI-545453

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 354354Bifunctional transcriptional activator/DNA repair enzyme Ada
PRO_0000018747

Regions

Domain85 – 18399HTH araC/xylS-type
DNA binding102 – 12120H-T-H motif
Region1 – 171171Methylphosphotriester-DNA--protein-cysteine methyltransferase
Region181 – 354174Methylated-DNA--protein-cysteine methyltransferase

Sites

Active site381Nucleophile; methyl group acceptor from methylphosphotriester Ref.20 Ref.21
Active site3211Nucleophile; methyl group acceptor from either O6-methylguanine or O4-methylthymine Ref.20
Metal binding381Zinc
Metal binding421Zinc
Metal binding691Zinc
Metal binding721Zinc
Binding site341DNA
Binding site431DNA
Binding site451DNA
Binding site671DNA
Site128 – 1292Cleavage
Site178 – 1792Cleavage

Natural variations

Natural variant751E → D in strain: B.
Natural variant79 – 802AQ → PR in strain: B.
Natural variant3181I → V in strain: B.
Natural variant3301T → S in strain: B.

Experimental info

Sequence conflict1341A → R in AAA23412. Ref.1

Secondary structure

..................................................... 354
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P06134 [UniParc].

Last modified February 1, 1994. Version 2.
Checksum: 4163E585C768C2F4

FASTA35439,324
        10         20         30         40         50         60 
MKKATCLTDD QRWQSVLARD PNADGEFVFA VRTTGIFCRP SCRARHALRE NVSFYANASE 

        70         80         90        100        110        120 
ALAAGFRPCK RCQPEKANAQ QHRLDKITHA CRLLEQETPV TLEALADQVA MSPFHLHRLF 

       130        140        150        160        170        180 
KATTGMTPKA WQQAWRARRL RESLAKGESV TTSILNAGFP DSSSYYRKAD ETLGMTAKQF 

       190        200        210        220        230        240 
RHGGENLAVR YALADCELGR CLVAESERGI CAILLGDDDA TLISELQQMF PAADNAPADL 

       250        260        270        280        290        300 
MFQQHVREVI ASLNQRDTPL TLPLDIRGTA FQQQVWQALR TIPCGETVSY QQLANAIGKP 

       310        320        330        340        350 
KAVRAVASAC AANKLAIIIP CHRVVRGDGT LSGYRWGVSR KAQLLRREAE NEER 

« Hide

References

« Hide 'large scale' references
[1]"Purification and structure of the intact Ada regulatory protein of Escherichia coli K12, O6-methylguanine-DNA methyltransferase."
Nakabeppu Y., Kondo H., Kawabata S., Iwanaga S., Sekiguchi M.
J. Biol. Chem. 260:7281-7288(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
Strain: K12.
[2]"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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: B.
[3]"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.
[4]"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. expand/collapse author list , 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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]"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 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[6]"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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]"Induction and autoregulation of ada, a positively acting element regulating the response of Escherichia coli K-12 to methylating agents."
Lemotte P.K., Walker G.C.
J. Bacteriol. 161:888-895(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-49.
Strain: K12.
[8]"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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 287-354.
[9]"The intracellular signal for induction of resistance to alkylating agents in E. coli."
Teo I., Sedgwick B., Kilpatrick M.W., McCarthy T.V., Lindahl T.
Cell 45:315-324(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-29.
[10]"Regulatory mechanisms for induction of synthesis of repair enzymes in response to alkylating agents: ada protein acts as a transcriptional regulator."
Nakabeppu Y., Sekiguchi M.
Proc. Natl. Acad. Sci. U.S.A. 83:6297-6301(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-27.
[11]"Methyl phosphotriesters in alkylated DNA are repaired by the Ada regulatory protein of E. coli."
McCarthy T.V., Lindahl T.
Nucleic Acids Res. 13:2683-2698(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY.
[12]"Functional domains and methyl acceptor sites of the Escherichia coli Ada protein."
Sedgwick B., Robins P., Totty N., Lindahl T.
J. Biol. Chem. 263:4430-4433(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: DOMAIN.
[13]"Zinc binding by the methylation signaling domain of the Escherichia coli Ada protein."
Myers L.C., Terranova M.P., Nash H.M., Markus M.A., Verdine G.L.
Biochemistry 31:4541-4547(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: ZINC-BINDING.
[14]"Specificities of human, rat and E. coli O6-methylguanine-DNA methyltransferases towards the repair of O6-methyl and O6-ethylguanine in DNA."
Liem L.-K., Lim A., Li B.F.L.
Nucleic Acids Res. 22:1613-1619(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION.
[15]"Escherichia coli proteome analysis using the gene-protein database."
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY 2D-GEL.
[16]"Folding topology and DNA binding of the N-terminal fragment of Ada protein."
Sakashita H., Sakuma T., Ohkubo T., Kainosho M., Sakumi K., Sekiguchi M., Morikawa K.
FEBS Lett. 323:252-256(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 1-129.
[17]"Repair of DNA methylphosphotriesters through a metalloactivated cysteine nucleophile."
Myers L.C., Terranova M.P., Ferentz A.E., Wagner G., Verdine G.L.
Science 261:1164-1167(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 1-92 IN COMPLEX WITH ZINC IONS.
[18]"Crystal structure of a suicidal DNA repair protein: the Ada O6-methylguanine-DNA methyltransferase from E. coli."
Moore M.H., Gulbis J.M., Dodson E.J., Demple B., Moody P.C.E.
EMBO J. 13:1495-1501(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 175-354.
Strain: B.
[19]"Structural basis for the functional switch of the E. coli Ada protein."
Lin Y., Doetsch V., Wintner T., Peariso K., Myers L.C., Penner-Hahn J.E., Verdine G.L., Wagner G.
Biochemistry 40:4261-4271(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 1-92 IN COMPLEX WITH ZINC IONS, INTERACTION WITH DNA.
[20]"A methylation-dependent electrostatic switch controls DNA repair and transcriptional activation by E. coli ada."
He C., Hus J.-C., Sun L.J., Zhou P., Norman D.P.G., Doetsch V., Wei H., Gross J.D., Lane W.S., Wagner G., Verdine G.L.
Mol. Cell 20:117-129(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 9-139 IN COMPLEX WITH DNA AND ZINC IONS, STRUCTURE BY NMR OF 9-139, IDENTIFICATION BY MASS SPECTROMETRY, ACTIVE SITE.
[21]"The solution structure of the methylated form of the N-terminal 16-kDa domain of Escherichia coli Ada protein."
Takinowaki H., Matsuda Y., Yoshida T., Kobayashi Y., Ohkubo T.
Protein Sci. 15:487-497(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 1-146 IN COMPLEX WITH ZINC IONS, IDENTIFICATION BY MASS SPECTROMETRY, ACTIVE SITE CYS-38.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M10211 Genomic DNA. Translation: AAA23412.1.
M10315 Genomic DNA. Translation: AAA23413.1.
U00008 Genomic DNA. Translation: AAA16408.1.
U00096 Genomic DNA. Translation: AAC75273.1.
AP009048 Genomic DNA. Translation: BAA15996.1.
J02607 Genomic DNA. Translation: AAA23415.1.
M13155 Genomic DNA. Translation: AAA23418.1.
M13828 Genomic DNA. Translation: AAA23417.1.
PIRXYECO2. C64991.
RefSeqNP_416717.1. NC_000913.3.
YP_490451.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1ADNNMR-A1-92[»]
1EYFNMR-A1-92[»]
1SFEX-ray2.10A175-354[»]
1U8BX-ray2.10A9-139[»]
1WPKNMR-A1-146[»]
1ZGWNMR-A1-139[»]
ProteinModelPortalP06134.
SMRP06134. Positions 1-146, 187-351.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-9055N.
IntActP06134. 13 interactions.
MINTMINT-1310041.
STRING511145.b2213.

Protein family/group databases

AraC-XylSSearch...

Proteomic databases

PRIDEP06134.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75273; AAC75273; b2213.
BAA15996; BAA15996; BAA15996.
GeneID12932929.
946710.
KEGGecj:Y75_p2174.
eco:b2213.
PATRIC32119785. VBIEscCol129921_2302.

Organism-specific databases

EchoBASEEB0028.
EcoGeneEG10029. ada.

Phylogenomic databases

eggNOGCOG2169.
HOGENOMHOG000244139.
KOK10778.
OMAGMRPRQY.
OrthoDBEOG6WMJ4F.
PhylomeDBP06134.
ProtClustDBPRK15435.

Enzyme and pathway databases

BioCycEcoCyc:PD00230.
ECOL316407:JW2201-MONOMER.
MetaCyc:PD00230.

Gene expression databases

GenevestigatorP06134.

Family and domain databases

Gene3D1.10.10.10. 1 hit.
1.10.10.60. 1 hit.
3.40.10.10. 1 hit.
InterProIPR004026. Ada_DNA_repair_Zn-bd.
IPR016221. Bifunct_regulatory_prot_Ada.
IPR009057. Homeodomain-like.
IPR018060. HTH_AraC.
IPR018062. HTH_AraC-typ_CS.
IPR001497. MethylDNA_cys_MeTrfase_AS.
IPR014048. MethylDNA_cys_MeTrfase_DNA-bd.
IPR008332. MethylG_MeTrfase_N.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamPF02805. Ada_Zn_binding. 1 hit.
PF01035. DNA_binding_1. 1 hit.
PF00165. HTH_AraC. 2 hits.
PF02870. Methyltransf_1N. 1 hit.
[Graphical view]
PIRSFPIRSF000409. Ada. 1 hit.
SMARTSM00342. HTH_ARAC. 1 hit.
[Graphical view]
SUPFAMSSF46689. SSF46689. 1 hit.
SSF46767. SSF46767. 1 hit.
SSF53155. SSF53155. 1 hit.
SSF57884. SSF57884. 1 hit.
TIGRFAMsTIGR00589. ogt. 1 hit.
PROSITEPS00041. HTH_ARAC_FAMILY_1. 2 hits.
PS01124. HTH_ARAC_FAMILY_2. 1 hit.
PS00374. MGMT. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP06134.
PROP06134.

Entry information

Entry nameADA_ECOLI
AccessionPrimary (citable) accession number: P06134
Secondary accession number(s): Q47032
Entry history
Integrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: February 1, 1994
Last modified: April 16, 2014
This is version 156 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene