P06134 (ADA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Bifunctional transcriptional activator/DNA repair enzyme Ada

Alternative name(s):
Regulatory protein of adaptative 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

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	354 AA.
Sequence status	Complete.
Protein existence	Evidence 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.

Ontologies

Keywords
Biological process	DNA damage DNA repair Transcription Transcription regulation
Ligand	DNA-binding Metal-binding Zinc
Molecular function	Activator Methyltransferase Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing Multifunctional enzyme Reference proteome
Gene Ontology (GO)
Biological_process	DNA dealkylation involved in DNA repair Inferred from direct assay PubMed 282622. Source: EcoliWiki DNA demethylation Inferred from direct assay PubMed 6754717. Source: EcoliWiki transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	intracellular Inferred from electronic annotation. Source: InterPro
Molecular_function	methylated-DNA-[protein]-cysteine S-methyltransferase activity Inferred from direct assay PubMed 6754717. Source: EcoliWiki sequence-specific DNA binding Inferred from electronic annotation. Source: InterPro sequence-specific DNA binding transcription factor activity Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from direct assay Ref.13. Source: EcoliWiki
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 354

354

Bifunctional transcriptional activator/DNA repair enzyme Ada

PRO_0000018747

Regions

Domain

85 – 183

99

HTH araC/xylS-type

DNA binding

102 – 121

20

H-T-H motif

Region

1 – 171

171

Methylphosphotriester-DNA--protein-cysteine methyltransferase

Region

181 – 354

174

Methylated-DNA--protein-cysteine methyltransferase

Sites

Active site

38

1

Nucleophile; methyl group acceptor from methylphosphotriester Ref.20 Ref.21

Active site

321

1

Nucleophile; methyl group acceptor from either O6-methylguanine or O4-methylthymine Ref.20

Metal binding

38

1

Zinc

Metal binding

42

1

Zinc

Metal binding

69

1

Zinc

Metal binding

72

1

Zinc

Binding site

34

1

DNA

Binding site

43

1

DNA

Binding site

45

1

DNA

Binding site

67

1

DNA

Site

128 – 129

2

Cleavage

Site

178 – 179

2

Cleavage

Natural variations

Natural variant

75

1

E → D in strain: B.

Natural variant

79 – 80

2

AQ → PR in strain: B.

Natural variant

318

1

I → V in strain: B.

Natural variant

330

1

T → S in strain: B.

Experimental info

Sequence conflict

134

1

A → R in AAA23412. Ref.1

Secondary structure

1

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354

Helix Strand Turn

Details...

Beta strand

4 – 6

3

Helix

9 – 17

9

Helix

21 – 23

3

Turn

24 – 26

3

Beta strand

27 – 31

5

Turn

32 – 34

3

Beta strand

36 – 38

3

Helix

49 – 51

3

Beta strand

52 – 57

6

Helix

58 – 63

6

Beta strand

67 – 69

3

Turn

70 – 72

3

Beta strand

76 – 78

3

Helix

79 – 93

15

Beta strand

96 – 98

3

Helix

102 – 109

8

Helix

113 – 123

11

Helix

128 – 137

10

Turn

142 – 144

3

Beta strand

190 – 196

7

Beta strand

199 – 205

7

Beta strand

207 – 217

11

Helix

219 – 229

11

Helix

240 – 254

15

Beta strand

255 – 257

3

Helix

270 – 279

10

Helix

290 – 296

7

Helix

303 – 311

9

Helix

321 – 323

3

Helix

338 – 348

11

Sequences

	Sequence		Length	Mass (Da)
	P06134 [UniParc]. Last modified February 1, 1994. Version 2. Checksum: 4163E585C768C2F4	FASTA	354	39,324
	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

References

	« Hide 'large scale' referencesShow '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. , 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 277:1453-1474(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, 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, 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.

PIR

XYECO2. C64991.

RefSeq

NP_416717.1. NC_000913.2.
YP_490451.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1ADN	NMR	-	A	1-92	[»]
1EYF	NMR	-	A	1-92	[»]
1SFE	X-ray	2.10	A	175-354	[»]
1U8B	X-ray	2.10	A	9-139	[»]
1WPK	NMR	-	A	1-146	[»]
1ZGW	NMR	-	A	1-139	[»]

ProteinModelPortal

P06134.

SMR

P06134. Positions 1-146, 187-351.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9055N.

IntAct

P06134. 9 interactions.

MINT

MINT-1310041.

STRING

511145.b2213.

Protein family/group databases

AraC-XylS

Search...

Proteomic databases

PRIDE

P06134.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75273; AAC75273; b2213.
BAA15996; BAA15996; BAA15996.

GeneID

12932929.
946710.

KEGG

ecj:Y75_p2174.
eco:b2213.

PATRIC

32119785. VBIEscCol129921_2302.

Organism-specific databases

EchoBASE

EB0028.

EcoGene

EG10029. ada.

Phylogenomic databases

eggNOG

COG2169.

HOGENOM

HOG000244139.

KO

K10778.

OMA

SNSRFYE.

ProtClustDB

PRK15435.

Enzyme and pathway databases

BioCyc

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

Gene expression databases

Genevestigator

P06134.

Family and domain databases

Gene3D

1.10.10.10. 1 hit.
1.10.10.60. 1 hit.
3.40.10.10. 1 hit.

InterPro

IPR004026. 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.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]

Pfam

PF02805. Ada_Zn_binding. 1 hit.
PF01035. DNA_binding_1. 1 hit.
PF02870. Methyltransf_1N. 1 hit.
[Graphical view]

PIRSF

PIRSF000409. Ada. 1 hit.

SMART

SM00342. HTH_ARAC. 1 hit.
[Graphical view]

SUPFAM

SSF57884. Ada_DNA_repair_Zn-bd. 1 hit.
SSF46689. Homeodomain_like. 1 hit.
SSF46767. MethylDNA_cys_mtrans_DNA_bd. 1 hit.

TIGRFAMs

TIGR00589. ogt. 1 hit.

PROSITE

PS00041. HTH_ARAC_FAMILY_1. 2 hits.
PS01124. HTH_ARAC_FAMILY_2. 1 hit.
PS00374. MGMT. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P06134.

Entry information

Entry name

ADA_ECOLI

Accession

Primary (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:	May 1, 2013
This is version 149 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program