Reviewed, UniProtKB/Swiss-Prot P06134 (ADA_ECOLI)

Names and origin

Protein names

Recommended name:
    Regulatory protein ada
Alternative name(s):
    Regulatory protein of adaptative response
Cleaved into the following chain:
    1- Recommended name:
            Methylated-DNA--protein-cysteine methyltransferase
              EC=2.1.1.63
        Alternative name(s):
            O-6-methylguanine-DNA alkyltransferase

Gene names

Name:	ada
Ordered Locus Names:	b2213, JW2201

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	354 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Repair of alkylated guanine in DNA by stoichiometrically transferring the alkyl group at the O-6 position to a cysteine residue in the enzyme. This is a suicide reaction: the enzyme is irreversibly inactivated. Can also repair O-4-methylthymine. The methylated ADA protein acts as a positive regulator of its own synthesis, as well as that of other proteins. The transcription-activating function of the ADA protein resides in its N-terminus. It activates the transcription of alkA, alkB and aidB.
Catalytic activity	DNA (containing 6-O-methylguanine) + protein L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L-cysteine.
Cofactor	Binds 1 zinc ion per subunit.
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
Gene Ontology (GO)
Biological process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription 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 electronic annotation. Source: EC sequence-specific DNA binding Inferred from electronic annotation. Source: InterPro transcription factor activity Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 354

354

Regulatory protein ada

PRO_0000018747

Chain

179 – 354

176

Methylated-DNA--protein-cysteine methyltransferase

PRO_0000018748

Regions

DNA binding

102 – 121

20

H-T-H motif

Sites

Active site

38

1

Nucleophile; methyl group acceptor from phosphotriester Ref.17 Ref.18

Active site

321

1

Nucleophile; methyl group acceptor Ref.17 Ref.18

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

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

354

Helix Strand Turn

Details...

Helix

9 – 17

9

Turn

24 – 26

3

Beta strand

28 – 31

4

Turn

32 – 34

3

Beta strand

36 – 38

3

Helix

49 – 51

3

Beta strand

52 – 57

6

Helix

58 – 63

6

Turn

70 – 72

3

Beta strand

79 – 81

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)
	P06134-1 [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: 2987251] [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: 3887409] [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: 9097040] [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: 9278503] [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: 16738553] [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: 2982792] [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: 3536913] [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: 3009022] [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: 3529081] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-27.
[11]	"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: 1581309] [Abstract] Cited for: ZINC-BINDING.
[12]	"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: 8202360] [Abstract] Cited for: CHARACTERIZATION.
[13]	"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: 8500619] [Abstract] Cited for: STRUCTURE BY NMR OF 1-129.
[14]	"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: 8395079] [Abstract] Cited for: STRUCTURE BY NMR OF 1-92 IN COMPLEX WITH ZINC IONS.
[15]	"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: 8156986] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 175-354. Strain: B.
[16]	"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: 11284682] [Abstract] Cited for: STRUCTURE BY NMR OF 1-92 IN COMPLEX WITH ZINC IONS, INTERACTION WITH DNA.
[17]	"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: 16209950] [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.
[18]	"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: 16452614] [Abstract] Cited for: STRUCTURE BY NMR OF 1-146 IN COMPLEX WITH ZINC IONS, MASS SPECTROMETRY, ACTIVE SITE.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

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

AP_002809.1.
NP_416717.1.

3D structure databases

PDBPDBe

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	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:9055N.

Protein family/group databases

AraC-XylS

Search...

2-D gel databases

ECO2DBASE

I039.5. 6TH EDITION.

Genome annotation databases

GeneID

946710.

GenomeReviews

Gene locus JW2201 in contig AP009048_GR.
Gene locus b2213 in contig U00096_GR.

KEGG

ecj:JW2201.
eco:b2213.

Organism-specific databases

EchoBASE

EB0028.

EcoGene

EG10029. ada.

CMR

Search...

Phylogenomic databases

HOGENOM

P06134.

OMA

P06134. SNSRFYE.

Enzyme and pathway databases

BioCyc

EcoCyc:PD00230.

Family and domain databases

InterPro

IPR004026. Ada_DNA_repair_Zn-bd.
IPR016221. Bifunct_regulatory_prot_Ada.
IPR000005. HTH_AraC-typ.
IPR018062. HTH_AraC-typ_sub_2.
IPR018060. HTH_AraC_domain.
IPR001497. MethylDNA_cys_MeTrfase_AS.
IPR014048. MethylDNA_cys_MeTrfase_DNA_bd.
IPR008332. MethylG_MeTrfase.
IPR011991. Wing_hlx_DNA_bd.
[Graphical view]

Gene3D

G3DSA:3.40.10.10. Ada_DNA_repair_Zn-bd. 1 hit.
G3DSA:1.10.10.10. Wing_hlx_DNA_bd. 1 hit.

PANTHER

PTHR10815. MethylDNA_cys_mtrans_DNA_bd. 1 hit.

Pfam

PF02805. Ada_Zn_binding. 1 hit.
PF01035. DNA_binding_1. 1 hit.
PF00165. HTH_AraC. 2 hits.
PF02870. Methyltransf_1N. 1 hit.
[Graphical view]

PIRSF

PIRSF000409. Ada. 1 hit.

SMART

SM00342. HTH_ARAC. 1 hit.
[Graphical view]

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...

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:	June 16, 2009
This is version 110 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)