Reviewed, UniProtKB/Swiss-Prot P04395 (3MG2_ECOLI)

Names and origin

Protein names

Recommended name:
    DNA-3-methyladenine glycosylase 2
    EC=3.2.2.21
Alternative name(s):
    DNA-3-methyladenine glycosylase II
    3-methyladenine-DNA glycosylase II, inducible
      Short name=TAG II
    DNA-3-methyladenine glycosidase II

Gene names

Name:	alkA
Synonyms:	aidA
Ordered Locus Names:	b2068, JW2053

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	282 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Hydrolysis of the deoxyribose N-glycosidic bond to excise 3-methyladenine, 3-methylguanine, 7-methylguanine, O2-methylthymine, and O2-methylcytosine from the damaged DNA polymer formed by alkylation lesions.
Catalytic activity	Hydrolysis of alkylated DNA, releasing 3-methyladenine, 3-methylguanine, 7-methylguanine and 7-methyladenine.
Subunit structure	Monomer.
Induction	When E.coli cells are exposed to doses of DNA alkylating agent. It is not inhibited by reaction products.
Sequence similarities	Belongs to the alkylbase DNA glycosidase alkA family.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	base-excision repair Inferred from electronic annotation. Source: InterPro
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro alkylbase DNA N-glycosylase activity Inferred from electronic annotation. Source: EC protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
aceF	P06959	1	EBI-544077,EBI-542707

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 282

282

DNA-3-methyladenine glycosylase 2

PRO_0000194878

Sites

Active site

238

1

Proton acceptor

Site

218

1

Determinant for substrate specificity and/or activity

Experimental info

Mutagenesis

124

1

Q → A: Methylmethane sulfonate-resistant.

Mutagenesis

218

1

W → A: No catalytic activity, methylmethane sulfonate-sensitive.

Mutagenesis

237

1

D → N: More than 30% catalytic activity, methylmethane sulfonate-resistant.

Mutagenesis

238

1

D → N: No catalytic activity, methylmethane sulfonate-sensitive.

Secondary structure

1

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282

Helix Strand Turn

Details...

Beta strand

2 – 5

4

Helix

12 – 22

11

Turn

25 – 27

3

Beta strand

28 – 30

3

Beta strand

35 – 41

7

Beta strand

44 – 53

10

Turn

54 – 57

4

Beta strand

58 – 63

6

Helix

65 – 70

6

Helix

71 – 82

12

Turn

83 – 85

3

Helix

88 – 95

8

Helix

96 – 99

4

Helix

113 – 122

10

Turn

123 – 125

3

Helix

128 – 142

15

Helix

158 – 162

5

Helix

166 – 171

6

Helix

176 – 190

15

Helix

202 – 209

8

Helix

217 – 227

11

Helix

239 – 244

6

Helix

250 – 257

8

Helix

258 – 260

3

Helix

264 – 272

9

Sequences

	Sequence		Length	Mass (Da)
	P04395-1 [UniParc]. Last modified March 20, 1987. Version 1. Checksum: B66BB5E23019899C	FASTA	282	31,393
	10 20 30 40 50 60 MYTLNWQPPY DWSWMLGFLA ARAVSSVETV ADSYYARSLA VGEYRGVVTA IPDIARHTLH 70 80 90 100 110 120 INLSAGLEPV AAECLAKMSR LFDLQCNPQI VNGALGRLGA ARPGLRLPGC VDAFEQGVRA 130 140 150 160 170 180 ILGQLVSVAM AAKLTARVAQ LYGERLDDFP EYICFPTPQR LAAADPQALK ALGMPLKRAE 190 200 210 220 230 240 ALIHLANAAL EGTLPMTIPG DVEQAMKTLQ TFPGIGRWTA NYFALRGWQA KDVFLPDDYL 250 260 270 280 IKQRFPGMTP AQIRRYAERW KPWRSYALLH IWYTEGWQPD EA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Structure and expression of the alkA gene of Escherichia coli involved in adaptive response to alkylating agents." Nakabeppu Y., Miyata T., Kondo H., Iwanaga S., Sekiguchi M. J. Biol. Chem. 259:13730-13736(1984) [PubMed: 6094528] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-12 AND 14-20.
[2]	"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.
[3]	"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.
[4]	"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.
[5]	"Cloning and characterization of the alkA gene of Escherichia coli that encodes 3-methyladenine DNA glycosylase II." Nakabeppu Y., Kondo H., Sekiguchi M. J. Biol. Chem. 259:13723-13729(1984) [PubMed: 6389535] [Abstract] Cited for: CHARACTERIZATION.
[6]	"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 1-2.
[7]	"Three-dimensional structure of a DNA repair enzyme, 3-methyladenine DNA glycosylase II, from Escherichia coli." Yamagata Y., Kato M., Odawara K., Tokuno Y., Nakashima Y., Matsushima N., Yasumura K., Tomita K., Ihara K., Fujii Y., Nakabeppu Y., Sekiguchi M., Fujii S. Cell 86:311-319(1996) [PubMed: 8706135] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS), MUTAGENESIS.
[8]	"Structural basis for the excision repair of alkylation-damaged DNA." Labahn J., Scharer O.D., Long A., Ezaz-Nikpay K., Verdine G.L., Ellenberger T.E. Cell 86:321-329(1996) [PubMed: 8706136] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

K02498 Genomic DNA. Translation: AAA23430.1.
U00096 Genomic DNA. Translation: AAC75129.1.
AP009048 Genomic DNA. Translation: BAA15926.1.
M13827 Genomic DNA. No translation available.

PIR

DGECMA. A00904.

RefSeq

AP_002668.1.
NP_416572.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DIZ	X-ray	2.50	A/B	1-282	[»]
1MPG	X-ray	1.80	A/B	1-282	[»]
1PVS	X-ray	2.40	A/B	1-282	[»]
3CVS	X-ray	2.40	A/B/C/D	1-282	[»]
3CVT	X-ray	2.50	A/B/C/D	1-282	[»]
3CW7	X-ray	2.30	A/B/C/D	1-282	[»]
3CWA	X-ray	2.40	A/B/C/D	1-282	[»]
3CWS	X-ray	2.30	A/B/C/D	1-282	[»]
3CWT	X-ray	2.30	A/B/C/D	1-282	[»]
3CWU	X-ray	2.80	A/B/C/D	1-282	[»]
3D4V	X-ray	2.90	A/B/C/D	1-282	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:9084N.

IntAct

P04395. 19 interactions.

STRING

P04395.

Genome annotation databases

GeneID

947371.

GenomeReviews

Gene locus JW2053 in contig AP009048_GR.
Gene locus b2068 in contig U00096_GR.

KEGG

ecj:JW2053.
eco:b2068.

Organism-specific databases

EchoBASE

EB1204.

EcoGene

EG11222. alkA.

CMR

Search...

Phylogenomic databases

HOGENOM

P04395.

OMA

GLARDPW.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11222-MON.

Gene expression databases

Genevestigator

P04395.

Family and domain databases

InterPro

IPR010316. AlkA_N.
IPR000035. Alkylbase_DNA_glycsylse_CS.
IPR003265. HhH-GPD_domain.
[Graphical view]

Gene3D

G3DSA:3.30.310.20. AlkA_N. 1 hit.

Pfam

PF06029. AlkA_N. 1 hit.
PF00730. HhH-GPD. 1 hit.
[Graphical view]

SMART

SM00478. ENDO3c. 1 hit.
[Graphical view]

PROSITE

PS00516. ALKYLBASE_DNA_GLYCOS. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

3MG2_ECOLI

Accession

Primary (citable) accession number: P04395

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 20, 1987
Last sequence update:	March 20, 1987
Last modified:	November 3, 2009
This is version 97 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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