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

Names and origin

Protein names

Recommended name:
DNA-3-methyladenine glycosylase 2
EC=3.2.2.21

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

Gene names

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

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	282 AA.
Sequence status	Complete.
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	Up-regulated by methylated Ada in response to the exposure to alkylating agents.
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 Reference proteome
Gene Ontology (GO)
Biological process	DNA dealkylation involved in DNA repair Inferred from mutant phenotype. Source: EcoliWiki base-excision repair Inferred from direct assay. Source: EcoliWiki
Cellular component	cytoplasm Inferred from direct assay. Source: EcoliWiki
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro DNA-3-methyladenine glycosylase activity Inferred from electronic annotation. Source: EC DNA-3-methylguanine glycosylase activity Inferred from electronic annotation. Source: EC DNA-7-methyladenine glycosylase activity Inferred from electronic annotation. Source: EC DNA-7-methylguanine glycosylase activity Inferred from electronic annotation. Source: EC
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

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

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 [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

EMBL
GenBank
DDBJ

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

NP_416572.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]
3OGD	X-ray	2.80	A	2-282	[»]
3OH6	X-ray	2.89	A	2-282	[»]
3OH9	X-ray	2.80	A	2-282	[»]

ProteinModelPortal

P04395.

SMR

P04395. Positions 1-282.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9084N.

IntAct

P04395. 19 interactions.

MINT

MINT-1227621.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000001174; EBESCP00000001174; EBESCG00000000970.
EBESCT00000016906; EBESCP00000016197; EBESCG00000015965.

GeneID

947371.

GenomeReviews

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

KEGG

ecj:JW2053.
eco:b2068.

PATRIC

32119469. VBIEscCol129921_2145.

Organism-specific databases

EchoBASE

EB1204.

EcoGene

EG11222. alkA.

Phylogenomic databases

eggNOG

COG0122.

GeneTree

EBGT00050000010546.

HOGENOM

HBG510250.

OMA

LHIWYTD.

PhylomeDB

P04395.

ProtClustDB

PRK10308.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11222-MONOMER.
MetaCyc:EG11222-MONOMER.

Gene expression databases

Genevestigator

P04395.

Family and domain databases

InterPro

IPR010316. AlkA_N.
IPR000035. Alkylbase_DNA_glycsylse_CS.
IPR011257. DNA_glycosylase.
IPR003265. HhH-GPD_domain.
IPR023170. HTH_base_excis_C.
IPR012294. TFIID_C/glycos_N.
[Graphical view]

Gene3D

G3DSA:3.30.310.20. AlkA_N. 1 hit.
G3DSA:1.10.340.30. DNA_glycosylase. 1 hit.
G3DSA:1.10.1670.10. HTH_base_excis_C. 1 hit.

KO

K01247.

Pfam

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

SMART

SM01009. AlkA_N. 1 hit.
SM00478. ENDO3c. 1 hit.
[Graphical view]

SUPFAM

SSF48150. DNA_glycsylse. 1 hit.
SSF55945. TFIID_C/glycos_N. 1 hit.

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:	January 25, 2012
This is version 117 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program