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Protein

DNA-3-methyladenine glycosylase 2

Gene

alkA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 activityi

Hydrolysis of alkylated DNA, releasing 3-methyladenine, 3-methylguanine, 7-methylguanine and 7-methyladenine.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei218 – 2181Determinant for substrate specificity and/or activity
Active sitei238 – 2381Proton acceptor

GO - Molecular functioni

GO - Biological processi

  • base-excision repair Source: EcoliWiki
  • cellular response to DNA damage stimulus Source: EcoliWiki
  • DNA dealkylation involved in DNA repair Source: EcoliWiki
  • DNA repair Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

DNA damage, DNA repair

Enzyme and pathway databases

BioCyciEcoCyc:EG11222-MONOMER.
ECOL316407:JW2053-MONOMER.
MetaCyc:EG11222-MONOMER.
BRENDAi3.2.2.21. 2026.

Names & Taxonomyi

Protein namesi
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 namesi
Name:alkA
Synonyms:aidA
Ordered Locus Names:b2068, JW2053
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11222. alkA.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: EcoliWiki
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi124 – 1241Q → A: Methylmethane sulfonate-resistant. 1 Publication
Mutagenesisi218 – 2181W → A: No catalytic activity, methylmethane sulfonate-sensitive. 1 Publication
Mutagenesisi237 – 2371D → N: More than 30% catalytic activity, methylmethane sulfonate-resistant. 1 Publication
Mutagenesisi238 – 2381D → N: No catalytic activity, methylmethane sulfonate-sensitive. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 282282DNA-3-methyladenine glycosylase 2PRO_0000194878Add
BLAST

Expressioni

Inductioni

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

Interactioni

Subunit structurei

Monomer.

Binary interactionsi

WithEntry#Exp.IntActNotes
aceFP069591EBI-544077,EBI-542707

Protein-protein interaction databases

DIPiDIP-9084N.
IntActiP04395. 19 interactions.
MINTiMINT-1227621.
STRINGi511145.b2068.

Structurei

Secondary structure

1
282
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 54Combined sources
Helixi12 – 2211Combined sources
Turni25 – 273Combined sources
Beta strandi28 – 303Combined sources
Beta strandi35 – 417Combined sources
Beta strandi44 – 5310Combined sources
Turni54 – 574Combined sources
Beta strandi58 – 636Combined sources
Helixi65 – 706Combined sources
Helixi71 – 8212Combined sources
Turni83 – 853Combined sources
Helixi88 – 958Combined sources
Helixi96 – 994Combined sources
Helixi113 – 12210Combined sources
Turni123 – 1253Combined sources
Helixi128 – 14215Combined sources
Beta strandi149 – 1535Combined sources
Helixi158 – 1625Combined sources
Helixi166 – 1716Combined sources
Helixi176 – 19015Combined sources
Helixi202 – 2098Combined sources
Helixi217 – 22711Combined sources
Helixi239 – 2446Combined sources
Beta strandi245 – 2473Combined sources
Helixi250 – 2578Combined sources
Helixi258 – 2603Combined sources
Helixi264 – 2729Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DIZX-ray2.50A/B1-282[»]
1MPGX-ray1.80A/B1-282[»]
1PVSX-ray2.40A/B1-282[»]
3CVSX-ray2.40A/B/C/D1-282[»]
3CVTX-ray2.50A/B/C/D1-282[»]
3CW7X-ray2.30A/B/C/D1-282[»]
3CWAX-ray2.40A/B/C/D1-282[»]
3CWSX-ray2.30A/B/C/D1-282[»]
3CWTX-ray2.30A/B/C/D1-282[»]
3CWUX-ray2.80A/B/C/D1-282[»]
3D4VX-ray2.90A/B/C/D1-282[»]
3OGDX-ray2.80A2-282[»]
3OH6X-ray2.89A2-282[»]
3OH9X-ray2.80A2-282[»]
ProteinModelPortaliP04395.
SMRiP04395. Positions 1-282.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04395.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0122.
HOGENOMiHOG000221908.
InParanoidiP04395.
KOiK01247.
OMAiLHIWYTD.
OrthoDBiEOG61VZ6W.
PhylomeDBiP04395.

Family and domain databases

Gene3Di1.10.1670.10. 1 hit.
1.10.340.30. 1 hit.
3.30.310.20. 1 hit.
InterProiIPR010316. AlkA_N.
IPR000035. Alkylbase_DNA_glycsylse_CS.
IPR011257. DNA_glycosylase.
IPR003265. HhH-GPD_domain.
IPR023170. HTH_base_excis_C.
[Graphical view]
PfamiPF06029. AlkA_N. 1 hit.
PF00730. HhH-GPD. 1 hit.
[Graphical view]
SMARTiSM01009. AlkA_N. 1 hit.
SM00478. ENDO3c. 1 hit.
[Graphical view]
SUPFAMiSSF48150. SSF48150. 1 hit.
PROSITEiPS00516. ALKYLBASE_DNA_GLYCOS. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P04395-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYTLNWQPPY DWSWMLGFLA ARAVSSVETV ADSYYARSLA VGEYRGVVTA
60 70 80 90 100
IPDIARHTLH INLSAGLEPV AAECLAKMSR LFDLQCNPQI VNGALGRLGA
110 120 130 140 150
ARPGLRLPGC VDAFEQGVRA ILGQLVSVAM AAKLTARVAQ LYGERLDDFP
160 170 180 190 200
EYICFPTPQR LAAADPQALK ALGMPLKRAE ALIHLANAAL EGTLPMTIPG
210 220 230 240 250
DVEQAMKTLQ TFPGIGRWTA NYFALRGWQA KDVFLPDDYL IKQRFPGMTP
260 270 280
AQIRRYAERW KPWRSYALLH IWYTEGWQPD EA
Length:282
Mass (Da):31,393
Last modified:March 20, 1987 - v1
Checksum:iB66BB5E23019899C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
K02498 Genomic DNA. Translation: AAA23430.1.
U00096 Genomic DNA. Translation: AAC75129.1.
AP009048 Genomic DNA. Translation: BAA15926.1.
M13827 Genomic DNA. No translation available.
PIRiA00904. DGECMA.
RefSeqiNP_416572.1. NC_000913.3.
WP_000288420.1. NZ_CP010445.1.

Genome annotation databases

EnsemblBacteriaiAAC75129; AAC75129; b2068.
BAA15926; BAA15926; BAA15926.
GeneIDi947371.
KEGGieco:b2068.
PATRICi32119469. VBIEscCol129921_2145.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
K02498 Genomic DNA. Translation: AAA23430.1.
U00096 Genomic DNA. Translation: AAC75129.1.
AP009048 Genomic DNA. Translation: BAA15926.1.
M13827 Genomic DNA. No translation available.
PIRiA00904. DGECMA.
RefSeqiNP_416572.1. NC_000913.3.
WP_000288420.1. NZ_CP010445.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DIZX-ray2.50A/B1-282[»]
1MPGX-ray1.80A/B1-282[»]
1PVSX-ray2.40A/B1-282[»]
3CVSX-ray2.40A/B/C/D1-282[»]
3CVTX-ray2.50A/B/C/D1-282[»]
3CW7X-ray2.30A/B/C/D1-282[»]
3CWAX-ray2.40A/B/C/D1-282[»]
3CWSX-ray2.30A/B/C/D1-282[»]
3CWTX-ray2.30A/B/C/D1-282[»]
3CWUX-ray2.80A/B/C/D1-282[»]
3D4VX-ray2.90A/B/C/D1-282[»]
3OGDX-ray2.80A2-282[»]
3OH6X-ray2.89A2-282[»]
3OH9X-ray2.80A2-282[»]
ProteinModelPortaliP04395.
SMRiP04395. Positions 1-282.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-9084N.
IntActiP04395. 19 interactions.
MINTiMINT-1227621.
STRINGi511145.b2068.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75129; AAC75129; b2068.
BAA15926; BAA15926; BAA15926.
GeneIDi947371.
KEGGieco:b2068.
PATRICi32119469. VBIEscCol129921_2145.

Organism-specific databases

EchoBASEiEB1204.
EcoGeneiEG11222. alkA.

Phylogenomic databases

eggNOGiCOG0122.
HOGENOMiHOG000221908.
InParanoidiP04395.
KOiK01247.
OMAiLHIWYTD.
OrthoDBiEOG61VZ6W.
PhylomeDBiP04395.

Enzyme and pathway databases

BioCyciEcoCyc:EG11222-MONOMER.
ECOL316407:JW2053-MONOMER.
MetaCyc:EG11222-MONOMER.
BRENDAi3.2.2.21. 2026.

Miscellaneous databases

EvolutionaryTraceiP04395.
PROiP04395.

Family and domain databases

Gene3Di1.10.1670.10. 1 hit.
1.10.340.30. 1 hit.
3.30.310.20. 1 hit.
InterProiIPR010316. AlkA_N.
IPR000035. Alkylbase_DNA_glycsylse_CS.
IPR011257. DNA_glycosylase.
IPR003265. HhH-GPD_domain.
IPR023170. HTH_base_excis_C.
[Graphical view]
PfamiPF06029. AlkA_N. 1 hit.
PF00730. HhH-GPD. 1 hit.
[Graphical view]
SMARTiSM01009. AlkA_N. 1 hit.
SM00478. ENDO3c. 1 hit.
[Graphical view]
SUPFAMiSSF48150. SSF48150. 1 hit.
PROSITEiPS00516. ALKYLBASE_DNA_GLYCOS. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-12 AND 14-20.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. 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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).

Entry informationi

Entry namei3MG2_ECOLI
AccessioniPrimary (citable) accession number: P04395
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 20, 1987
Last sequence update: March 20, 1987
Last modified: July 22, 2015
This is version 142 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.