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P04395

- 3MG2_ECOLI

UniProt

P04395 - 3MG2_ECOLI

Protein

DNA-3-methyladenine glycosylase 2

Gene

alkA

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 135 (01 Oct 2014)
      Sequence version 1 (20 Mar 1987)
      Previous versions | rss
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    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

    1. alkylbase DNA N-glycosylase activity Source: EcoliWiki
    2. DNA-3-methyladenine glycosylase activity Source: UniProtKB-EC
    3. DNA-3-methylguanine glycosylase activity Source: UniProtKB-EC
    4. DNA-7-methyladenine glycosylase activity Source: UniProtKB-EC
    5. DNA-7-methylguanine glycosylase activity Source: UniProtKB-EC

    GO - Biological processi

    1. base-excision repair Source: EcoliWiki
    2. cellular response to DNA damage stimulus Source: EcoliWiki
    3. DNA dealkylation involved in DNA repair Source: EcoliWiki
    4. DNA repair Source: EcoliWiki

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    DNA damage, DNA repair

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11222-MONOMER.
    ECOL316407:JW2053-MONOMER.
    MetaCyc:EG11222-MONOMER.

    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: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG11222. alkA.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: EcoliWiki

    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.

    Gene expression databases

    GenevestigatoriP04395.

    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 – 54
    Helixi12 – 2211
    Turni25 – 273
    Beta strandi28 – 303
    Beta strandi35 – 417
    Beta strandi44 – 5310
    Turni54 – 574
    Beta strandi58 – 636
    Helixi65 – 706
    Helixi71 – 8212
    Turni83 – 853
    Helixi88 – 958
    Helixi96 – 994
    Helixi113 – 12210
    Turni123 – 1253
    Helixi128 – 14215
    Beta strandi149 – 1535
    Helixi158 – 1625
    Helixi166 – 1716
    Helixi176 – 19015
    Helixi202 – 2098
    Helixi217 – 22711
    Helixi239 – 2446
    Beta strandi245 – 2473
    Helixi250 – 2578
    Helixi258 – 2603
    Helixi264 – 2729

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    KOiK01247.
    OMAiQIKEKSM.
    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

    MYTLNWQPPY DWSWMLGFLA ARAVSSVETV ADSYYARSLA VGEYRGVVTA    50
    IPDIARHTLH INLSAGLEPV AAECLAKMSR LFDLQCNPQI VNGALGRLGA 100
    ARPGLRLPGC VDAFEQGVRA ILGQLVSVAM AAKLTARVAQ LYGERLDDFP 150
    EYICFPTPQR LAAADPQALK ALGMPLKRAE ALIHLANAAL EGTLPMTIPG 200
    DVEQAMKTLQ TFPGIGRWTA NYFALRGWQA KDVFLPDDYL IKQRFPGMTP 250
    AQIRRYAERW KPWRSYALLH IWYTEGWQPD EA 282
    Length:282
    Mass (Da):31,393
    Last modified:March 20, 1987 - v1
    Checksum:iB66BB5E23019899C
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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.
    YP_490310.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75129; AAC75129; b2068.
    BAA15926; BAA15926; BAA15926.
    GeneIDi12930687.
    947371.
    KEGGiecj:Y75_p2031.
    eco:b2068.
    PATRICi32119469. VBIEscCol129921_2145.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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.
    PIRi A00904. DGECMA.
    RefSeqi NP_416572.1. NC_000913.3.
    YP_490310.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    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 [» ]
    ProteinModelPortali P04395.
    SMRi P04395. Positions 1-282.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-9084N.
    IntActi P04395. 19 interactions.
    MINTi MINT-1227621.
    STRINGi 511145.b2068.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC75129 ; AAC75129 ; b2068 .
    BAA15926 ; BAA15926 ; BAA15926 .
    GeneIDi 12930687.
    947371.
    KEGGi ecj:Y75_p2031.
    eco:b2068.
    PATRICi 32119469. VBIEscCol129921_2145.

    Organism-specific databases

    EchoBASEi EB1204.
    EcoGenei EG11222. alkA.

    Phylogenomic databases

    eggNOGi COG0122.
    HOGENOMi HOG000221908.
    KOi K01247.
    OMAi QIKEKSM.
    OrthoDBi EOG61VZ6W.
    PhylomeDBi P04395.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG11222-MONOMER.
    ECOL316407:JW2053-MONOMER.
    MetaCyc:EG11222-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P04395.
    PROi P04395.

    Gene expression databases

    Genevestigatori P04395.

    Family and domain databases

    Gene3Di 1.10.1670.10. 1 hit.
    1.10.340.30. 1 hit.
    3.30.310.20. 1 hit.
    InterProi IPR010316. AlkA_N.
    IPR000035. Alkylbase_DNA_glycsylse_CS.
    IPR011257. DNA_glycosylase.
    IPR003265. HhH-GPD_domain.
    IPR023170. HTH_base_excis_C.
    [Graphical view ]
    Pfami PF06029. AlkA_N. 1 hit.
    PF00730. HhH-GPD. 1 hit.
    [Graphical view ]
    SMARTi SM01009. AlkA_N. 1 hit.
    SM00478. ENDO3c. 1 hit.
    [Graphical view ]
    SUPFAMi SSF48150. SSF48150. 1 hit.
    PROSITEi PS00516. ALKYLBASE_DNA_GLYCOS. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 135 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