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P05523

- FPG_ECOLI

UniProt

P05523 - FPG_ECOLI

Protein

Formamidopyrimidine-DNA glycosylase

Gene

mutM

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 149 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases. Has a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG) and its derivatives such as guanidinohydantoin:C and spiroiminodihydantoin:C, however it also acts on thymine glycol:G, 5,6-dihydrouracil:G and 5-hydroxyuracil:G. Has AP (apurinic/apyrimidinic) lyase activity and introduces nicks in the DNA strand. Cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Cleaves ssDNA containing an AP site.2 Publications

    Catalytic activityi

    Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine.
    The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.

    Cofactori

    Binds 1 zinc ion per subunit.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei2 – 21Schiff-base intermediate with DNA
    Active sitei3 – 31Proton donorCurated
    Active sitei57 – 571Proton donor; for beta-elimination activityCurated
    Binding sitei90 – 901DNA1 Publication
    Binding sitei109 – 1091DNA1 Publication
    Binding sitei150 – 1501DNA1 Publication
    Active sitei259 – 2591Proton donor; for delta-elimination activityCurated

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri235 – 26935FPG-typeAdd
    BLAST

    GO - Molecular functioni

    1. damaged DNA binding Source: EcoCyc
    2. DNA-(apurinic or apyrimidinic site) lyase activity Source: EcoliWiki
    3. DNA N-glycosylase activity Source: EcoliWiki
    4. endonuclease activity Source: EcoliWiki
    5. metal ion binding Source: EcoliWiki
    6. oxidized purine nucleobase lesion DNA N-glycosylase activity Source: EcoCyc
    7. oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity Source: EcoCyc
    8. zinc ion binding Source: EcoliWiki

    GO - Biological processi

    1. base-excision repair, AP site formation Source: EcoCyc
    2. cellular response to DNA damage stimulus Source: EcoliWiki
    3. DNA catabolic process, endonucleolytic Source: GOC
    4. nucleic acid phosphodiester bond hydrolysis Source: GOC
    5. nucleotide-excision repair Source: InterPro

    Keywords - Molecular functioni

    Glycosidase, Hydrolase, Lyase

    Keywords - Biological processi

    DNA damage, DNA repair

    Keywords - Ligandi

    DNA-binding, Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10329-MONOMER.
    ECOL316407:JW3610-MONOMER.
    MetaCyc:EG10329-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Formamidopyrimidine-DNA glycosylase (EC:3.2.2.23)
    Short name:
    Fapy-DNA glycosylase
    Alternative name(s):
    DNA-(apurinic or apyrimidinic site) lyase MutM (EC:4.2.99.18)
    Short name:
    AP lyase MutM
    Gene namesi
    Name:mutM
    Synonyms:fpg
    Ordered Locus Names:b3635, JW3610
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10329. mutM.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi3 – 31E → Q: Strong decrease of glycosylase activity; slight decrease of AP lyase activity. 1 Publication
    Mutagenesisi6 – 61E → Q: Decrease of glycosylase activity; no effect on AP lyase activity. 1 Publication
    Mutagenesisi90 – 901H → A: Increase of substrate affinity and decrease of activity. 1 Publication
    Mutagenesisi107 – 1071D → N: No effect on glycosylase and AP lyase activity. 1 Publication
    Mutagenesisi109 – 1091R → A: Over 100-fold decrease of activity. 1 Publication
    Mutagenesisi110 – 1101R → A: Over 100-fold increase of substrate affinity and decrease of activity. 1 Publication
    Mutagenesisi132 – 1321E → Q: Decrease of glycosylase activity; slight decrease of AP lyase activity. 1 Publication
    Mutagenesisi160 – 1601D → N: No effect on glycosylase and AP lyase activity. 1 Publication
    Mutagenesisi174 – 1741E → Q: Strong decrease of glycosylase activity; slight decrease of AP lyase activity. 1 Publication
    Mutagenesisi218 – 2181K → T: Slight increase of substrate affinity and decrease of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 269268Formamidopyrimidine-DNA glycosylasePRO_0000170822Add
    BLAST

    Proteomic databases

    PaxDbiP05523.
    PRIDEiP05523.

    Expressioni

    Gene expression databases

    GenevestigatoriP05523.

    Interactioni

    Subunit structurei

    Monomer.2 Publications

    Protein-protein interaction databases

    DIPiDIP-10286N.
    IntActiP05523. 12 interactions.
    STRINGi511145.b3635.

    Structurei

    Secondary structure

    1
    269
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi4 – 1815
    Beta strandi22 – 298
    Beta strandi32 – 365
    Helixi39 – 435
    Beta strandi46 – 494
    Beta strandi51 – 555
    Beta strandi58 – 625
    Beta strandi67 – 715
    Turni73 – 753
    Beta strandi77 – 848
    Beta strandi93 – 975
    Beta strandi102 – 1065
    Beta strandi113 – 1186
    Beta strandi120 – 1234
    Helixi124 – 1263
    Helixi140 – 1478
    Helixi154 – 1585
    Turni161 – 1633
    Helixi169 – 17911
    Helixi187 – 1893
    Helixi192 – 21120
    Helixi231 – 2333
    Turni245 – 2473
    Beta strandi252 – 2565
    Beta strandi259 – 2635
    Turni265 – 2673

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1K82X-ray2.10A/B/C/D2-269[»]
    ProteinModelPortaliP05523.
    SMRiP05523. Positions 2-269.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP05523.

    Family & Domainsi

    Domaini

    The zinc-finger is necessary for DNA binding.

    Sequence similaritiesi

    Belongs to the FPG family.Curated
    Contains 1 FPG-type zinc finger.Curated

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri235 – 26935FPG-typeAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiCOG0266.
    HOGENOMiHOG000020881.
    KOiK10563.
    OMAiDHVDLKL.
    OrthoDBiEOG6QP131.
    PhylomeDBiP05523.

    Family and domain databases

    HAMAPiMF_00103. Fapy_DNA_glycosyl.
    InterProiIPR015886. DNA_glyclase/AP_lyase_DNA-bd.
    IPR015887. DNA_glyclase_Znf_dom_DNA_BS.
    IPR000191. DNA_glycosylase/AP_lyase.
    IPR012319. DNA_glycosylase/AP_lyase_cat.
    IPR020629. Formamido-pyr_DNA_Glyclase.
    IPR010979. Ribosomal_S13-like_H2TH.
    IPR000214. Znf_DNA_glyclase/AP_lyase.
    IPR010663. Znf_DNA_glyclase/IsotRNA_synth.
    [Graphical view]
    PfamiPF01149. Fapy_DNA_glyco. 1 hit.
    PF06831. H2TH. 1 hit.
    PF06827. zf-FPG_IleRS. 1 hit.
    [Graphical view]
    SMARTiSM00898. Fapy_DNA_glyco. 1 hit.
    [Graphical view]
    SUPFAMiSSF46946. SSF46946. 1 hit.
    SSF81624. SSF81624. 1 hit.
    TIGRFAMsiTIGR00577. fpg. 1 hit.
    PROSITEiPS51068. FPG_CAT. 1 hit.
    PS01242. ZF_FPG_1. 1 hit.
    PS51066. ZF_FPG_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P05523-1 [UniParc]FASTAAdd to Basket

    « Hide

    MPELPEVETS RRGIEPHLVG ATILHAVVRN GRLRWPVSEE IYRLSDQPVL    50
    SVQRRAKYLL LELPEGWIII HLGMSGSLRI LPEELPPEKH DHVDLVMSNG 100
    KVLRYTDPRR FGAWLWTKEL EGHNVLTHLG PEPLSDDFNG EYLHQKCAKK 150
    KTAIKPWLMD NKLVVGVGNI YASESLFAAG IHPDRLASSL SLAECELLAR 200
    VIKAVLLRSI EQGGTTLKDF LQSDGKPGYF AQELQVYGRK GEPCRVCGTP 250
    IVATKHAQRA TFYCRQCQK 269
    Length:269
    Mass (Da):30,290
    Last modified:January 23, 2007 - v3
    Checksum:i01826F7E0E4686EC
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M86305 Genomic DNA. Translation: AAA03747.1.
    X06036 Genomic DNA. Translation: CAA29431.1.
    L10328 Genomic DNA. Translation: AAA61988.1.
    U00039 Genomic DNA. Translation: AAB18612.1.
    U00096 Genomic DNA. Translation: AAC76659.1.
    AP009048 Genomic DNA. Translation: BAE77657.1.
    M60670 Genomic DNA. Translation: AAA24045.1.
    PIRiA30254. DGECFP.
    RefSeqiNP_418092.1. NC_000913.3.
    YP_491798.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76659; AAC76659; b3635.
    BAE77657; BAE77657; BAE77657.
    GeneIDi12933569.
    946765.
    KEGGiecj:Y75_p3539.
    eco:b3635.
    PATRICi32122757. VBIEscCol129921_3755.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M86305 Genomic DNA. Translation: AAA03747.1 .
    X06036 Genomic DNA. Translation: CAA29431.1 .
    L10328 Genomic DNA. Translation: AAA61988.1 .
    U00039 Genomic DNA. Translation: AAB18612.1 .
    U00096 Genomic DNA. Translation: AAC76659.1 .
    AP009048 Genomic DNA. Translation: BAE77657.1 .
    M60670 Genomic DNA. Translation: AAA24045.1 .
    PIRi A30254. DGECFP.
    RefSeqi NP_418092.1. NC_000913.3.
    YP_491798.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1K82 X-ray 2.10 A/B/C/D 2-269 [» ]
    ProteinModelPortali P05523.
    SMRi P05523. Positions 2-269.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-10286N.
    IntActi P05523. 12 interactions.
    STRINGi 511145.b3635.

    Proteomic databases

    PaxDbi P05523.
    PRIDEi P05523.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC76659 ; AAC76659 ; b3635 .
    BAE77657 ; BAE77657 ; BAE77657 .
    GeneIDi 12933569.
    946765.
    KEGGi ecj:Y75_p3539.
    eco:b3635.
    PATRICi 32122757. VBIEscCol129921_3755.

    Organism-specific databases

    EchoBASEi EB0325.
    EcoGenei EG10329. mutM.

    Phylogenomic databases

    eggNOGi COG0266.
    HOGENOMi HOG000020881.
    KOi K10563.
    OMAi DHVDLKL.
    OrthoDBi EOG6QP131.
    PhylomeDBi P05523.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG10329-MONOMER.
    ECOL316407:JW3610-MONOMER.
    MetaCyc:EG10329-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P05523.
    PROi P05523.

    Gene expression databases

    Genevestigatori P05523.

    Family and domain databases

    HAMAPi MF_00103. Fapy_DNA_glycosyl.
    InterProi IPR015886. DNA_glyclase/AP_lyase_DNA-bd.
    IPR015887. DNA_glyclase_Znf_dom_DNA_BS.
    IPR000191. DNA_glycosylase/AP_lyase.
    IPR012319. DNA_glycosylase/AP_lyase_cat.
    IPR020629. Formamido-pyr_DNA_Glyclase.
    IPR010979. Ribosomal_S13-like_H2TH.
    IPR000214. Znf_DNA_glyclase/AP_lyase.
    IPR010663. Znf_DNA_glyclase/IsotRNA_synth.
    [Graphical view ]
    Pfami PF01149. Fapy_DNA_glyco. 1 hit.
    PF06831. H2TH. 1 hit.
    PF06827. zf-FPG_IleRS. 1 hit.
    [Graphical view ]
    SMARTi SM00898. Fapy_DNA_glyco. 1 hit.
    [Graphical view ]
    SUPFAMi SSF46946. SSF46946. 1 hit.
    SSF81624. SSF81624. 1 hit.
    TIGRFAMsi TIGR00577. fpg. 1 hit.
    PROSITEi PS51068. FPG_CAT. 1 hit.
    PS01242. ZF_FPG_1. 1 hit.
    PS51066. ZF_FPG_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Formamidopyrimidine-DNA glycosylase of Escherichia coli: cloning and sequencing of the fpg structural gene and overproduction of the protein."
      Boiteux S., O'Connor T.R., Laval J.
      EMBO J. 6:3177-3183(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes."
      Sofia H.J., Burland V., Daniels D.L., Plunkett G. III, Blattner F.R.
      Nucleic Acids Res. 22:2576-2586(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    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. "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication."
      Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.
      Genomics 16:551-561(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] OF 1-182.
      Strain: K12 / MG1655 / ATCC 47076.
    6. "A gene coding for 3-deoxy-D-manno-octulosonic-acid transferase in Escherichia coli. Identification, mapping, cloning, and sequencing."
      Clementz T., Raetz C.R.H.
      J. Biol. Chem. 266:9687-9696(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 181-269.
      Strain: K12.
    7. "Homogeneous Escherichia coli FPG protein. A DNA glycosylase which excises imidazole ring-opened purines and nicks DNA at apurinic/apyrimidinic sites."
      Boiteux S., O'Connor T.R., Lederer F., Gouyette A., Laval J.
      J. Biol. Chem. 265:3916-3922(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-24, FUNCTION, SUBUNIT, COFACTOR.
    8. "Fpg protein of Escherichia coli is a zinc finger protein whose cysteine residues have a structural and/or functional role."
      O'Connor T.E., Graves R.J., de Murcia G., Castaing B., Laval J.
      J. Biol. Chem. 268:9063-9070(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    9. "Involvement of phylogenetically conserved acidic amino acid residues in catalysis by an oxidative DNA damage enzyme formamidopyrimidine glycosylase."
      Lavrukhin O.V., Lloyd R.S.
      Biochemistry 39:15266-15271(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF GLU-3; GLU-6; ASP-107; GLU-132; ASP-160 AND GLU-174.
    10. "The oxidative DNA glycosylases of Mycobacterium tuberculosis exhibit different substrate preferences from their Escherichia coli counterparts."
      Guo Y., Bandaru V., Jaruga P., Zhao X., Burrows C.J., Iwai S., Dizdaroglu M., Bond J.P., Wallace S.S.
      DNA Repair 9:177-190(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBSTRATES.
    11. "Substrate discrimination by formamidopyrimidine-DNA glycosylase: a mutational analysis."
      Zaika E.I., Perlow R.A., Matz E., Broyde S., Gilboa R., Grollman A.P., Zharkov D.O.
      J. Biol. Chem. 279:4849-4861(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF HIS-90; ARG-109; ARG-110 AND LYS-218.
    12. "Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA."
      Gilboa R., Zharkov D.O., Golan G., Fernandes A.S., Gerchman S.E., Matz E., Kycia J.H., Grollman A.P., Shoham G.
      J. Biol. Chem. 277:19811-19816(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 1-269 IN COMPLEX WITH DNA.

    Entry informationi

    Entry nameiFPG_ECOLI
    AccessioniPrimary (citable) accession number: P05523
    Secondary accession number(s): Q2M7U9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1988
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 149 of the entry and version 3 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, Multifunctional enzyme, 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