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P84131

- P84131_GEOSE

UniProt

P84131 - P84131_GEOSE

Protein

Formamidopyrimidine-DNA glycosylase

Gene

mutM

Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
Status
Unreviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 77 (01 Oct 2014)
      Sequence version 1 (13 Sep 2004)
      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). 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.UniRule annotationSAAS annotation

    Catalytic activityi

    Hydrolysis of DNA containing ring-opened 7-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimidine.UniRule annotationSAAS annotation
    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.UniRule annotationSAAS annotation

    Cofactori

    Binds 1 zinc ion per subunit.UniRule annotationSAAS annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei2 – 21Schiff-base intermediate with DNAUniRule annotation
    Active sitei60 – 601Proton donor; for beta-elimination activityUniRule annotation
    Binding sitei93 – 931DNAUniRule annotation
    Binding sitei112 – 1121DNAUniRule annotation
    Metal bindingi249 – 2491ZincImported
    Metal bindingi252 – 2521ZincImported
    Active sitei264 – 2641Proton donor; for delta-elimination activityUniRule annotation
    Metal bindingi269 – 2691ZincImported
    Metal bindingi272 – 2721ZincImported

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri240 – 27435FPG-typeUniRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. damaged DNA binding Source: InterPro
    2. oxidized purine nucleobase lesion DNA N-glycosylase activity Source: UniProtKB-HAMAP
    3. zinc ion binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. base-excision repair Source: InterPro
    2. nucleotide-excision repair Source: InterPro

    Keywords - Molecular functioni

    GlycosidaseUniRule annotationSAAS annotation, Hydrolase, LyaseUniRule annotationSAAS annotation

    Keywords - Biological processi

    DNA damage, DNA repairUniRule annotationSAAS annotation

    Keywords - Ligandi

    DNA-bindingUniRule annotationSAAS annotation, Metal-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Formamidopyrimidine-DNA glycosylaseUniRule annotation (EC:3.2.2.23UniRule annotation)
    Short name:
    Fapy-DNA glycosylaseUniRule annotation
    Alternative name(s):
    DNA-(apurinic or apyrimidinic site) lyase MutMUniRule annotation
    Gene namesi
    Name:mutMUniRule annotation
    Synonyms:fpgUniRule annotation
    OrganismiGeobacillus stearothermophilus (Bacillus stearothermophilus)Imported
    Taxonomic identifieri1422 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

    Interactioni

    Subunit structurei

    Monomer.UniRule annotationSAAS annotation

    Structurei

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1L1TX-ray1.80A1-274[»]
    1L1ZX-ray1.70A1-274[»]
    1L2BX-ray2.40A1-274[»]
    1L2CX-ray2.20A1-274[»]
    1R2YX-ray2.34A1-274[»]
    1R2ZX-ray1.63A1-274[»]
    2F5NX-ray2.00A1-274[»]
    2F5OX-ray2.05A1-274[»]
    2F5PX-ray2.00A1-274[»]
    2F5QX-ray2.35A1-274[»]
    2F5SX-ray2.35A1-274[»]
    3GO8X-ray1.89A2-274[»]
    3GP1X-ray2.05A2-274[»]
    3GPPX-ray2.15A2-274[»]
    3GPUX-ray1.62A2-274[»]
    3GPXX-ray1.78A2-274[»]
    3GPYX-ray1.85A2-274[»]
    3GQ3X-ray1.83A2-274[»]
    3GQ4X-ray1.70A2-274[»]
    3GQ5X-ray1.90A2-274[»]
    3JR4X-ray2.60A2-274[»]
    3JR5X-ray1.70A2-274[»]
    3SARX-ray1.95A2-274[»]
    3SASX-ray2.05A2-274[»]
    3SATX-ray2.15A2-274[»]
    3SAUX-ray1.65A2-274[»]
    3SAVX-ray2.12A2-274[»]
    3SAWX-ray2.35A2-274[»]
    3SBJX-ray2.10A2-274[»]
    3U6CX-ray1.80A2-274[»]
    3U6DX-ray1.87A2-274[»]
    3U6EX-ray1.70A2-274[»]
    3U6LX-ray1.97A2-274[»]
    3U6MX-ray2.10A2-274[»]
    3U6OX-ray1.90A2-274[»]
    3U6PX-ray1.60A2-274[»]
    3U6QX-ray1.98A2-274[»]
    3U6SX-ray1.77A2-274[»]
    4G4NX-ray1.85A2-274[»]
    4G4OX-ray1.95A2-274[»]
    4G4QX-ray1.86A2-274[»]
    4G4RX-ray1.95A2-274[»]
    ProteinModelPortaliP84131.
    SMRiP84131. Positions 2-274.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP84131.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the FPG family.UniRule annotation
    Contains 1 FPG-type zinc finger.UniRule annotation
    Contains FPG-type zinc finger.SAAS annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri240 – 27435FPG-typeUniRule annotationAdd
    BLAST

    Keywords - Domaini

    Zinc-fingerUniRule annotationSAAS annotation

    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.

    P84131-1 [UniParc]FASTAAdd to Basket

    « Hide

    MPQLPEVETI RRTLLPLIVG KTIEDVRIFW PNIIRHPRDS EAFAARMIGQ    50
    TVRGLERRGK FLKFLLDRDA LISHLRMEGR YAVASALEPL EPHTHVVFCF 100
    TDGSELRYRD VRKFGTMHVY AKEEADRRPP LAELGPEPLS PAFSPAVLAE 150
    RAVKTKRSVK ALLLDQTVVA GFGNIYVDES LFRAGILPGR PAASLSSKEI 200
    ERLHEEMVAT IGEAVMKGGS TVRTYVNTQG EAGTFQHHLY VYGRQGNPCK 250
    RCGTPIEKTV VAGRGTHYCP RCQR 274
    Length:274
    Mass (Da):30,689
    Last modified:September 13, 2004 - v1
    Checksum:iC260712E9E1B7FD9
    GO

    Cross-referencesi

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1L1T X-ray 1.80 A 1-274 [» ]
    1L1Z X-ray 1.70 A 1-274 [» ]
    1L2B X-ray 2.40 A 1-274 [» ]
    1L2C X-ray 2.20 A 1-274 [» ]
    1R2Y X-ray 2.34 A 1-274 [» ]
    1R2Z X-ray 1.63 A 1-274 [» ]
    2F5N X-ray 2.00 A 1-274 [» ]
    2F5O X-ray 2.05 A 1-274 [» ]
    2F5P X-ray 2.00 A 1-274 [» ]
    2F5Q X-ray 2.35 A 1-274 [» ]
    2F5S X-ray 2.35 A 1-274 [» ]
    3GO8 X-ray 1.89 A 2-274 [» ]
    3GP1 X-ray 2.05 A 2-274 [» ]
    3GPP X-ray 2.15 A 2-274 [» ]
    3GPU X-ray 1.62 A 2-274 [» ]
    3GPX X-ray 1.78 A 2-274 [» ]
    3GPY X-ray 1.85 A 2-274 [» ]
    3GQ3 X-ray 1.83 A 2-274 [» ]
    3GQ4 X-ray 1.70 A 2-274 [» ]
    3GQ5 X-ray 1.90 A 2-274 [» ]
    3JR4 X-ray 2.60 A 2-274 [» ]
    3JR5 X-ray 1.70 A 2-274 [» ]
    3SAR X-ray 1.95 A 2-274 [» ]
    3SAS X-ray 2.05 A 2-274 [» ]
    3SAT X-ray 2.15 A 2-274 [» ]
    3SAU X-ray 1.65 A 2-274 [» ]
    3SAV X-ray 2.12 A 2-274 [» ]
    3SAW X-ray 2.35 A 2-274 [» ]
    3SBJ X-ray 2.10 A 2-274 [» ]
    3U6C X-ray 1.80 A 2-274 [» ]
    3U6D X-ray 1.87 A 2-274 [» ]
    3U6E X-ray 1.70 A 2-274 [» ]
    3U6L X-ray 1.97 A 2-274 [» ]
    3U6M X-ray 2.10 A 2-274 [» ]
    3U6O X-ray 1.90 A 2-274 [» ]
    3U6P X-ray 1.60 A 2-274 [» ]
    3U6Q X-ray 1.98 A 2-274 [» ]
    3U6S X-ray 1.77 A 2-274 [» ]
    4G4N X-ray 1.85 A 2-274 [» ]
    4G4O X-ray 1.95 A 2-274 [» ]
    4G4Q X-ray 1.86 A 2-274 [» ]
    4G4R X-ray 1.95 A 2-274 [» ]
    ProteinModelPortali P84131.
    SMRi P84131. Positions 2-274.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Miscellaneous databases

    EvolutionaryTracei P84131.

    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. "Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM."
      Fromme J.C., Verdine G.L.
      Nat. Struct. Biol. 9:544-552(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEX WITH ZINC.
    2. "DNA lesion recognition by the bacterial repair enzyme MutM."
      Fromme J.C., Verdine G.L.
      J. Biol. Chem. 278:51543-51548(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.63 ANGSTROMS) IN COMPLEX WITH ZINC.
    3. "Structure of a DNA glycosylase searching for lesions."
      Banerjee A., Santos W.L., Verdine G.L.
      Science 311:1153-1157(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH ZINC.
    4. "Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme."
      Qi Y., Spong M.C., Nam K., Banerjee A., Jiralerspong S., Karplus M., Verdine G.L.
      Nature 462:762-766(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.62 ANGSTROMS) OF 2-274 IN COMPLEX WITH ZINC.
    5. "Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM."
      Qi Y., Spong M.C., Nam K., Karplus M., Verdine G.L.
      J. Biol. Chem. 285:1468-1478(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 2-274 IN COMPLEX WITH ZINC.
    6. "Sequence-dependent structural variation in DNA undergoing intrahelical inspection by the DNA glycosylase MutM."
      Sung R.J., Zhang M., Qi Y., Verdine G.L.
      J. Biol. Chem. 287:18044-18054(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 2-274 IN COMPLEX WITH ZINC.
    7. Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF 2-274 IN COMPLEX WITH ZINC.
    8. "Structural and biochemical analysis of DNA helix invasion by the bacterial 8-oxoguanine DNA glycosylase MutM."
      Sung R.J., Zhang M., Qi Y., Verdine G.L.
      J. Biol. Chem. 288:10012-10023(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 2-274 IN COMPLEX WITH ZINC.

    Entry informationi

    Entry nameiP84131_GEOSE
    AccessioniPrimary (citable) accession number: P84131
    Entry historyi
    Integrated into UniProtKB/TrEMBL: September 13, 2004
    Last sequence update: September 13, 2004
    Last modified: October 1, 2014
    This is version 77 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiUnreviewed (UniProtKB/TrEMBL)

    Miscellaneousi

    Keywords - Technical termi

    3D-structureImported, Multifunctional enzymeUniRule annotationSAAS annotation

    External Data

    Dasty 3