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P42371

- FPG_LACLC

UniProt

P42371 - FPG_LACLC

Protein

Formamidopyrimidine-DNA glycosylase

Gene

mutM

Organism
Lactococcus lactis subsp. cremoris (Streptococcus cremoris)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 107 (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). 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.1 Publication

    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.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei2 – 21Schiff-base intermediate with DNACurated
    Active sitei3 – 31Proton donorCurated
    Active sitei58 – 581Proton donor; for beta-elimination activityCurated
    Binding sitei92 – 921DNA
    Binding sitei110 – 1101DNA
    Active sitei262 – 2621Proton donor; for delta-elimination activityCurated

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri238 – 27235FPG-typeAdd
    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

    Glycosidase, Hydrolase, Lyase

    Keywords - Biological processi

    DNA damage, DNA repair

    Keywords - Ligandi

    DNA-binding, Metal-binding, Zinc

    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
    OrganismiLactococcus lactis subsp. cremoris (Streptococcus cremoris)
    Taxonomic identifieri1359 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeLactococcus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi2 – 21P → G: Loss of activity.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 273272Formamidopyrimidine-DNA glycosylasePRO_0000170830Add
    BLAST

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Structurei

    Secondary structure

    1
    273
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi4 – 1815
    Beta strandi25 – 295
    Helixi31 – 333
    Helixi38 – 458
    Beta strandi49 – 568
    Beta strandi59 – 646
    Turni65 – 673
    Beta strandi68 – 736
    Turni75 – 773
    Beta strandi79 – 835
    Beta strandi93 – 986
    Beta strandi103 – 1075
    Beta strandi114 – 1196
    Helixi120 – 1223
    Helixi123 – 1297
    Helixi144 – 1529
    Helixi158 – 1636
    Beta strandi165 – 1695
    Helixi173 – 18210
    Helixi191 – 1933
    Helixi196 – 21520
    Beta strandi221 – 2233
    Turni227 – 2304
    Helixi233 – 2364
    Turni248 – 2503
    Beta strandi255 – 2595
    Beta strandi262 – 2665
    Turni268 – 2703

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1KFVX-ray2.55A/B2-273[»]
    1NNJX-ray1.90A2-273[»]
    1PJIX-ray1.90A2-273[»]
    1PJJX-ray1.90A2-273[»]
    1PM5X-ray1.95A2-273[»]
    1TDZX-ray1.80A1-273[»]
    1XC8X-ray1.95A2-273[»]
    2XZFX-ray1.80A2-273[»]
    2XZUX-ray1.82A2-273[»]
    3C58X-ray1.90A2-273[»]
    ProteinModelPortaliP42371.
    SMRiP42371. Positions 2-273.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP42371.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni58 – 7619DNA bindingAdd
    BLAST
    Regioni162 – 17211DNA bindingAdd
    BLAST

    Sequence similaritiesi

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

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri238 – 27235FPG-typeAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    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.

    P42371-1 [UniParc]FASTAAdd to Basket

    « Hide

    MPELPEVETV RRELEKRIVG QKIISIEATY PRMVLTGFEQ LKKELTGKTI    50
    QGISRRGKYL IFEIGDDFRL ISHLRMEGKY RLATLDAPRE KHDHLTMKFA 100
    DGQLIYADVR KFGTWELIST DQVLPYFLKK KIGPEPTYDE DFDEKLFREK 150
    LRKSTKKIKP YLLEQTLVAG LGNIYVDEVL WLAKIHPEKE TNQLIESSIH 200
    LLHDSIIEIL QKAIKLGGSS IRTYSALGST GKMQNELQVY GKTGEKCSRC 250
    GAEIQKIKVA GRGTHFCPVC QQK 273
    Length:273
    Mass (Da):31,310
    Last modified:January 23, 2007 - v3
    Checksum:iEB16055C5E09840F
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X74298 Genomic DNA. Translation: CAA52351.1.
    M88106 Genomic DNA. No translation available.
    PIRiS39200.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X74298 Genomic DNA. Translation: CAA52351.1 .
    M88106 Genomic DNA. No translation available.
    PIRi S39200.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1KFV X-ray 2.55 A/B 2-273 [» ]
    1NNJ X-ray 1.90 A 2-273 [» ]
    1PJI X-ray 1.90 A 2-273 [» ]
    1PJJ X-ray 1.90 A 2-273 [» ]
    1PM5 X-ray 1.95 A 2-273 [» ]
    1TDZ X-ray 1.80 A 1-273 [» ]
    1XC8 X-ray 1.95 A 2-273 [» ]
    2XZF X-ray 1.80 A 2-273 [» ]
    2XZU X-ray 1.82 A 2-273 [» ]
    3C58 X-ray 1.90 A 2-273 [» ]
    ProteinModelPortali P42371.
    SMRi P42371. Positions 2-273.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Miscellaneous databases

    EvolutionaryTracei P42371.

    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. "Repair of oxidative DNA damage in Gram-positive bacteria: the Lactococcus lactis Fpg protein."
      Duwat P., de Oliveira R., Ehrlich S.D., Boiteux S.
      Microbiology 141:411-417(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-22, FUNCTION.
      Strain: NCDO 763 / ML3.
    2. "Use of degenerate primers for polymerase chain reaction cloning and sequencing of the Lactococcus lactis subsp. lactis recA gene."
      Duwat P., Ehrlich S.D., Gruss A.
      Appl. Environ. Microbiol. 58:2674-2678(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 194-273.
      Strain: NCDO 763 / ML3.
    3. "Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA."
      Serre L., Pereira de Jesus K., Boiteux S., Zelwer C., Castaing B.
      EMBO J. 21:2854-2865(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 1-273 OF MUTANT GLY-2 IN COMPLEX WITH SUBSTRATE ANALOG.

    Entry informationi

    Entry nameiFPG_LACLC
    AccessioniPrimary (citable) accession number: P42371
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 107 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The zinc finger is important for DNA binding.

    Keywords - Technical termi

    3D-structure, Direct protein sequencing, Multifunctional enzyme

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3