3c58 Summary


Crystal structure of a complex between the wild-type lactococcus lactis Fpg (MutM) and a N7-Benzyl-Fapy-dG containing DNA

The structure was published by Coste, F., Ober, M., Le Bihan, Y.V., et al., Mueller, H., Carell, T., and Castaing, B., in 2008 in a paper entitled "Bacterial base excision repair enzyme Fpg recognizes bulky N7-substituted-FapydG lesion via unproductive binding mode" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 1.9 Å and deposited in 2008.

The experimental data on which the structure is based was also deposited.

This PDB entry contains a complex of 3 biomacromolecules, namely DNA (5'-D(*DGP*DCP*DGP*DAP*DGP*DAP*DAP*DAP*DCP*DAP*DAP*DAP*DGP*DA)-3'), DNA (5'-D(*DCP*DTP*DCP*DTP*DTP*DTP*(SOS)P*DTP*DTP*DTP*DCP*DTP*DCP*DG)-3'), and DNA glycosylase.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule most likely forms heterotrimers.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):

Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A DNA glycosylase P42371 (2-273) (FPG_LACLC)search Lactococcus lactis subsp. cremorissearch 99% 271 99%

This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
P42371 (2 - 273) DNA glycosylase Lactococcus lactis subsp. cremoris MG1363

Chain Sequence family (Pfam)
A (P42371) PF01149: Formamidopyrimidine-DNA glycosylase N-terminal domainsearch, PF06827: Zinc finger found in FPG and IleRSsearch, PF06831: Formamidopyrimidine-DNA glycosylase H2TH domainsearch

Chain ID Molecular function (GO) Biological process (GO)
A (P42371) zinc ion bindingsearch hydrolase activity, hydrolyzing N-glycosyl compoundssearch metal ion bindingsearch DNA-(apurinic or apyrimidinic site) lyase activitysearch oxidized purine nucleobase lesion DNA N-glycosylase activitysearch nucleic acid bindingsearch DNA bindingsearch hydrolase activity, acting on glycosyl bondssearch hydrolase activitysearch catalytic activitysearch damaged DNA bindingsearch lyase activitysearch metabolic processsearch DNA repairsearch DNA catabolic process, endonucleolyticsearch cellular response to DNA damage stimulussearch nucleotide-excision repairsearch base-excision repairsearch

Chain InterPro annotation
A DNA glycosylase/AP lyasesearch Zinc finger, DNA glycosylase/AP lyase-typesearch Zinc finger, DNA glycosylase/AP lyase/isoleucyl tRNA synthetasesearch Ribosomal protein S13-like, H2THsearch DNA glycosylase/AP lyase, catalytic domainsearch DNA glycosylase/AP lyase, H2TH DNA-bindingsearch DNA glycosylase/AP lyase, zinc finger domain, DNA-binding sitesearch Formamidopyrimidine-DNA glycosylasesearch