1k82 Summary

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Crystal structure of E.coli formamidopyrimidine-DNA glycosylase (Fpg) covalently trapped with DNA

The structure was published by Gilboa, R., Zharkov, D.O., Golan, G., et al., Kycia, J.H., Grollman, A.P., and Shoham, G., in 2002 in a paper entitled "Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.1 Å and deposited in 2001.

The experimental data on which the structure is based was not deposited.

This PDB entry contains a complex of 3 biomacromolecules, namely 5'-D(*GP*GP*CP*TP*TP*CP*CP*TP*CP*CP*TP*GP*G)-3', 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3', and formamidopyrimidine-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 has more than one probable quaternary state observed. For more details see the quaternary structure page.

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 formamidopyrimidine-DNA glycosylase P05523 (2-269) (FPG_ECOLI)search Escherichia coli K-12search 100% 268 97%
B formamidopyrimidine-DNA glycosylase P05523 (2-269) (FPG_ECOLI)search Escherichia coli K-12search 100% 268 97%
C formamidopyrimidine-DNA glycosylase P05523 (2-269) (FPG_ECOLI)search Escherichia coli K-12search 100% 268 97%
D formamidopyrimidine-DNA glycosylase P05523 (2-269) (FPG_ECOLI)search Escherichia coli K-12search 100% 268 97%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
P05523 (2 - 269) formamidopyrimidine-DNA glycosylase Escherichia coli

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
A, B, C, D (P05523) Middle domain of MutM-like DNA repair proteinssearch, N-terminal domain of MutM-like DNA repair proteinssearch, C-terminal, Zn-finger domain of MutM-like DNA repair proteinssearch Helicase, Ruva Protein; domain 3search, N-terminal domain of MutM-like DNA repair proteinssearch 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, B, C, D (P05523) DNA-(apurinic or apyrimidinic site) lyase activitysearch hydrolase activitysearch oxidized purine nucleobase lesion DNA N-glycosylase activitysearch zinc ion bindingsearch hydrolase activity, acting on glycosyl bondssearch DNA N-glycosylase activitysearch catalytic activitysearch oxidized pyrimidine nucleobase lesion DNA N-glycosylase activitysearch damaged DNA bindingsearch nucleic acid bindingsearch DNA bindingsearch hydrolase activity, hydrolyzing N-glycosyl compoundssearch metal ion bindingsearch endonuclease activitysearch lyase activitysearch DNA catabolic process, endonucleolyticsearch nucleic acid phosphodiester bond hydrolysissearch base-excision repairsearch DNA repairsearch nucleotide-excision repairsearch cellular response to DNA damage stimulussearch metabolic processsearch base-excision repair, AP site formationsearch

Chain InterPro annotation
A, B, C, D 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