2f5n Summary


MutM crosslinked to undamaged DNA sampling A:T base pair IC1

The structure was published by Banerjee, A., Santos, W.L., and Verdine, G.L., in 2006 in a paper entitled "Structure of a DNA glycosylase searching for lesions." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.0 Å and deposited in 2005.

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

This PDB entry contains a complex of 3 biomacromolecules, namely 5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3', 5'-D(*TP*GP*C*GP*TP*CP*CP*AP*GP*GP*TP*CP*TP*AP*CP*C)-3', and formamidopyrimidine-DNA glycosidase.

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 formamidopyrimidine-DNA glycosidase P84131 (1-274) (P84131_GEOSE)search Geobacillus stearothermophilussearch 93% 274 91%

This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
P84131 (1 - 274) formamidopyrimidine-DNA glycosidase Geobacillus stearothermophilus

Chain Sequence family (Pfam)
A (P84131) 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 (P84131) zinc ion bindingsearch damaged DNA bindingsearch lyase activitysearch metal ion bindingsearch hydrolase activity, hydrolyzing N-glycosyl compoundssearch DNA-(apurinic or apyrimidinic site) lyase activitysearch oxidized purine nucleobase lesion DNA N-glycosylase activitysearch DNA bindingsearch catalytic activitysearch hydrolase activity, acting on glycosyl bondssearch nucleic acid bindingsearch hydrolase activitysearch DNA repairsearch DNA catabolic process, endonucleolyticsearch base-excision repairsearch metabolic processsearch cellular response to DNA damage stimulussearch nucleotide-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