2f5q Summary

pdbe.org/2f5q
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Catalytically inactive (E3Q) MutM crosslinked to oxoG:C containing DNA CC2

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 2.35 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*G*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3', 5'-D(*TP*GP*CP*G*TP*CP*CP*AP*(8OG)P*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 99%


This entry contains 1 unique UniProt protein:

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

Chain Structural classification (SCOP) Sequence family (Pfam)
A (P84131) 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 PF01149: Formamidopyrimidine-DNA glycosylase N-terminal domainsearch, PF06827: Zinc finger found in FPG and IleRSsearch, PF06831: Formamidopyrimidine-DNA glycosylase H2TH domainsearch

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

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