4EJZ

Structure of MBOgg1 in complex with low affinity DNA ligand

Summary for 4EJZ

• Entry DOI: 10.2210/pdb4ejz/pdb
• Related: 4EJY
• Descriptor: 3-Methyladenine DNA glycosylase, DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3'), DNA (5'-D(*T*GP*GP*TP*AP*GP*AP*CP*TP*TP*GP*GP*AP*CP*GP*C)-3') (3 entities in total)
• Functional Keywords: 8-oxoguanine dna glycosylase, dna, hydrolase-dna complex, hydrolase/dna
• Biological source: Thermoanaerobacter tengcongensis
• Total number of polymer chains: 6
• Total formula weight: 91707.06

Authors

Jiang, T.,Yu, H.J.,Bi, L.J.,Zhang, X.E.,Yang, M.Z. (deposition date: 2012-04-08, release date: 2013-03-20, Last modification date: 2023-11-08)

Primary citation

Yu, H.J.,Yang, M.Z.,Zhang, X.E.,Bi, L.J.,Jiang, T.
Crystal structures of MBOgg1 in complex with two abasic DNA ligands
J.Struct.Biol., 181:252-263, 2013

PubMed Abstract: 7,8-Dihydro-8-oxoguanine (8-oxoG) is one of the most common oxidative DNA lesions. 8-oxoguanine DNA glycosylases (Oggs) detect and excise 8-oxoG through a multiple-step process. To better understand the basis for estranged base recognition, we have solved the crystal structures of MBOgg1, the 8-oxoguanine DNA glycosylase of Thermoanaerobacter tengcongensis, in complex with DNA containing a tetrahydrofuranyl site (THF, a stable abasic site analog) paired with an estranged cytosine (MBOgg1/DNA(THF:C)) or thymine (MBOgg1/DNA(THF:T)). Different states of THF (extrahelical or intrahelical) are observed in the two complexes of the ASU of MBOgg1/DNA(THF:C) structure. Analyses of their different interaction modes reveal that variable contacts on the 5' region flanking the THF abasic site are correlated with the states of the THF. Comparison of MBOgg1/DNA(THF:T) with MBOgg1/DNA(THF:C) indicates that the non-preferred estranged T may affect MBOgg1's contacts with the 5' flank of the lesion strand. Furthermore, we identified a region in MBOgg1 that is rich in positive charges and interacts with the 5' region flanking the lesion. This region is conserved only in non-eukaryotic Oggs, and additional mutagenesis and biochemical assays reveal that it may contribute to the distinct estranged base specificities between eukaryotic and non-eukaryotic Oggs.

PubMed: 23246782
DOI: 10.1016/j.jsb.2012.12.003

Experimental method

X-RAY DIFFRACTION (3.05 Å)