3KNT image
Entry Detail
PDB ID:
3KNT
Title:
Crystal structure of Methanocaldococcus jannaschii 8-oxoguanine glycosylase/lyase in complex with 15mer DNA containing 8-oxoguanine
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2009-11-12
Release Date:
2010-02-02
Method Details:
Experimental Method:
Resolution:
2.70 Å
R-Value Free:
0.22
R-Value Work:
0.18
R-Value Observed:
0.19
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:N-glycosylase/DNA lyase
Mutations:K129Q
Chain IDs:A, B, C, D
Chain Length:207
Number of Molecules:4
Biological Source:Methanocaldococcus jannaschii
Polymer Type:polydeoxyribonucleotide
Description:5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3'
Chain IDs:E, G, I, K
Chain Length:15
Number of Molecules:4
Biological Source:
Polymer Type:polydeoxyribonucleotide
Description:5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'
Chain IDs:F, H, J, L
Chain Length:15
Number of Molecules:4
Biological Source:
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
8OG E DG ?
Ligand Molecules
Primary Citation
The C-terminal Lysine of Ogg2 DNA Glycosylases is a Major Molecular Determinant for Guanine/8-Oxoguanine Distinction.
J.Mol.Biol. 397 46 56 (2010)
PMID: 20083120 DOI: 10.1016/j.jmb.2010.01.024

Abstact

7,8-Dihydro-8-oxoguanine (8-oxoG) is a major oxidative lesion found in DNA. The 8-oxoguanine DNA glycosylases (Ogg) responsible for the removal of 8-oxoG are divided into three families Ogg1, Ogg2 and AGOG. The Ogg2 members are devoid of the recognition loop used by Ogg1 to discriminate between 8-oxoG and guanine and it was unclear until recently how Ogg2 enzymes recognize the oxidized base. We present here the first crystallographic structure of an Ogg2 member, Methanocaldococcus janischii Ogg, in complex with a DNA duplex containing the 8-oxoG lesion. This structure highlights the crucial role of the C-terminal lysine, strictly conserved in Ogg2, in the recognition of 8-oxoG. The structure also reveals that Ogg2 undergoes a conformational change upon DNA binding similar to that observed in Ogg1 glycosylases. Furthermore, this work provides a structural rationale for the lack of opposite base specificity in this family of enzymes.

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