3GPY: Sequence-matched MutM Lesion Recognition Complex 3 (LRC3)

How living systems detect the presence of genotoxic damage embedded in a million-fold excess of undamaged DNA is an unresolved question in biology. Here we have captured and structurally elucidated a base-excision DNA repair enzyme, MutM, at the stage of initial encounter with a damaged nucleobase, 8-oxoguanine (oxoG), nested within a DNA duplex. Three structures of intrahelical oxoG-encounter complexes are compared with sequence-matched structures containing a normal G base in place of an oxoG lesion. Although the protein-DNA interfaces in the matched complexes differ by only two atoms-those that distinguish oxoG from G-their pronounced structural differences indicate that MutM can detect a lesion in DNA even at the earliest stages of encounter. All-atom computer simulations show the pathway by which encounter of the enzyme with the lesion causes extrusion from the DNA duplex, and they elucidate the critical free energy difference between oxoG and G along the extrusion pathway.
PDB ID: 3GPYDownload
MMDB ID: 77992
PDB Deposition Date: 2009/3/23
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 1.85  Å
Source Organism:
Geobacillus stearothermophilus
Similar Structures:
Biological Unit for 3GPY: trimeric; determined by author and by software (PISA)
Molecular Components in 3GPY
Label Count Molecule
Protein (1 molecule)
DNA Glycosylase
Molecule annotation
Nucleotides(2 molecules)
DNA (5'-d(*ap*gp*gp*tp*ap*gp*ap*tp*cp*cp*gp*gp*ap*cp*gp*c)-3')
Molecule annotation
DNA (5'-d(*t*gp*cp*gp*tp*cp*cp*(8og)p*gp*ap*tp*cp*tp*ap*cp*c)-3')
Molecule annotation
Chemical (1 molecule)
* Click molecule labels to explore molecular sequence information.

Citing MMDB