8DWE

Adenine glycosylase MutY variant E43Q in complex with DNA containing d(8-oxo-G) paired with substrate purine

Summary for 8DWE

• Entry DOI: 10.2210/pdb8dwe/pdb
• Related: 8DWD 8DWE 8DWF
• Descriptor: Adenine DNA glycosylase, DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3'), DNA (5'-D(*TP*GP*TP*CP*CP*AP*(PRN)P*GP*TP*CP*T)-3'), ... (8 entities in total)
• Functional Keywords: protein-dna complex, dna repair, base excision repair, hydrolase, hydrolase-dna complex, hydrolase/dna
• Biological source: Geobacillus stearothermophilus; More
• Total number of polymer chains: 6
• Total formula weight: 98242.08

Authors

Russelburg, L.P.,Demir, M.,David, S.S.,Horvath, M.P. (deposition date: 2022-08-01, release date: 2023-08-09, Last modification date: 2026-06-03)

Primary citation

Russelburg, L.P.,Demir, M.,Cedeno, K.,David, S.S.,Horvath, M.P.
Structural Basis for Nucleobase Activation by the Adenine DNA Glycosylase MutY.
Biorxiv, 2026

PubMed Abstract: MutY excises adenine (A) from 8-oxo-guanine:adenine (OG:A) lesions in DNA to initiate base excision repair (BER) and thereby prevent mutations. A catalytic Glu, found at position 43 in the enzyme from ( MutY), protonates the nucleobase at N to labilize the N-glycosidic bond. The resulting oxocarbenium ion transition state is stabilized by a covalent DNA-enzyme intermediate and resolved by nucleophilic attack to yield the -anomer abasic AP site product. The retaining SN1 mechanism for MutY posits deprotonation of the nucleophile by the catalytic Glu. Here we tested kinetic and structural consequences of Glu replacement and found that E43Q and E43S substitution variants were severely impaired, retained measurable activity, but engage the substrate nucleobase in an conformation, rotated by 180 ° from the conformation seen in previous substrate complexes. The enzyme-generated AP product is observed in its -anomer configuration for these Glu-replacement variants. Comparison with inverting adenine glycosylases that act on RNA or nucleosides shows that MutY's mechanism is uniquely reliant on one catalytic residue for both leaving group and nucleophile activation, a situation that may serve to ensure only rare adenines paired with OG are excised.

PubMed: 41648512
DOI: 10.64898/2026.01.22.701053

Experimental method

X-RAY DIFFRACTION (2.2 Å)