8DW4

Glycosylase MutY variant N146S in complex with DNA containing d(8-oxo-G) paired with an abasic site product (AP) generated by the enzyme in crystals by removal of calcium

Summary for 8DW4

• Entry DOI: 10.2210/pdb8dw4/pdb
• Related: 8DVP
• Descriptor: Adenine DNA glycosylase, DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3'), DNA (5'-D(P*GP*TP*CP*CP*AP*(AAB)P*GP*TP*CP*T)-3'), ... (7 entities in total)
• Functional Keywords: protein-dna complex, dna repair, apurinic/apyrimidinic, base excision repair, hydrolase, hydrolase-dna complex, hydrolase/dna
• Biological source: Geobacillus stearothermophilus; More
• Total number of polymer chains: 3
• Total formula weight: 48810.57

Authors

Demir, M.,Russelburg, L.P.,Horvath, M.P.,David, S.S. (deposition date: 2022-07-31, release date: 2022-11-30, Last modification date: 2023-10-25)

Primary citation

Demir, M.,Russelburg, L.P.,Lin, W.J.,Trasvina-Arenas, C.H.,Huang, B.,Yuen, P.K.,Horvath, M.P.,David, S.S.
Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism.
Nucleic Acids Res., 51:1034-1049, 2023

PubMed Abstract: DNA glycosylase MutY plays a critical role in suppression of mutations resulted from oxidative damage, as highlighted by cancer-association of the human enzyme. MutY requires a highly conserved catalytic Asp residue for excision of adenines misinserted opposite 8-oxo-7,8-dihydroguanine (OG). A nearby Asn residue hydrogen bonds to the catalytic Asp in structures of MutY and its mutation to Ser is an inherited variant in human MUTYH associated with colorectal cancer. We captured structural snapshots of N146S Geobacillus stearothermophilus MutY bound to DNA containing a substrate, a transition state analog and enzyme-catalyzed abasic site products to provide insight into the base excision mechanism of MutY and the role of Asn. Surprisingly, despite the ability of N146S to excise adenine and purine (P) in vitro, albeit at slow rates, N146S-OG:P complex showed a calcium coordinated to the purine base altering its conformation to inhibit hydrolysis. We obtained crystal structures of N146S Gs MutY bound to its abasic site product by removing the calcium from crystals of N146S-OG:P complex to initiate catalysis in crystallo or by crystallization in the absence of calcium. The product structures of N146S feature enzyme-generated β-anomer abasic sites that support a retaining mechanism for MutY-catalyzed base excision.

PubMed: 36631987
DOI: 10.1093/nar/gkac1246

Experimental method

X-RAY DIFFRACTION (2.49 Å)