9VR3

Trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA containing G opposite the crosslink

Summary for 9VR3

• Entry DOI: 10.2210/pdb9vr3/pdb
• Related: 9VR4 9VRM
• Descriptor: DNA (5'-D(P*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*G)-3'), DNA (5'-D(P*GP*CP*TP*TP*CP*GP*TP*CP*CP*TP*GP*G)-3'), Endonuclease 8, ... (6 entities in total)
• Functional Keywords: dna-glycosylase, dna-protein crosslink, repair, hydrolase, hydrolase-dna complex, hydrolase/dna
• Biological source: Escherichia coli BL21; More
• Total number of polymer chains: 3
• Total formula weight: 38102.76

Authors

Bulgakov, N.A.,Endutkin, A.V.,Shevtsov, M.B.,Kapranov, I.A.,Yudkina, A.V.,Borshchevskiy, V.I.,Zharkov, D.O. (deposition date: 2025-07-05, release date: 2026-10-07, Last modification date: 2026-10-14)

Primary citation

Bulgakov, N.A.,Endutkin, A.V.,MacCarthy, C.,Shevtsov, M.B.,Kapranov, I.A.,Yudkina, A.V.,Borshchevskiy, V.I.,Zharkov, D.O.
Unique structural mode for opposite-base tolerance in endonuclease VIII.
DNA Repair (Amst), 167:103962-103962, 2026

PubMed Abstract: Endonuclease VIII (Nei) is a DNA repair enzyme with broad substrate specificity for oxidative lesions, excising damaged bases paired with any normal base. The structural basis for this opposite-base tolerance is unknown, since only the structure of the Nei-DNA complex with A opposite the lesion had been determined. Here we address this question by solving crystal structures of Escherichia coli Nei conjugates with DNA duplexes containing C, G, or T opposite the lesion. While estranged purine bases are recognized by Nei via a non-specific hydrogen bond to N3, pyrimidine bases undergo a 180° rotation into the syn conformation. In this unique orientation, their Watson-Crick edge faces the major groove, forming no specific contacts with Nei. Substrates with 5-hydroxyuracil opposite T analogs carrying bulky C5-substitutions are cleaved by Nei less efficiently, consistent with the intrahelical location of the C5-C6 edge of the estranged pyrimidine bases. We have also identified several hydrogen bond networks within the Nei molecule that may facilitate accommodation of different DNA structures and stabilize the catalytic conformation of the enzyme. The mechanism of opposite-base tolerance through pyrimidine flipping is unprecedented among DNA glycosylases and may allow Nei to recognize a wide spectrum of oxidative lesions.

PubMed: 42804861
DOI: 10.1016/j.dnarep.2026.103962

Experimental method

X-RAY DIFFRACTION (1.85 Å)