PDBsum entry 4ppx

Transferase, lyase/DNA

PDB id: 4ppx

Contents

Protein chain

314 a.a.

DNA/RNA

Metals

_NA ×2

Waters ×348

References listed in PDB file

Key reference

• Title: Crystal structure of DNA polymerase β with DNA containing the base lesion spiroiminodihydantoin in a templating position.
• Authors: B.E.Eckenroth, A.M.Fleming, J.B.Sweasy, C.J.Burrows, S.Doublié.
• Ref.: Biochemistry, 2014, 53, 2075-2077. [DOI no: 10.1021/bi500270e]
• PubMed id: 24649945

Abstract

The first high-resolution crystal structure of spiroiminodihydantoin (dSp1) was obtained in the context of the DNA polymerase β active site and reveals two areas of significance. First, the structure verifies the recently determined S configuration at the spirocyclic carbon. Second, the distortion of the DNA duplex is similar to that of the single-oxidation product 8-oxoguanine. For both oxidized lesions, adaptation of the syn conformation results in similar backbone distortions in the DNA duplex. The resulting conformation positions the dSp1 A-ring as the base-pairing face whereas the B-ring of dSp1 protrudes into the major groove.