Non-flipping DNA glycosylase AlkD scans DNA without formation of a stable interrogation complex

Arash Ahmadi; Katharina Till; Paul Hoff Backe; Pernille Blicher; Robin Diekmann; Mark Schüttpelz; Kyrre Glette; Jim Tørresen; Magnar Bjørås; Alexander D Rowe; Bjørn Dalhus

doi:10.1038/s42003-021-02400-x

Non-flipping DNA glycosylase AlkD scans DNA without formation of a stable interrogation complex

Commun Biol. 2021 Jul 15;4(1):876. doi: 10.1038/s42003-021-02400-x.

Authors

Arash Ahmadi¹, Katharina Till^{2

3}, Paul Hoff Backe^{1

4}, Pernille Blicher¹, Robin Diekmann³, Mark Schüttpelz³, Kyrre Glette⁵, Jim Tørresen⁵, Magnar Bjørås^{4

6}, Alexander D Rowe^{1

7}, Bjørn Dalhus^{8

9}

Affiliations

¹ Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.
² FOM Institute AMOLF, Science Park 104, Amsterdam, The Netherlands.
³ Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany.
⁴ Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, Oslo, Norway.
⁵ Department of Informatics, University of Oslo, Oslo, Norway.
⁶ Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
⁷ Department of Newborn Screening, Division of Child and Adolescent Medicine, Oslo University Hospital, Oslo, Norway.
⁸ Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway. bjorn.dalhus@medisin.uio.no.
⁹ Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, Oslo, Norway. bjorn.dalhus@medisin.uio.no.

Abstract

The multi-step base excision repair (BER) pathway is initiated by a set of enzymes, known as DNA glycosylases, able to scan DNA and detect modified bases among a vast number of normal bases. While DNA glycosylases in the BER pathway generally bend the DNA and flip damaged bases into lesion specific pockets, the HEAT-like repeat DNA glycosylase AlkD detects and excises bases without sequestering the base from the DNA helix. We show by single-molecule tracking experiments that AlkD scans DNA without forming a stable interrogation complex. This contrasts with previously studied repair enzymes that need to flip bases into lesion-recognition pockets and form stable interrogation complexes. Moreover, we show by design of a loss-of-function mutant that the bimodality in scanning observed for the structural homologue AlkF is due to a key structural differentiator between AlkD and AlkF; a positively charged β-hairpin able to protrude into the major groove of DNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bacterial Proteins / genetics*
Bacterial Proteins / metabolism
DNA Glycosylases / genetics*
DNA Glycosylases / metabolism
DNA, Bacterial / genetics*

Substances

Bacterial Proteins
DNA, Bacterial
DNA Glycosylases