Thumb-domain dynamics modulate the functional repertoire of DNA-Polymerase IV (DinB)

• Published in: Nucleic acids research 2023-07, Vol.51 (13), p.7036-7052
• Main Authors: Okeke, Damasus C, Lidman, Jens, Matečko-Burmann, Irena, Burmann, Björn M
• Format: Article
• Language: English
• Subjects: DNA - genetics; DNA - metabolism; DNA Polymerase beta - genetics; Escherichia coli - metabolism; Escherichia coli Proteins - metabolism; Mutation; Structural Biology; Strukturbiologi
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkad490

Abstract In order to cope with the risk of stress-induced mutagenesis, cells in all kingdoms of life employ Y-family DNA polymerases to resolve resulting DNA lesions and thus maintaining the integrity of the genome. In Escherichia coli, the DNA polymerase IV, or DinB, plays this crucial role in coping with these type of mutations via the so-called translesion DNA synthesis. Despite the availability of several high-resolution crystal structures, important aspects of the functional repertoire of DinB remain elusive. In this study, we use advanced solution NMR spectroscopy methods in combination with biophysical characterization to elucidate the crucial role of the Thumb domain within DinB’s functional cycle. We find that the inherent dynamics of this domain guide the recognition of double-stranded (ds) DNA buried within the interior of the DinB domain arrangement and trigger allosteric signals through the DinB protein. Subsequently, we characterized the RNA polymerase interaction with DinB, revealing an extended outside surface of DinB and thus not mutually excluding the DNA interaction. Altogether the obtained results lead to a refined model of the functional repertoire of DinB within the translesion DNA synthesis pathway. Graphical Abstract Graphical Abstract