Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase

• Published in: Nucleic acids research Vol. 47; no. 13; pp. 6973 - 6983
• Main Authors: Jackson, Lynnette N, Chim, Nicholas, Shi, Changhua, Chaput, John C
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 26.07.2019
• Subjects: Arabinonucleotides - metabolism; Bacterial Proteins - chemistry; Bacterial Proteins - isolation & purification; Bacterial Proteins - metabolism; Catalytic Domain; Crystallography, X-Ray; DNA Polymerase I - chemistry; DNA Polymerase I - isolation & purification; DNA Polymerase I - metabolism; DNA, Bacterial - metabolism; Geobacillus stearothermophilus - enzymology; Models, Molecular; Nucleic Acid Enzymes; Nucleic Acid Hybridization; Nucleosides - metabolism; Protein Binding; Protein Conformation; RNA-Directed DNA Polymerase - chemistry; RNA-Directed DNA Polymerase - isolation & purification; RNA-Directed DNA Polymerase - metabolism; Structure-Activity Relationship; Templates, Genetic
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkz513

Replicative DNA polymerases are highly efficient enzymes that maintain stringent geometric control over shape and orientation of the template and incoming nucleoside triphosphate. In a surprising twist to this paradigm, a naturally occurring bacterial DNA polymerase I member isolated from Geobacillus stearothermophilus (Bst) exhibits an innate ability to reverse transcribe RNA and other synthetic congeners (XNAs) into DNA. This observation raises the interesting question of how a replicative DNA polymerase is able to recognize templates of diverse chemical composition. Here, we present crystal structures of natural Bst DNA polymerase that capture the post-translocated product of DNA synthesis on templates composed entirely of 2'-deoxy-2'-fluoro-β-d-arabino nucleic acid (FANA) and α-l-threofuranosyl nucleic acid (TNA). Analysis of the enzyme active site reveals the importance of structural plasticity as a possible mechanism for XNA-dependent DNA synthesis and provides insights into the construction of variants with improved activity.