Structural basis of interaction between Pol1 and DnaN from Mycobacterium tuberculosis

DNA polymerases generally interact with the processivity clamp (DnaN/{beta}-clamp) during replication via clamp-binding motifs (CBMs). Since a CBM was not detected in DNA Polymerase I (PolI) from E. coli, it is generally believed that PolI performs its functions in genome replication and repair, independently of the {beta}-clamp. We observe that, while PolI and {beta}-clamp proteins from E. coli do not interact, their homologs from Mycobacterium tuberculosis bind strongly, and the binding site localises to the Klenow fragment of PolI. The cryo-EM structure (4.9 [A]) of the Mtb-PolI-Klenow: Mtb-{beta}-clamp complex, coupled with continuous heterogeneity analysis of the cryo-EM data and binding experiments, showed that the primary CBM in PolI may be defined by the stretch 457QLSLLDD463. The crystal structure (2.9 [A]) of the {beta}-clamp with the CBM peptide revealed specific interactions that stabilise the peptide within the {beta}-clamp's canonical binding site. Phylogenetic analyses across different bacteria showed that the identified CBM is present only in PolI from members of the order Mycobacteriales. Overall, the interaction between PolI with the {beta}-clamp, mediated by a CBM unique to the Mycobacteriales order, highlights the mechanistic distinctiveness of genome replication in Mtb and phylogenetically related organisms, and has important implications for drug discovery.